1
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Jorrin B, Haskett TL, Knights HE, Martyn A, Underwood TJ, Dolliver J, Ledermann R, Poole PS. Stable, fluorescent markers for tracking synthetic communities and assembly dynamics. MICROBIOME 2024; 12:81. [PMID: 38715147 PMCID: PMC11075435 DOI: 10.1186/s40168-024-01792-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/09/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND After two decades of extensive microbiome research, the current forefront of scientific exploration involves moving beyond description and classification to uncovering the intricate mechanisms underlying the coalescence of microbial communities. Deciphering microbiome assembly has been technically challenging due to their vast microbial diversity but establishing a synthetic community (SynCom) serves as a key strategy in unravelling this process. Achieving absolute quantification is crucial for establishing causality in assembly dynamics. However, existing approaches are primarily designed to differentiate a specific group of microorganisms within a particular SynCom. RESULTS To address this issue, we have developed the differential fluorescent marking (DFM) strategy, employing three distinguishable fluorescent proteins in single and double combinations. Building on the mini-Tn7 transposon, DFM capitalises on enhanced stability and broad applicability across diverse Proteobacteria species. The various DFM constructions are built using the pTn7-SCOUT plasmid family, enabling modular assembly, and facilitating the interchangeability of expression and antibiotic cassettes in a single reaction. DFM has no detrimental effects on fitness or community assembly dynamics, and through the application of flow cytometry, we successfully differentiated, quantified, and tracked a diverse six-member SynCom under various complex conditions like root rhizosphere showing a different colonisation assembly dynamic between pea and barley roots. CONCLUSIONS DFM represents a powerful resource that eliminates dependence on sequencing and/or culturing, thereby opening new avenues for studying microbiome assembly. Video Abstract.
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Affiliation(s)
- Beatriz Jorrin
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Timothy L Haskett
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Hayley E Knights
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Anna Martyn
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Thomas J Underwood
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Jessica Dolliver
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Raphael Ledermann
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Philip S Poole
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
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2
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Stojan I, Šantić D, Villena-Alemany C, Trumbić Ž, Matić F, Vrdoljak Tomaš A, Lepen Pleić I, Piwosz K, Kušpilić G, Ninčević Gladan Ž, Šestanović S, Šolić M. Ecology of aerobic anoxygenic phototrophs on a fine-scale taxonomic resolution in Adriatic Sea unravelled by unsupervised neural network. ENVIRONMENTAL MICROBIOME 2024; 19:28. [PMID: 38685092 PMCID: PMC11059731 DOI: 10.1186/s40793-024-00573-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 04/22/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND Aerobic anoxygenic phototrophs are metabolically highly active, diverse and widespread polyphyletic members of bacterioplankton whose photoheterotrophic capabilities shifted the paradigm about simplicity of the microbial food chain. Despite their considerable contribution to the transformation of organic matter in marine environments, relatively little is still known about their community structure and ecology at fine-scale taxonomic resolution. Up to date, there is no comprehensive (i.e. qualitative and quantitative) analysis of their community composition in the Adriatic Sea. RESULTS Analysis was based on pufM gene metabarcoding and quantitative FISH-IR approach with the use of artificial neural network. Significant seasonality was observed with regards to absolute abundances (maximum average abundances in spring 2.136 ± 0.081 × 104 cells mL-1, minimum in summer 0.86 × 104 cells mL-1), FISH-IR groups (Roseobacter clade prevalent in autumn, other Alpha- and Gammaproteobacteria in summer) and pufM sequencing data agglomerated at genus-level. FISH-IR results revealed heterogeneity with the highest average relative contribution of AAPs assigned to Roseobacter clade (37.66%), followed by Gammaproteobacteria (35.25%) and general Alphaproteobacteria (31.15%). Community composition obtained via pufM sequencing was dominated by Gammaproteobacteria clade NOR5/OM60, specifically genus Luminiphilus, with numerous rare genera present in relative abundances below 1%. The use of artificial neural network connected this community to biotic (heterotrophic bacteria, HNA and LNA bacteria, Synechococcus, Prochlorococcus, picoeukaryotes, heterotrophic nanoflagellates, bacterial production) and abiotic environmental factors (temperature, salinity, chlorophyll a and nitrate, nitrite, ammonia, total nitrogen, silicate, and orthophosphate concentration). A type of neural network, neural gas analysis at order-, genus- and ASV-level, resulted in five distinct best matching units (representing particular environments) and revealed that high diversity was generally independent of temperature, salinity, and trophic status of the environment, indicating a potentially dissimilar behaviour of aerobic anoxygenic phototrophs compared to the general bacterioplankton. CONCLUSION This research represents the first comprehensive analysis of aerobic anoxygenic phototrophs in the Adriatic Sea on a trophic gradient during a year-round period. This study is also one of the first reports of their genus-level ecology linked to biotic and abiotic environmental factors revealed by unsupervised neural network algorithm, paving the way for further research of substantial contribution of this important bacterial functional group to marine ecosystems.
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Affiliation(s)
- Iva Stojan
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
- Doctoral Study of Biophysics, Faculty of Science, University of Split, Ruđera Boškovića 37, Split, Croatia
| | - Danijela Šantić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia.
| | - Cristian Villena-Alemany
- Laboratory of Anoxygenic Phototrophs, Institute of Microbiology, Czech Academy of Sciences, 379 81, Třeboň, Czechia
- Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Željka Trumbić
- University Department of Marine Studies, University of Split, Ruđera Boškovića 37, Split, Croatia
| | - Frano Matić
- University Department of Marine Studies, University of Split, Ruđera Boškovića 37, Split, Croatia
| | - Ana Vrdoljak Tomaš
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
| | - Ivana Lepen Pleić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
| | - Kasia Piwosz
- Department of Fisheries, Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Gdynia, Poland
| | - Grozdan Kušpilić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
| | | | - Stefanija Šestanović
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
| | - Mladen Šolić
- Institute of Oceanography and Fisheries, Šetalište Ivana Meštrovića 63, Split, Croatia
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3
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Man DKW, Hermans SM, Taubert M, Garcia SL, Hengoju S, Küsel K, Rosenbaum MA. Enrichment of different taxa of the enigmatic candidate phyla radiation bacteria using a novel picolitre droplet technique. ISME COMMUNICATIONS 2024; 4:ycae080. [PMID: 38946848 PMCID: PMC11214157 DOI: 10.1093/ismeco/ycae080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 03/24/2024] [Accepted: 06/20/2024] [Indexed: 07/02/2024]
Abstract
The candidate phyla radiation (CPR) represents a distinct monophyletic clade and constitutes a major portion of the tree of life. Extensive efforts have focused on deciphering the functional diversity of its members, primarily using sequencing-based techniques. However, cultivation success remains scarce, presenting a significant challenge, particularly in CPR-dominated groundwater microbiomes characterized by low biomass. Here, we employ an advanced high-throughput droplet microfluidics technique to enrich CPR taxa from groundwater. Utilizing a low-volume filtration approach, we successfully harvested a microbiome resembling the original groundwater microbial community. We assessed CPR enrichment in droplet and aqueous bulk cultivation for 30 days using a novel CPR-specific primer to rapidly track the CPR fraction through the cultivation attempts. The combination of soil extract and microbial-derived necromass provided the most supportive conditions for CPR enrichment. Employing these supplemented conditions, droplet cultivation proved superior to bulk cultivation, resulting in up to a 13-fold CPR enrichment compared to a 1- to 2-fold increase in bulk cultivation. Amplicon sequencing revealed 10 significantly enriched CPR orders. The highest enrichment in CPRs was observed for some unknown members of the Parcubacteria order, Cand. Jorgensenbacteria, and unclassified UBA9983. Furthermore, we identified co-enriched putative host taxa, which may guide more targeted CPR isolation approaches in subsequent investigations.
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Affiliation(s)
- DeDe Kwun Wai Man
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), 07745 Jena, Germany
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
| | - Syrie M Hermans
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
- Food Science and Microbiology, School of Science, Faculty of Health and Environmental Sciences, Auckland University of Technology, 1142 Auckland, New Zealand
- Aquatic Geomicrobiology, Institute of Biodiversity, Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
| | - Martin Taubert
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
- Aquatic Geomicrobiology, Institute of Biodiversity, Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
| | - Sarahi L Garcia
- Department of Ecology, Environment and Plant Sciences, Science for Life Laboratory, Stockholm University, 106 91 Stockholm, Sweden
- Institute for Chemistry and Biology of the Marine Environment (ICBM), School of Mathematics and Science, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg, Germany
| | - Sundar Hengoju
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), 07745 Jena, Germany
| | - Kirsten Küsel
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
- Aquatic Geomicrobiology, Institute of Biodiversity, Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
| | - Miriam A Rosenbaum
- Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute (HKI), 07745 Jena, Germany
- Balance of the Microverse, Cluster of Excellence, Friedrich Schiller University, 07743 Jena, Germany
- Institute of Microbiology, Faculty of Biological Sciences, Friedrich Schiller University, 07743 Jena, Germany
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Kułak K, Wojciechowska N, Samelak-Czajka A, Jackowiak P, Bagniewska-Zadworna A. How to explore what is hidden? A review of techniques for vascular tissue expression profile analysis. PLANT METHODS 2023; 19:129. [PMID: 37981669 PMCID: PMC10659056 DOI: 10.1186/s13007-023-01109-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 11/10/2023] [Indexed: 11/21/2023]
Abstract
The evolution of plants to efficiently transport water and assimilates over long distances is a major evolutionary success that facilitated their growth and colonization of land. Vascular tissues, namely xylem and phloem, are characterized by high specialization, cell heterogeneity, and diverse cell components. During differentiation and maturation, these tissues undergo an irreversible sequence of events, leading to complete protoplast degradation in xylem or partial degradation in phloem, enabling their undisturbed conductive function. Due to the unique nature of vascular tissue, and the poorly understood processes involved in xylem and phloem development, studying the molecular basis of tissue differentiation is challenging. In this review, we focus on methods crucial for gene expression research in conductive tissues, emphasizing the importance of initial anatomical analysis and appropriate material selection. We trace the expansion of molecular techniques in vascular gene expression studies and discuss the application of single-cell RNA sequencing, a high-throughput technique that has revolutionized transcriptomic analysis. We explore how single-cell RNA sequencing will enhance our knowledge of gene expression in conductive tissues.
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Affiliation(s)
- Karolina Kułak
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
| | - Natalia Wojciechowska
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland
| | - Anna Samelak-Czajka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Paulina Jackowiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704, Poznan, Poland
| | - Agnieszka Bagniewska-Zadworna
- Department of General Botany, Institute of Experimental Biology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614, Poznan, Poland.
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5
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Kostešić E, Mitrović M, Kajan K, Marković T, Hausmann B, Orlić S, Pjevac P. Microbial Diversity and Activity of Biofilms from Geothermal Springs in Croatia. MICROBIAL ECOLOGY 2023; 86:2305-2319. [PMID: 37209180 PMCID: PMC10640420 DOI: 10.1007/s00248-023-02239-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 05/07/2023] [Indexed: 05/22/2023]
Abstract
Hot spring biofilms are stable, highly complex microbial structures. They form at dynamic redox and light gradients and are composed of microorganisms adapted to the extreme temperatures and fluctuating geochemical conditions of geothermal environments. In Croatia, a large number of poorly investigated geothermal springs host biofilm communities. Here, we investigated the microbial community composition of biofilms collected over several seasons at 12 geothermal springs and wells. We found biofilm microbial communities to be temporally stable and highly dominated by Cyanobacteria in all but one high-temperature sampling site (Bizovac well). Of the physiochemical parameters recorded, temperature had the strongest influence on biofilm microbial community composition. Besides Cyanobacteria, the biofilms were mainly inhabited by Chloroflexota, Gammaproteobacteria, and Bacteroidota. In a series of incubations with Cyanobacteria-dominated biofilms from Tuhelj spring and Chloroflexota- and Pseudomonadota-dominated biofilms from Bizovac well, we stimulated either chemoorganotrophic or chemolithotrophic community members, to determine the fraction of microorganisms dependent on organic carbon (in situ predominantly produced via photosynthesis) versus energy derived from geochemical redox gradients (here simulated by addition of thiosulfate). We found surprisingly similar levels of activity in response to all substrates in these two distinct biofilm communities, and observed microbial community composition and hot spring geochemistry to be poor predictors of microbial activity in the study systems.
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Affiliation(s)
- Ema Kostešić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Maja Mitrović
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
| | - Katarina Kajan
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia
| | | | - Bela Hausmann
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Sandi Orlić
- Division of Materials Chemistry, Ruđer Bošković Institute, Zagreb, Croatia
- Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia
| | - Petra Pjevac
- Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria.
- Centre for Microbiology and Environmental Systems Science, Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria.
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6
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Urasaki K, Li YY, Kubota K. A novel method for the whole-cell detection of environmental microorganisms using hemin and tyramide signal amplification (Hemin-TSA) with a desired fluorescent dye. Syst Appl Microbiol 2023; 46:126473. [PMID: 37977040 DOI: 10.1016/j.syapm.2023.126473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 10/28/2023] [Accepted: 11/09/2023] [Indexed: 11/19/2023]
Abstract
A method called hemin-tyramide signal amplification (Hemin-TSA) was developed for visualization of environmental microorganisms using hemin and tyramide signal amplification. In Hemin-TSA, hemin, which has peroxidase activity, is bound to microbial cells, and a desired fluorescent dye is deposited on the microbial cells by a hemin-catalyzed TSA reaction. The protocol was initially optimized in terms of hemin concentration, hemin binding time and repeated reaction times of TSA. Hemin-TSA showed a comparative or improved signal-to-noise ratio compared to DAPI staining. The shapes of fluorescent signals obtained from microbial cells were almost morphologically identical to those observed in phase contrast microscopy. Hemin-TSA staining provided more accurate cell counts than DAPI staining, especially for actively growing cells, for which two or three spotty DAPI signals were obtained from a single cell. In addition, microbial cells that were not detected by DAPI staining were detected by Hemin-TSA with fluorescein, which enabled us to avoid high non-specific fluorescence under UV excitation. The method developed in this study allows us to visually detect microbial cells in various environments with the characteristics of better cell morphological identification, improved enumeration accuracy and selectivity of fluorescent dyes.
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Affiliation(s)
- Kampachiro Urasaki
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Graduate School of Engineering, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan; Department of Frontier Sciences for Advanced Environment, Graduate School of Environmental Studies, Tohoku University, 6-6-06 Aoba, Aramaki, Aoba-ku, Sendai, Miyagi 980-8579, Japan.
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Mermans F, Mattelin V, Van den Eeckhoudt R, García-Timermans C, Van Landuyt J, Guo Y, Taurino I, Tavernier F, Kraft M, Khan H, Boon N. Opportunities in optical and electrical single-cell technologies to study microbial ecosystems. Front Microbiol 2023; 14:1233705. [PMID: 37692384 PMCID: PMC10486927 DOI: 10.3389/fmicb.2023.1233705] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/03/2023] [Indexed: 09/12/2023] Open
Abstract
New techniques are revolutionizing single-cell research, allowing us to study microbes at unprecedented scales and in unparalleled depth. This review highlights the state-of-the-art technologies in single-cell analysis in microbial ecology applications, with particular attention to both optical tools, i.e., specialized use of flow cytometry and Raman spectroscopy and emerging electrical techniques. The objectives of this review include showcasing the diversity of single-cell optical approaches for studying microbiological phenomena, highlighting successful applications in understanding microbial systems, discussing emerging techniques, and encouraging the combination of established and novel approaches to address research questions. The review aims to answer key questions such as how single-cell approaches have advanced our understanding of individual and interacting cells, how they have been used to study uncultured microbes, which new analysis tools will become widespread, and how they contribute to our knowledge of ecological interactions.
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Affiliation(s)
- Fabian Mermans
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
- Department of Oral Health Sciences, KU Leuven, Leuven, Belgium
| | - Valérie Mattelin
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Ruben Van den Eeckhoudt
- Micro- and Nanosystems (MNS), Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
| | - Cristina García-Timermans
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Josefien Van Landuyt
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Yuting Guo
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Irene Taurino
- Micro- and Nanosystems (MNS), Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
- Semiconductor Physics, Department of Physics and Astronomy, KU Leuven, Leuven, Belgium
| | - Filip Tavernier
- MICAS, Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
| | - Michael Kraft
- Micro- and Nanosystems (MNS), Department of Electrical Engineering (ESAT), KU Leuven, Leuven, Belgium
- Leuven Institute of Micro- and Nanoscale Integration (LIMNI), KU Leuven, Leuven, Belgium
| | - Hira Khan
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
| | - Nico Boon
- Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University, Ghent, Belgium
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Barbosa A, Miranda S, Azevedo NF, Cerqueira L, Azevedo AS. Imaging biofilms using fluorescence in situ hybridization: seeing is believing. Front Cell Infect Microbiol 2023; 13:1195803. [PMID: 37284501 PMCID: PMC10239779 DOI: 10.3389/fcimb.2023.1195803] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 05/08/2023] [Indexed: 06/08/2023] Open
Abstract
Biofilms are complex structures with an intricate relationship between the resident microorganisms, the extracellular matrix, and the surrounding environment. Interest in biofilms is growing exponentially given its ubiquity in so diverse fields such as healthcare, environmental and industry. Molecular techniques (e.g., next-generation sequencing, RNA-seq) have been used to study biofilm properties. However, these techniques disrupt the spatial structure of biofilms; therefore, they do not allow to observe the location/position of biofilm components (e.g., cells, genes, metabolites), which is particularly relevant to explore and study the interactions and functions of microorganisms. Fluorescence in situ hybridization (FISH) has been arguably the most widely used method for an in situ analysis of spatial distribution of biofilms. In this review, an overview on different FISH variants already applied on biofilm studies (e.g., CLASI-FISH, BONCAT-FISH, HiPR-FISH, seq-FISH) will be explored. In combination with confocal laser scanning microscopy, these variants emerged as a powerful approach to visualize, quantify and locate microorganisms, genes, and metabolites inside biofilms. Finally, we discuss new possible research directions for the development of robust and accurate FISH-based approaches that will allow to dig deeper into the biofilm structure and function.
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Affiliation(s)
- Ana Barbosa
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Sónia Miranda
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - Nuno F. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Laura Cerqueira
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
| | - Andreia S. Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
- ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP-Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
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Kreth J, Merritt J. Illuminating the oral microbiome and its host interactions: tools and approaches for molecular ecological studies. FEMS Microbiol Rev 2023; 47:fuac052. [PMID: 36564013 PMCID: PMC9936263 DOI: 10.1093/femsre/fuac052] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 12/25/2022] Open
Abstract
A more comprehensive understanding of oral diseases like caries and periodontitis is dependent on an intimate understanding of the microbial ecological processes that are responsible for disease development. With this review, we provide a comprehensive overview of relevant molecular ecology techniques that have played critical roles in the current understanding of human oral biofilm development, interspecies interactions, and microbiome biogeography. The primary focus is on relevant technologies and examples available in the oral microbiology literature. However, most, if not all, of the described technologies should be readily adaptable for studies of microbiomes from other mucosal sites in the body. Therefore, this review is intended to serve as a reference guide used by microbiome researchers as they inevitably transition into molecular mechanistic studies of the many significant phenotypes observed clinically.
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Affiliation(s)
- Jens Kreth
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, MRB433, 3181 SW Sam Jackson Park Rd., #L595, Portland, OR 97239, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, United States
| | - Justin Merritt
- Department of Restorative Dentistry, School of Dentistry, Oregon Health and Science University, MRB433, 3181 SW Sam Jackson Park Rd., #L595, Portland, OR 97239, United States
- Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, OR, United States
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Application of Fluorescence In Situ Hybridization (FISH) in Oral Microbial Detection. Pathogens 2022; 11:pathogens11121450. [PMID: 36558784 PMCID: PMC9788346 DOI: 10.3390/pathogens11121450] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Revised: 11/26/2022] [Accepted: 11/29/2022] [Indexed: 12/02/2022] Open
Abstract
Varieties of microorganisms reside in the oral cavity contributing to the occurrence and development of microbes associated with oral diseases; however, the distribution and in situ abundance in the biofilm are still unclear. In order to promote the understanding of the ecosystem of oral microbiota and the diagnosis of oral diseases, it is necessary to monitor and compare the oral microorganisms from different niches of the oral cavity in situ. The fluorescence in situ hybridization (FISH) has proven to be a powerful tool for representing the status of oral microorganisms in the oral cavity. FISH is one of the most routinely used cytochemical techniques for genetic detection, identification, and localization by a fluorescently labeled nucleic acid probe, which can hybridize with targeted nucleic acid sequences. It has the advantages of rapidity, safety, high sensitivity, and specificity. FISH allows the identification and quantification of different oral microorganisms simultaneously. It can also visualize microorganisms by combining with other molecular biology technologies to represent the distribution of each microbial community in the oral biofilm. In this review, we summarized and discussed the development of FISH technology and the application of FISH in oral disease diagnosis and oral ecosystem research, highlighted its advantages in oral microbiology, listed the existing problems, and provided suggestions for future development..
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11
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Compendium of analytical methods for sampling, characterization and quantification of bioaerosols. ADV ECOL RES 2022. [DOI: 10.1016/bs.aecr.2022.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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12
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Diakoumopoulou D, Magana M, Karoussis IK, Nikolaou C, Chatzipanagiotou S, Ioannidis A. The ever-changing landscape in modern dentistry therapeutics - Enhancing the emptying quiver of the periodontist. Heliyon 2021; 7:e08342. [PMID: 34816039 PMCID: PMC8591475 DOI: 10.1016/j.heliyon.2021.e08342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 09/12/2021] [Accepted: 11/04/2021] [Indexed: 11/29/2022] Open
Abstract
Introduction/Objectives Periodontitis comprises of a wide range of inflammatory conditions of the gums leading to soft tissue damage and attachment loss. The initiation of periodontitis constitutes a rather complex disease pathogenesis which is based on pathogenic shifts of the oral microbiota combined with the host-microbiome interactions. The severity of the periodontitis is multifactorial depending on genetic, environmental, as well as host immunity factors. Data and sources To make an inclusive analysis on the periodontitis therapeutics, reading of the recent relevant literature was carried out using the MEDLINE/PubMed database, Google Scholar and the NIH public online database for clinical trials (http://www.clinicaltrials.gov). Conclusions Tackling the inflammation associated periodontal defects can be succeeded with conventional therapy or resective and regenerative treatment. To date, the mechanical removal of the supragingival and subgingival biofilm is considered the “gold standard” of periodontal therapy in combination with the use of antibacterial compounds. The antimicrobial resistance phenomenon tends to turn all the currently applied antibacterials into “endangered species”. Ongoing efforts through the conduct of clinical trials should be focused on understanding the advantages of modern approaches in comparison to traditional therapies.
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Affiliation(s)
- Dimitra Diakoumopoulou
- Department of Clinical Microbiology, Athens Medical School, Aeginition Hospital, Athens, Greece
| | - Maria Magana
- Department of Clinical Microbiology, Athens Medical School, Aeginition Hospital, Athens, Greece
| | - Ioannis K Karoussis
- Department of Periodontology, School of Dental Medicine, National and Kapodistrian University of Athens, Athens, Greece
| | - Chrysoula Nikolaou
- Department of Clinical Microbiology, Athens Medical School, Aeginition Hospital, Athens, Greece
| | | | - Anastasios Ioannidis
- Department of Clinical Microbiology, Athens Medical School, Aeginition Hospital, Athens, Greece.,Department of Nursing, Faculty of Health Sciences, University of Peloponnese, Tripolis, Greece
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Jia Z, Dong Y, Xu H, Wang F. Optimizing the hybridization chain reaction-fluorescence in situ hybridization (HCR-FISH) protocol for detection of microbes in sediments. MARINE LIFE SCIENCE & TECHNOLOGY 2021; 3:529-541. [PMID: 37073263 PMCID: PMC10077247 DOI: 10.1007/s42995-021-00098-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 02/17/2021] [Indexed: 05/03/2023]
Abstract
Fluorescence in situ hybridization (FISH) is a canonical tool commonly used in environmental microbiology research to visualize targeted cells. However, the problems of low signal intensity and false-positive signals impede its widespread application. Alternatively, the signal intensity can be amplified by incorporating Hybridization Chain Reaction (HCR) with FISH, while the specificity can be improved through protocol modification and proper counterstaining. Here we optimized the HCR-FISH protocol for studying microbes in environmental samples, particularly marine sediments. Firstly, five sets of HCR initiator/amplifier pairs were tested on the laboratory-cultured bacterium Escherichia coli and the archaeon Methanococcoides methylutens, and two sets displayed high hybridization efficiency and specificity. Secondly, we tried to find the best combination of sample pretreatment methods and HCR-FISH protocol for environmental sample analysis with the aim of producing less false positive signals. Various detachment methods, extraction methods and formulas of hybridization buffer were tested using sediment samples. Thirdly, an image processing method was developed to enhance the DAPI signal of microbial cells against that of abiotic particles, providing a reliable reference for FISH imaging. In summary, our optimized HCR-FISH protocol showed promise to serve as an addendum to traditional FISH for research on environmental microbes. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-021-00098-8.
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Affiliation(s)
- Zeyu Jia
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Yijing Dong
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Heng Xu
- School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, 200240 China
- Institute of Natural Science, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
- School of Oceanography, Shanghai Jiao Tong University, Shanghai, 200240 China
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14
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Wang X, Howe S, Deng F, Zhao J. Current Applications of Absolute Bacterial Quantification in Microbiome Studies and Decision-Making Regarding Different Biological Questions. Microorganisms 2021; 9:1797. [PMID: 34576694 PMCID: PMC8467167 DOI: 10.3390/microorganisms9091797] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 08/16/2021] [Accepted: 08/21/2021] [Indexed: 11/17/2022] Open
Abstract
High throughput sequencing has emerged as one of the most important techniques for characterizing microbial dynamics and revealing bacteria and host interactions. However, data interpretation using this technique is mainly based on relative abundance and ignores total bacteria load. In certain cases, absolute abundance is more important than compositional relative data, and interpretation of microbiota data based solely on relative abundance can be misleading. The available approaches for absolute quantification are highly diverse and challenging, especially for quantification in differing biological situations, such as distinguishing between live and dead cells, quantification of specific taxa, enumeration of low biomass samples, large sample size feasibility, and the detection of various other cellular features. In this review, we first illustrate the importance of integrating absolute abundance into microbiome data interpretation. Second, we briefly discuss the most widely used cell-based and molecular-based bacterial load quantification methods, including fluorescence spectroscopy, flow cytometry, 16S qPCR, 16S qRT-PCR, ddPCR, and reference spike-in. Last, we present a specific decision-making scheme for absolute quantification methods based on different biological questions and some of the latest quantitative methods and procedure modifications.
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Affiliation(s)
- Xiaofan Wang
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Samantha Howe
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
| | - Feilong Deng
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, College of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Jiangchao Zhao
- Department of Animal Science, Division of Agriculture, University of Arkansas, Fayetteville, AR 72701, USA
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15
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Cahn JKB, Piel J. Anwendungen von Einzelzellmethoden in der mikrobiellen Naturstoffforschung. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.201900532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jackson K. B. Cahn
- Institut für Mikrobiologie Eidgenössische Technische Hochschule Zürich (ETH) 8093 Zürich Schweiz
| | - Jörn Piel
- Institut für Mikrobiologie Eidgenössische Technische Hochschule Zürich (ETH) 8093 Zürich Schweiz
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16
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Sequence-specific capture of oligonucleotide probes (SCOPE): A simple and rapid microbial rRNA quantification method using molecular weight cut-off membrane. Appl Environ Microbiol 2021; 87:e0116721. [PMID: 34319794 DOI: 10.1128/aem.01167-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A method named sequence-specific capture of oligonucleotide probes (SCOPE) was developed for quantification of microbial rRNA molecules in a multiplex manner. In this method, molecular weight cut-off membrane (MWCOM) was used for the separation of fluorescent-labeled oligonucleotide probes hybridized with rRNA from free unhybridized probes. To demonstrate proof-of-concept, probes targeting bacteria or archaea at different taxonomic levels were prepared and were hybridized with rRNAs. The hybridization stringency was controlled by adjusting reaction temperature and urea concentration in the mixture. Then, the mixture was filtered through the MWCOM. The rRNA and hybridized probes collected on the MWCOM were recovered and quantified using spectrophotometer and fluorospectrometer, respectively. The method showed high accuracy in detecting specific microbial rRNA in a defined nucleic acid mixture. Furthermore, the method was capable of simultaneous detection and quantification of multiple target rRNAs in a sample with sensitivity up to a single-base mismatch. The SCOPE method was tested and benchmarked against the reverse transcription-quantitative PCR (RT-qPCR) for the quantification of Bacteria, Archaea and some key methanogens in anaerobic sludge samples. It was observed that the SCOPE method produced comparatively more reliable and coherent results. In this way, the SCOPE method allows a simple and rapid detection and quantification of target microbial rRNAs for environmental microbial population analysis without any need for enzymatic reactions. Importance Microorganisms play integral roles in the earth's ecosystem. Microbial population and their activities significantly affect the global nutrient cycles. Quantification of key microorganisms provides important information that is required to understand their roles in the environment. Sequence-based analysis of microbial population is a powerful tool, but it only provides information on relative abundance of microorganisms. Hence, the development of a simpler and quick method for the quantification of microorganisms is necessary. To address the shortcomings of a variety of molecular methods reported so far, we developed a simple, rapid, accurate and multiplexed microbial rRNA quantification method to evaluate the abundance of specific microbial population in complex ecosystems. The developed method demonstrated high specificity, reproducibility, and applicability to such samples. The method is useful for quantitative detection of particular microbial members in the environment.
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17
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Cahn JKB, Piel J. Opening up the Single-Cell Toolbox for Microbial Natural Products Research. Angew Chem Int Ed Engl 2021; 60:18412-18428. [PMID: 30748086 DOI: 10.1002/anie.201900532] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Indexed: 02/06/2023]
Abstract
The diverse microbes that produce natural products represent an important source of novel therapeutics, drug leads, and scientific tools. However, the vast majority have not been grown in axenic culture and are members of complex communities. While meta-'omic methods such as metagenomics, -transcriptomics, and -proteomics reveal collective molecular features of this "microbial dark matter", the study of individual microbiome members can be challenging. To address these limits, a number of techniques with single-bacterial resolution have been developed in the last decade and a half. While several of these are embraced by microbial ecologists, there has been less use by researchers interested in mining microbes for natural products. In this review, we discuss the available and emerging techniques for targeted single-cell analysis with a particular focus on applications to the discovery and study of natural products.
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Affiliation(s)
- Jackson K B Cahn
- Instit. of Microbiol., Eidgenössische Technische Hochschule Zürich (ETH), 8093, Zurich, Switzerland
| | - Jörn Piel
- Instit. of Microbiol., Eidgenössische Technische Hochschule Zürich (ETH), 8093, Zurich, Switzerland
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18
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Delpech LM, Vonnahme TR, McGovern M, Gradinger R, Præbel K, Poste AE. Terrestrial Inputs Shape Coastal Bacterial and Archaeal Communities in a High Arctic Fjord (Isfjorden, Svalbard). Front Microbiol 2021; 12:614634. [PMID: 33717004 PMCID: PMC7952621 DOI: 10.3389/fmicb.2021.614634] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/29/2021] [Indexed: 11/13/2022] Open
Abstract
The Arctic is experiencing dramatic changes including increases in precipitation, glacial melt, and permafrost thaw, resulting in increasing freshwater runoff to coastal waters. During the melt season, terrestrial runoff delivers carbon- and nutrient-rich freshwater to Arctic coastal waters, with unknown consequences for the microbial communities that play a key role in determining the cycling and fate of terrestrial matter at the land-ocean interface. To determine the impacts of runoff on coastal microbial (bacteria and archaea) communities, we investigated changes in pelagic microbial community structure between the early (June) and late (August) melt season in 2018 in the Isfjorden system (Svalbard). Amplicon sequences of the 16S rRNA gene were generated from water column, river and sediment samples collected in Isfjorden along fjord transects from shallow river estuaries and glacier fronts to the outer fjord. Community shifts were investigated in relation to environmental gradients, and compared to river and marine sediment microbial communities. We identified strong temporal and spatial reorganizations in the structure and composition of microbial communities during the summer months in relation to environmental conditions. Microbial diversity patterns highlighted a reorganization from rich communities in June toward more even and less rich communities in August. In June, waters enriched in dissolved organic carbon (DOC) provided a niche for copiotrophic taxa including Sulfitobacter and Octadecabacter. In August, lower DOC concentrations and Atlantic water inflow coincided with a shift toward more cosmopolitan taxa usually associated with summer stratified periods (e.g., SAR11 Clade Ia), and prevalent oligotrophic marine clades (OM60, SAR92). Higher riverine inputs of dissolved inorganic nutrients and suspended particulate matter also contributed to spatial reorganizations of communities in August. Sentinel taxa of this late summer fjord environment included taxa from the class Verrucomicrobiae (Roseibacillus, Luteolibacter), potentially indicative of a higher fraction of particle-attached bacteria. This study highlights the ecological relevance of terrestrial runoff for Arctic coastal microbial communities and how its impacts on biogeochemical conditions may make these communities susceptible to climate change.
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Affiliation(s)
- Lisa-Marie Delpech
- Department of Biology, École Normale Supérieure de Lyon, Université de Lyon, Lyon, France.,Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway.,Norwegian Institute for Water Research (NIVA), Tromsø, Norway
| | - Tobias R Vonnahme
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Maeve McGovern
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway.,Norwegian Institute for Water Research (NIVA), Tromsø, Norway
| | - Rolf Gradinger
- Department of Arctic and Marine Biology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Kim Præbel
- Norwegian College of Fishery Science, UiT The Arctic University of Norway, Tromsø, Norway
| | - Amanda E Poste
- Norwegian Institute for Water Research (NIVA), Tromsø, Norway
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19
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Borics G, Abonyi A, Salmaso N, Ptacnik R. Freshwater phytoplankton diversity: models, drivers and implications for ecosystem properties. HYDROBIOLOGIA 2021; 848:53-75. [PMID: 32836348 PMCID: PMC7334633 DOI: 10.1007/s10750-020-04332-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/09/2020] [Accepted: 06/13/2020] [Indexed: 05/20/2023]
Abstract
Our understanding on phytoplankton diversity has largely been progressing since the publication of Hutchinson on the paradox of the plankton. In this paper, we summarise some major steps in phytoplankton ecology in the context of mechanisms underlying phytoplankton diversity. Here, we provide a framework for phytoplankton community assembly and an overview of measures on taxonomic and functional diversity. We show how ecological theories on species competition together with modelling approaches and laboratory experiments helped understand species coexistence and maintenance of diversity in phytoplankton. The non-equilibrium nature of phytoplankton and the role of disturbances in shaping diversity are also discussed. Furthermore, we discuss the role of water body size, productivity of habitats and temperature on phytoplankton species richness, and how diversity may affect the functioning of lake ecosystems. At last, we give an insight into molecular tools that have emerged in the last decades and argue how it has broadened our perspective on microbial diversity. Besides historical backgrounds, some critical comments have also been made.
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Affiliation(s)
- Gábor Borics
- Department of Tisza Research, Centre for Ecological Research, Danube Research Institute, Bem tér 18/c, 4026 Debrecen, Hungary
- GINOP Sustainable Ecosystems Group, Centre for Ecological Research, Klebelsberg Kuno u. 3, 8237 Tihany, Hungary
| | - András Abonyi
- Centre for Ecological Research, Institute of Ecology and Botany, Alkotmány u. 2-4, 2163 Vácrátót, Hungary
- WasserCluster Lunz – Biologische Station GmbH, Dr. Carl Kupelwieser-Promenade 5, 3293 Lunz am See, Austria
| | - Nico Salmaso
- Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Italy
| | - Robert Ptacnik
- WasserCluster Lunz – Biologische Station GmbH, Dr. Carl Kupelwieser-Promenade 5, 3293 Lunz am See, Austria
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20
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Abstract
Fluorescence in situ hybridization (FISH) is a molecular biology technique that enables the localization, quantification, and identification of microorganisms in a sample. This technique has found applications in several areas, most notably the environmental, for quantification and diversity assessment of microorganisms and, the clinical, for the rapid diagnostics of infectious agents. The FISH method is based on the hybridization of a fluorescently labeled nucleic acid probe with a complementary sequence that is present inside the microbial cell, typically in the form of ribosomal RNA (rRNA). In fact, an hybridized cell is typically only detectable because a large number of multiple fluorescent particles (as many as the number of target sequences available) are present inside the cell. Here, we will review the major steps involved in a standard FISH protocol, namely, fixation/permeabilization, hybridization, washing, and visualization/detection. For each step, the major variables/parameters are identified and, subsequently, their impact on the overall hybridization performance is assessed in detail.
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Affiliation(s)
- Carina Almeida
- INIAV - National Institute for Agrarian and Veterinarian Research, Rua dos Lagidos, Lugar da Madalena, Vairão, Vila do Conde, Portugal.
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal.
- CEB - Centre of Biological Engineering, Universidade do Minho, Campus de Gualtar, Braga, Portugal.
| | - Nuno F Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Porto, Portugal
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21
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Wakade VS, Shende P. Strategic advancements and multimodal applications of biofilm therapy. Expert Opin Biol Ther 2020; 21:395-412. [PMID: 32933329 DOI: 10.1080/14712598.2020.1822319] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
INTRODUCTION Biofilm is a layer of mucilage consisting of bacterial species like Escherichia coli and Streptococcus aureus adhering to the solid cell surface. Biofilm is an important and novel approach in a delivery system consisting of six elements that includes extracellular DNA, enzymes, proteins, bacteria, exopolysaccharides and water channels. The biofilm formation is based on two mechanisms: extra polymeric substance and quorum sensing. The microbes present in biofilm prevent direct interaction between the cell surface and foreign materials, like allergens, or toxic gases, like carbon-monoxide and chlorofluorocarbon, entering the body. AREAS COVERED The authors focus on the novel applications of biofilms such as adhesives, tissue engineering, targeted delivery system, probiotics, nutrients delivery, etc. Moreover, the information of the factors for biofilm formation, techniques useful in biofilm formation, and clinical studies are also covered in this article. EXPERT OPINION Many people believe that biofilms have a negative impact on human health, but the expert opinion states that biofilm is a futuristic approach useful in therapeutics for the treatment of tumors and cancer. Biofilms can be combined with novel delivery systems such as nanoparticles, microparticles, etc. for better therapeutic action.
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Affiliation(s)
- Varun S Wakade
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM's NMIMS, Vile Parle (W), India
| | - Pravin Shende
- Shobhaben Pratapbhai Patel School of Pharmacy and Technology Management, SVKM's NMIMS, Vile Parle (W), India
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22
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Gallego S, Barkay T, Fahrenfeld NL. Tagging the vanA gene in wastewater microbial communities for cell sorting and taxonomy of vanA carrying cells. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 732:138865. [PMID: 32417556 DOI: 10.1016/j.scitotenv.2020.138865] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/18/2020] [Accepted: 04/19/2020] [Indexed: 06/11/2023]
Abstract
Failure to understand the microbial ecology driving the proliferation of antibiotic resistance in the environment prevents us from developing strategies to limit the spread of antibiotic resistant infectious disease. In this study, we developed for the first time a tyramide signal amplification-fluorescence in situ hybridization-fluorescence-activated cell sorting protocol (TSA-FISH-FACS) for the characterization of all vanA carrying bacteria in wastewater samples. Firstly, we validated the TSA-FISH protocol through microscopy in pure cultures and wastewater influent. Then, samples were sorted and quantified by FACS and qPCR. Significantly higher percentage tagging of cells was detected in vanA carrying pure cultures and wastewater samples spiked with vanA carrying cells as compared to vanA negative Gram positive strains and non-spiked wastewater samples respectively. qPCR analysis targeting vanZ, a regulating gene in the vanA cluster, showed its relative abundance was significantly greater in Enterococcus faecium ATCC 700221-spiked and positively sorted samples compared to the E. faecium spiked and negatively sorted samples. Phylogenetic analysis was then performed. Although further efforts are needed to overcome technical problems, we have, for the first time, demonstrated sorting bacterial-cells carrying antibiotic resistance genes from wastewater samples through a TSA-FISH-FACS protocol and provided insight into the microbial ecology of vancomycin resistant bacteria. Future potential applications using this approach will include the separation of members of an environmental microbial community (cultured and hard-to-culture) to allow for metagenomics on single cells or, in the case of clumping, targeting a smaller portion of the community with a priori knowledge that the target gene is present.
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Affiliation(s)
- Sara Gallego
- Civil & Environmental Engineering, Rutgers, The State University of New Jersey, 500 Bartholomew Rd., Piscataway, NJ 08854, United States of America
| | - Tamar Barkay
- Department of Biochemistry and Microbiology, 76 Lipman Dr, Rutgers, The State University of New Jersey, New Brunswick, NJ 08901, United States of America
| | - N L Fahrenfeld
- Civil & Environmental Engineering, Rutgers, The State University of New Jersey, 500 Bartholomew Rd., Piscataway, NJ 08854, United States of America.
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Morono Y, Kubota K, Tsukagoshi D, Terada T. EDTA-FISH: A Simple and Effective Approach to Reduce Non-specific Adsorption of Probes in Fluorescence in situ Hybridization (FISH) for Environmental Samples. Microbes Environ 2020; 35. [PMID: 32595184 PMCID: PMC7511785 DOI: 10.1264/jsme2.me20062] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is a widely used molecular technique in microbial ecology. However, the non-specific adsorption of fluorescent probes and resulting high intensity of background signals from mineral particles hampers the specific detection of microbial cells in grain-rich environmental samples, such as subseafloor sediments. We herein demonstrated that a new buffer composition containing EDTA efficiently reduced the adsorption of probes without compromising the properties of the FISH-based probing of microbes. The inclusion of a high concentration of EDTA in the buffer in our protocol provides a simple and effective approach for reducing the background in FISH for environmental samples.
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Affiliation(s)
- Yuki Morono
- Geomicrobiology Group, Kochi Institute for Core Sample Research, Japan Agency for Earth-Marine Science and Technology (JAMSTEC)
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University
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Liu JM, Bao ZH, Cao WW, Han JJ, Zhao J, Kang ZZ, Wang LX, Zhao J. Enrichment of Type I Methanotrophs with nirS Genes of Three Emergent Macrophytes in a Eutrophic Wetland in China. Microbes Environ 2020; 35. [PMID: 31969532 PMCID: PMC7104278 DOI: 10.1264/jsme2.me19098] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The pmoA gene, encoding particulate methane monooxygenase in methanotrophs, and nirS and nirK genes, encoding bacterial nitrite reductases, were examined in the root and rhizosphere sediment of three common emergent macrophytes (Phragmites australis, Typha angustifolia, and Scirpus triqueter) and unvegetated sediment from eutrophic Wuliangsuhai Lake in China. Sequencing analyses indicated that 334 out of 351 cloned pmoA sequences were phylogenetically the most closely related to type I methanotrophs (Gammaproteobacteria), and Methylomonas denitrificans-like organisms accounted for 44.4% of the total community. In addition, 244 out of 250 cloned nirS gene sequences belonged to type I methanotrophs, and 31.2% of nirS genes were the most closely related to paddy rice soil clone SP-2-12 in Methylomonas of the total community. Three genera of type I methanotrophs, Methylomonas, Methylobacter, and Methylovulum, were common in both pmoA and nirS clone libraries in each sample. A quantitative PCR (qPCR) analysis demonstrated that the copy numbers of the nirS and nirK genes were significantly higher in rhizosphere sediments than in unvegetated sediments in P. australis and T. angustifolia plants. In the same sample, the nirS gene copy number was significantly higher than that of nirK. Furthermore, type I methanotrophs were localized in the root tissues according to catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Thus, nirS-carrying type I methanotrophs were enriched in macrophyte root and rhizosphere sediment and are expected to play important roles in carbon/nitrogen cycles in a eutrophic wetland.
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Affiliation(s)
- Ju-Mei Liu
- College of Life Sciences, Inner Mongolia University.,College of Chemistry and Environmental Engineering, Chongqing Key Laboratory of Environmental Materials & Remediation Technologies, Chongqing University of Arts and Sciences
| | - Zhi-Hua Bao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University.,Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University
| | - Wei-Wei Cao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University
| | - Jing-Jing Han
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University
| | - Jun Zhao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University
| | - Zhen-Zhong Kang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University
| | - Li-Xin Wang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University
| | - Ji Zhao
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University.,Inner Mongolia Key Laboratory of Environmental Pollution Control & Waste Resource Reuse, Inner Mongolia University
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25
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Rodriguez-Mateos P, Azevedo NF, Almeida C, Pamme N. FISH and chips: a review of microfluidic platforms for FISH analysis. Med Microbiol Immunol 2020; 209:373-391. [PMID: 31965296 PMCID: PMC7248050 DOI: 10.1007/s00430-019-00654-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 12/19/2019] [Indexed: 12/12/2022]
Abstract
Fluorescence in situ hybridization (FISH) allows visualization of specific nucleic acid sequences within an intact cell or a tissue section. It is based on molecular recognition between a fluorescently labeled probe that penetrates the cell membrane of a fixed but intact sample and hybridizes to a nucleic acid sequence of interest within the cell, rendering a measurable signal. FISH has been applied to, for example, gene mapping, diagnosis of chromosomal aberrations and identification of pathogens in complex samples as well as detailed studies of cellular structure and function. However, FISH protocols are complex, they comprise of many fixation, incubation and washing steps involving a range of solvents and temperatures and are, thus, generally time consuming and labor intensive. The complexity of the process, the relatively high-priced fluorescent probes and the fairly high-end microscopy needed for readout render the whole process costly and have limited wider uptake of this powerful technique. In recent years, there have been attempts to transfer FISH assay protocols onto microfluidic lab-on-a-chip platforms, which reduces the required amount of sample and reagents, shortens incubation times and, thus, time to complete the protocol, and finally has the potential for automating the process. Here, we review the wide variety of approaches for lab-on-chip-based FISH that have been demonstrated at proof-of-concept stage, ranging from FISH analysis of immobilized cell layers, and cells trapped in arrays, to FISH on tissue slices. Some researchers have aimed to develop simple devices that interface with existing equipment and workflows, whilst others have aimed to integrate the entire FISH protocol into a fully autonomous FISH on-chip system. Whilst the technical possibilities for FISH on-chip are clearly demonstrated, only a small number of approaches have so far been converted into off-the-shelf products for wider use beyond the research laboratory.
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Affiliation(s)
- Pablo Rodriguez-Mateos
- Department of Chemistry and Biochemistry, University of Hull, Cottingham Road, Hull, HU6 7RX, UK
| | - Nuno Filipe Azevedo
- LEPABE-Laboratory for Process Engineering, Environment, Biotechnology and Energy, Department of Chemical Engineering, Faculty of Engineering of University of Porto, Rua Dr. Roberto Frias, s/n, 4200-465, Porto, Portugal.,Biomode SA, Av. Mestre José Veiga, 4715-330, Braga, Portugal
| | - Carina Almeida
- Biomode SA, Av. Mestre José Veiga, 4715-330, Braga, Portugal.,INIAV, I.P.-National Institute for Agricultural and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão, 4485-655, Vila Do Conde, Portugal.,CEB-Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Nicole Pamme
- Department of Chemistry and Biochemistry, University of Hull, Cottingham Road, Hull, HU6 7RX, UK.
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26
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Baña Z, Abad N, Uranga A, Azúa I, Artolozaga I, Unanue M, Iriberri J, Arrieta JM, Ayo B. Recurrent seasonal changes in bacterial growth efficiency, metabolism and community composition in coastal waters. Environ Microbiol 2019; 22:369-380. [PMID: 31713276 DOI: 10.1111/1462-2920.14853] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Revised: 09/25/2019] [Accepted: 11/03/2019] [Indexed: 11/28/2022]
Abstract
The microbial response to environmental changes in coastal waters of the eastern Cantabrian Sea was explored for four years by analysing a broad set of environmental variables along with bacterial community metabolism and composition. A recurrent seasonal cycle emerged, consisting of two stable periods, characterized by low bacterial metabolic activity (winter) from October to March, and high bacterial metabolic activity (summer) from May to August. These two contrasting periods were linked by short transition periods in April (TA ) and September (TS ). The phylogenetic groups Alphaproteobacteria and Bacteroidetes were dominant during winter and summer respectively, and their recurrent alternation was mainly driven by the bloom of eukaryotic phytoplankton before TA and the bloom of prokaryotic phytoplankton before TS . Bacterial growth efficiency remained high and stable during the winter and summer periods but dropped during the two short transition periods. Our results suggest that bacterial growth efficiency should be considered a very resilient property that reflects different stages in the adaptation of the bacterial community composition to the environmental changes occurring throughout the seasonal cycle in this coastal ecosystem.
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Affiliation(s)
- Zuriñe Baña
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Sarriena S/N, Leioa, 48940, Spain
| | - Naiara Abad
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Sarriena S/N, Leioa, 48940, Spain
| | - Ainhoa Uranga
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Sarriena S/N, Leioa, 48940, Spain
| | - Iñigo Azúa
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Sarriena S/N, Leioa, 48940, Spain
| | - Itxaso Artolozaga
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Sarriena S/N, Leioa, 48940, Spain
| | - Marian Unanue
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Sarriena S/N, Leioa, 48940, Spain
| | - Juan Iriberri
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Sarriena S/N, Leioa, 48940, Spain.,Research Centre for Experimental Marine Biology and Biotechnology PiE-UPV/EHU, Areatza Hiribidea 47, Plentzia, 48620, Spain
| | - Jesus M Arrieta
- Oceanographic Center of Canary Island, Spanish Institute of Oceanography IEO, Vía Espaldón, Parcela 8, Santa Cruz De Tenerife, 38180, Spain
| | - Begoña Ayo
- Department of Immunology, Microbiology and Parasitology, Faculty of Science and Technology, University of Basque Country (UPV/EHU), Sarriena S/N, Leioa, 48940, Spain.,Research Centre for Experimental Marine Biology and Biotechnology PiE-UPV/EHU, Areatza Hiribidea 47, Plentzia, 48620, Spain
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27
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Cattò C, Cappitelli F. Testing Anti-Biofilm Polymeric Surfaces: Where to Start? Int J Mol Sci 2019; 20:E3794. [PMID: 31382580 PMCID: PMC6696330 DOI: 10.3390/ijms20153794] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 08/02/2019] [Indexed: 12/11/2022] Open
Abstract
Present day awareness of biofilm colonization on polymeric surfaces has prompted the scientific community to develop an ever-increasing number of new materials with anti-biofilm features. However, compared to the large amount of work put into discovering potent biofilm inhibitors, only a small number of papers deal with their validation, a critical step in the translation of research into practical applications. This is due to the lack of standardized testing methods and/or of well-controlled in vivo studies that show biofilm prevention on polymeric surfaces; furthermore, there has been little correlation with the reduced incidence of material deterioration. Here an overview of the most common methods for studying biofilms and for testing the anti-biofilm properties of new surfaces is provided.
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Affiliation(s)
- Cristina Cattò
- Department of Food Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy
| | - Francesca Cappitelli
- Department of Food Environmental and Nutritional Sciences, Università degli Studi di Milano, via Celoria 2, 20133 Milano, Italy.
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28
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Panferova NA, Panferov VG, Safenkova IV, Varitsev YA, Zherdev AV, Dzantiev BB. Development of Enzyme-Linked Immunosorbent Assay with Tiramine Amplification for the Detection of Potato Virus X. APPL BIOCHEM MICRO+ 2019. [DOI: 10.1134/s0003683819040136] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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29
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Caracciolo AB, Dejana L, Fajardo C, Grenni P, Martin M, Mengs G, Sánchez-Fortún S, Lettieri T, Saccà M, Medlin L. A new fluorescent oligonucleotide probe for in-situ identification of Microcystis aeruginosa in freshwater. Microchem J 2019. [DOI: 10.1016/j.microc.2019.05.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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30
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Zhou Z, Pan J, Wang F, Gu JD, Li M. Bathyarchaeota: globally distributed metabolic generalists in anoxic environments. FEMS Microbiol Rev 2018; 42:639-655. [PMID: 29790926 DOI: 10.1093/femsre/fuy023] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 05/18/2018] [Indexed: 11/12/2022] Open
Abstract
Bathyarchaeota, formerly known as the Miscellaneous Crenarchaeotal Group, is a phylum of global generalists that are widespread in anoxic sediments, which host relatively high abundance archaeal communities. Until now, 25 subgroups have been identified in the Bathyarchaeota. The distinct bathyarchaeotal subgroups diverged to adapt to marine and freshwater environments. Based on the physiological and genomic evidence, acetyl-coenzyme A-centralized heterotrophic pathways of energy conservation have been proposed to function in Bathyarchaeota; these microbes are able to anaerobically utilize (i) detrital proteins, (ii) polymeric carbohydrates, (iii) fatty acids/aromatic compounds, (iv) methane (or short chain alkane) and methylated compounds, and/or (v) potentially other organic matter. Furthermore, bathyarchaeotal members have wide metabolic capabilities, including acetogenesis, methane metabolism, and dissimilatory nitrogen and sulfur reduction, and they also have potential interactions with anaerobic methane-oxidizing archaea, acetoclastic methanogens and heterotrophic bacteria. These results have not only demonstrated multiple and important ecological functions of this archaeal phylum, but also paved the way for a detailed understanding of the evolution and metabolism of archaea as such. This review summarizes the recent findings pertaining to the ecological, physiological and genomic aspects of Bathyarchaeota, highlighting the vital role of this phylum in global carbon cycling.
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Affiliation(s)
- Zhichao Zhou
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China.,Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Jie Pan
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China
| | - Fengping Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.,State Key Laboratory of Ocean Engineering, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Ji-Dong Gu
- Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People's Republic of China
| | - Meng Li
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, People's Republic of China
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31
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Salgado-Salazar C, Bauchan GR, Wallace EC, Crouch JA. Visualization of the impatiens downy mildew pathogen using fluorescence in situ hybridization (FISH). PLANT METHODS 2018; 14:92. [PMID: 30386410 PMCID: PMC6199785 DOI: 10.1186/s13007-018-0362-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 10/19/2018] [Indexed: 05/04/2023]
Abstract
BACKGROUND Plasmopara obducens is the biotrophic oomycete responsible for impatiens downy mildew, a destructive disease of Impatiens that causes high crop loss. Currently, there are no available methods for the microscopic detection of P. obducens from leaves of impatiens, which may be contributing to the spread of the disease. Fluorescence in situ hybridization (FISH) is a sensitive and robust method that uses sequence-specific, fluorescence-labeled oligonucleotide probes to detect target organisms from the environment. To study this important pathogen, we developed and standardized a FISH technique for the visualization of P. obducens from Impatiens walleriana tissues using a species-specific 24-mer oligonucleotide probe designed to target a region of the rRNA internal transcribed spacer 2 (ITS2). RESULTS Since P. obducens cannot be propagated in vitro, we developed a custom E. coli expression vector that transcribes the P. obducens rRNA-ITS target sequence (clone-FISH) for use as a control and to optimize hybridization conditions. The FISH assay could detect P. obducens sporangiophores, sporangia and oospores, and hyphae from naturally infected I. walleriana leaves and stems. Cross-reactivity was not observed from plant tissue, and the assay did not react when applied to E. coli with self-ligated plasmids and non-target oomycete species. CONCLUSIONS This FISH protocol may provide a valuable tool for the study of this disease and could potentially be used to improve early monitoring of P. obducens, substantially reducing the persistence and spread of this destructive plant pathogen.
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Affiliation(s)
- Catalina Salgado-Salazar
- Agriculture Research Service (ARS), Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, 10300 Baltimore Avenue, Beltsville, MD 20705 USA
- ARS Research Participation Program, Oak Ridge Institute for Science and Education, MC-100-44, P.O. Box 117, Oak Ridge, TN 37831 USA
| | - Gary R. Bauchan
- Agriculture Research Service, Electron and Confocal Microscopy Unit, U.S. Department of Agriculture, 10300 Baltimore Avenue, Beltsville, MD 20705 USA
| | - Emma C. Wallace
- Agriculture Research Service (ARS), Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, 10300 Baltimore Avenue, Beltsville, MD 20705 USA
- ARS Research Participation Program, Oak Ridge Institute for Science and Education, MC-100-44, P.O. Box 117, Oak Ridge, TN 37831 USA
- Present Address: Department of Plant Pathology and Environmental Microbiology, The Pennsylvania State University, 120 Buckhout Lab, University Park, PA 16802 USA
| | - Jo Anne Crouch
- Agriculture Research Service (ARS), Mycology and Nematology Genetic Diversity and Biology Laboratory, U.S. Department of Agriculture, 10300 Baltimore Avenue, Beltsville, MD 20705 USA
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32
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Huang T, Wang R, Xiao L, Wang H, Martínez JM, Escudero C, Amils R, Cheng Z, Xu Y. Dalangtan Playa (Qaidam Basin, NW China): Its microbial life and physicochemical characteristics and their astrobiological implications. PLoS One 2018; 13:e0200949. [PMID: 30067805 PMCID: PMC6070256 DOI: 10.1371/journal.pone.0200949] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Accepted: 07/04/2018] [Indexed: 01/29/2023] Open
Abstract
Dalangtan Playa is the second largest salt playa in the Qaidam Basin, north-western China. The hyper saline deposition, extremely arid climate and high UV radiation make Dalangtan a Mars analogue both for geomorphology and life preservation. To better understand microbial life at Dalangtan, both culture-dependent and culture-independent methods were examined and simultaneously, environment conditions and the evaporitic mineral assemblages were investigated. Ten and thirteen subsurface samples were collected along a 595-cm deep profile (P1) and a 685-cm deep profile (P2) respectively, and seven samples were gathered from surface sediments. These samples are composed of salt minerals, minor silicate mineral fragments and clays. The total bacterial cell numbers are (1.54±0.49) ×10(5) g-1 for P1 and (3.22±0.95) ×10(5) g-1 for P2 as indicated by the CAtalyzed Reporter Deposition- Fluorescent in situ Hybridization (CARD-FISH). 76.6% and 75.7% of the bacteria belong to Firmicutes phylum respectively from P1 and P2. In total, 47 bacteria and 6 fungi were isolated from 22 subsurface samples. In contrast, only 3 bacteria and 1 fungus were isolated from 3 surface samples. The isolated bacteria show high homology (≥97%) with members of the Firmicutes phylum (47 strains, 8 genera) and the Actinobacteria phylum (3 strains, 2 genera), which agrees with the result of CARD-FISH. Isolated fungi showed ≥98% ITS1 homology with members of the phylum Ascomycota. Moisture content and TOC values may control the sediments colonization. Given the deliquescence of salts, evaporites may provide refuge for microbial life, which merits further investigation. Halotolerant and spore-forming microorganisms are the dominant microbial groups capable of surviving under extreme conditions. Our results offer brand-new information on microbial biomass in Dalangtan Playa and shed light on understanding the potential microbial life in the dried playa or paleo-lakes on Mars.
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Affiliation(s)
- Ting Huang
- State Key Laboratory of Geological Process and Mineral Resources, Planetary Science Institute, China University of Geosciences, Wuhan, Hubei, China
| | - Ruicheng Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
| | - Long Xiao
- State Key Laboratory of Geological Process and Mineral Resources, Planetary Science Institute, China University of Geosciences, Wuhan, Hubei, China
- Space Science Institute, Macau University of Science and Technology, Macau, China
- * E-mail: (LX); (HW)
| | - Hongmei Wang
- State Key Laboratory of Biogeology and Environmental Geology, China University of Geosciences, Wuhan, Hubei, China
- * E-mail: (LX); (HW)
| | - José M. Martínez
- Centro de Biología Molecular “Severo Ochoa” (UAM-CSIC), Madrid, Spain
| | - Cristina Escudero
- Centro de Biología Molecular “Severo Ochoa” (UAM-CSIC), Madrid, Spain
| | - Ricardo Amils
- Centro de Biología Molecular “Severo Ochoa” (UAM-CSIC), Madrid, Spain
- Centro de Astrobiología (CSIC-INTA), Torrejón de Ardoz, Madrid, Spain
| | - Ziye Cheng
- State Key Laboratory of Geological Process and Mineral Resources, Planetary Science Institute, China University of Geosciences, Wuhan, Hubei, China
| | - Yi Xu
- Space Science Institute, Macau University of Science and Technology, Macau, China
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33
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Influence of the fixation/permeabilization step on peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) for the detection of bacteria. PLoS One 2018; 13:e0196522. [PMID: 29851961 PMCID: PMC5979007 DOI: 10.1371/journal.pone.0196522] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 03/14/2018] [Indexed: 11/19/2022] Open
Abstract
Fluorescence in situ Hybridization (FISH) is a versatile, widespread and widely- used technique in microbiology. The first step of FISH—fixation/permeabilization—is crucial to the outcome of the method. This work aimed to systematically evaluate fixation/permeabilization protocols employing ethanol, triton X-100 and lysozyme in conjugation with paraformaldehyde for Peptide Nucleic Acid (PNA)-FISH. Response surface methodology was used to optimize these protocols for Gram-negative (Escherichia coli and Pseudomonas fluorescens) and Gram-positive species (Listeria innocua, Staphylococcus epidermidis and Bacillus cereus). In general, the optimal PNA-FISH fluorescent outcome in Gram-positive bacteria was obtained employing harsher permeabilization conditions when compared to Gram-negative optimal protocols. The observed differences arise from the intrinsic cell envelope properties of each species and the ability of the fixation/permeabilization compounds to effectively increase the permeability of these structures while maintaining structural integrity. Ultimately, the combination of paraformaldehyde and ethanol proved to have significantly superior performance for all tested bacteria, especially for Gram-positive species (p<0.05).
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34
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Methane fluxes from coastal sediments are enhanced by macrofauna. Sci Rep 2017; 7:13145. [PMID: 29030563 PMCID: PMC5640653 DOI: 10.1038/s41598-017-13263-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 09/22/2017] [Indexed: 11/08/2022] Open
Abstract
Methane and nitrous oxide are potent greenhouse gases (GHGs) that contribute to climate change. Coastal sediments are important GHG producers, but the contribution of macrofauna (benthic invertebrates larger than 1 mm) inhabiting them is currently unknown. Through a combination of trace gas, isotope, and molecular analyses, we studied the direct and indirect contribution of two macrofaunal groups, polychaetes and bivalves, to methane and nitrous oxide fluxes from coastal sediments. Our results indicate that macrofauna increases benthic methane efflux by a factor of up to eight, potentially accounting for an estimated 9.5% of total emissions from the Baltic Sea. Polychaetes indirectly enhance methane efflux through bioturbation, while bivalves have a direct effect on methane release. Bivalves host archaeal methanogenic symbionts carrying out preferentially hydrogenotrophic methanogenesis, as suggested by analysis of methane isotopes. Low temperatures (8 °C) also stimulate production of nitrous oxide, which is consumed by benthic denitrifying bacteria before it reaches the water column. We show that macrofauna contributes to GHG production and that the extent is dependent on lineage. Thus, macrofauna may play an important, but overlooked role in regulating GHG production and exchange in coastal sediment ecosystems.
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35
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A Keystone Methylobacterium Strain in Biofilm Formation in Drinking Water. WATER 2017. [DOI: 10.3390/w9100778] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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36
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Haruta S, Iino T, Ohkuma M, Suzuki KI, Igarashi Y. Ca 2+ in Hybridization Solutions for Fluorescence in situ Hybridization Facilitates the Detection of Enterobacteriaceae. Microbes Environ 2017; 32:142-146. [PMID: 28515389 PMCID: PMC5478537 DOI: 10.1264/jsme2.me16186] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) has been employed to identify microorganisms at the single cell level under a microscope. Extensive efforts have been made to improve and extend the FISH technique; however, the development of a widely applicable protocol is a continuing challenge. The present study evaluated the effects of divalent cations in the hybridization solution on the FISH-based detection of various species of bacteria and archaea with rRNA-targeted probes. A flow cytometric analysis after FISH with a standard hybridization buffer detected positive signals from less than 30% of Escherichia coli IAM 1264 cells. However, the number of cells with positive signals increased to more than 90% after the addition of calcium chloride to the hybridization buffer. Mn2+ also had positive effects, whereas Mg2+ did not. The positive effects of Ca2+ were similarly observed for bacteria belonging to Enterobacteriaceae, including Enterobacter sakazakii IAM 12660T, E. aerogenes IAM 12348, Klebsiella planticola IAM 14202, and Salmonella enterica subsp. enterica serovar Typhimurium strain LT2. These results indicate that the supplementation of Ca2+ to the hybridization buffer for FISH contributes to the efficient detection of Enterobacteriaceae cells.
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Affiliation(s)
- Shin Haruta
- Department of Biological Sciences, Tokyo Metropolitan University.,Graduate School of Agricultural and Life Sciences, The University of Tokyo
| | - Takao Iino
- Japan Collection of Microorganisms, RIKEN BioResource Center.,NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE)
| | - Moriya Ohkuma
- Japan Collection of Microorganisms, RIKEN BioResource Center
| | - Ken-Ichiro Suzuki
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE)
| | - Yasuo Igarashi
- Graduate School of Agricultural and Life Sciences, The University of Tokyo.,Research Center of Bioenergy and Bioremediation, Southwest University
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Matsubayashi M, Shimada Y, Li YY, Harada H, Kubota K. Phylogenetic diversity and in situ detection of eukaryotes in anaerobic sludge digesters. PLoS One 2017; 12:e0172888. [PMID: 28264042 PMCID: PMC5338771 DOI: 10.1371/journal.pone.0172888] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Accepted: 02/10/2017] [Indexed: 12/11/2022] Open
Abstract
Eukaryotic communities in aerobic wastewater treatment processes are well characterized, but little is known about them in anaerobic processes. In this study, abundance, diversity and morphology of eukaryotes in anaerobic sludge digesters were investigated by quantitative real-time PCR (qPCR), 18S rRNA gene clone library construction and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). Samples were taken from four different anaerobic sludge digesters in Japan. Results of qPCR of rRNA genes revealed that Eukarya accounted from 0.1% to 1.4% of the total number of microbial rRNA gene copy numbers. The phylogenetic affiliations of a total of 251 clones were Fungi, Alveolata, Viridiplantae, Amoebozoa, Rhizaria, Stramenopiles and Metazoa. Eighty-five percent of the clones showed less than 97.0% sequence identity to described eukaryotes, indicating most of the eukaryotes in anaerobic sludge digesters are largely unknown. Clones belonging to the uncultured lineage LKM11 in Cryptomycota of Fungi were most abundant in anaerobic sludge, which accounted for 50% of the total clones. The most dominant OTU in each library belonged to either the LKM11 lineage or the uncultured lineage A31 in Alveolata. Principal coordinate analysis indicated that the eukaryotic and prokaryotic community structures were related. The detection of anaerobic eukaryotes, including the members of the LKM11 and A31 lineages in anaerobic sludge digesters, by CARD-FISH revealed their sizes in the range of 2–8 μm. The diverse and uncultured eukaryotes in the LKM11 and the A31 lineages are common and ecologically relevant members in anaerobic sludge digester.
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Affiliation(s)
- Miri Matsubayashi
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Yusuke Shimada
- Department of Frontier Science for Advanced Environment, Tohoku University, Sendai, Miyagi, Japan
| | - Yu-You Li
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Miyagi, Japan
| | - Hideki Harada
- New Industry Creation Hatchery Center, Tohoku University, Sendai, Miyagi, Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, Sendai, Miyagi, Japan
- * E-mail:
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39
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Mizuno M, Suzuki Y, Higashide K, Sei Y, Iguchi D, Sakata F, Horie M, Maruyama S, Matsuo S, Morgan BP, Ito Y. High Levels of Soluble C5b-9 Complex in Dialysis Fluid May Predict Poor Prognosis in Peritonitis in Peritoneal Dialysis Patients. PLoS One 2017; 12:e0169111. [PMID: 28046064 PMCID: PMC5207753 DOI: 10.1371/journal.pone.0169111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 12/12/2016] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND We searched for indicators to predict the prognosis of infectious peritonitis by measuring levels of complement proteins and activation products in peritoneal dialysis (PD) fluid (PDF) of patients at early stages of peritonitis. We retrospectively analyzed the relationship between the levels of sC5b-9, C3 and C4 in PDF and the subsequent clinical prognosis. METHODS We measured levels of sC5b-9, C3 and C4 in PDF on days 1, 2 and 5 post-onset of peritonitis in 104 episodes of infectious peritonitis in PD patients from 2008 and retrospectively compared levels with clinical outcomes. Further analysis for the presence of causative microorganisms or to demonstrate bacterial culture negative peritonitis was performed and correlated with change of levels of sC5b-9 in PDF. RESULTS When PD patients with peritonitis were divided into groups that either failed to recover from peritonitis and were finally withdrawn from PD (group 1; n = 25) or recovered (group 2; n = 79), levels of sC5b-9, C3 and C4 in PDF were significantly higher in group 1 patients compared to those in group 2 on day5. Analysis of microorganisms showed significantly higher sC5b-9 levels in PDF of peritonitis cases caused by culture negative peritonitis in group 1 compared with group 2 when we analyzed for individual microorganisms. Of note, on day5, the sC5b-9 levels in PDF were similarly high in peritonitis caused by fungi or other organisms. CONCLUSION Our results suggested that levels of complement markers in PDF, especially sC5b-9, have potential as surrogate markers to predict prognosis of PD-related peritonitis.
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Affiliation(s)
- Masashi Mizuno
- Renal Replacement Therapy, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Division of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yasuhiro Suzuki
- Division of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keiko Higashide
- Division of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yumi Sei
- Division of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Daiki Iguchi
- Division of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Fumiko Sakata
- Division of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | | | - Shoichi Maruyama
- Division of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Seiichi Matsuo
- Division of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - B. Paul Morgan
- Complement Biology Group, Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, United Kingdom
| | - Yasuhiko Ito
- Renal Replacement Therapy, Nagoya University Graduate School of Medicine, Nagoya, Japan
- Division of Nephrology, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Zeller P, Méjean A, Biegala I, Contremoulins V, Ploux O. Fluorescence in situ hybridization of Microcystis strains producing microcystin using specific mRNA probes. Lett Appl Microbiol 2016; 63:376-383. [PMID: 27538762 DOI: 10.1111/lam.12634] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/29/2016] [Accepted: 08/12/2016] [Indexed: 11/29/2022]
Abstract
Cyanobacteria are ubiquitous micro-organisms that can produce toxic compounds, the cyanotoxins. The monitoring of such producers in the environment is of prime importance for human health. An attractive technology for such monitoring is fluorescence in situ hybridization (FISH), which allows the detection and enumeration of environmental micro-organisms. We present here the application of tyramide signal amplification fluorescence in situ hybridization (TSA-FISH) to the detection of microcystin-producing Microcystis strains. We used a 16S rRNA-specific probe, MICR3, to specifically label and observe by epifluorescence microscopy Microcystis aeruginosa strains. Using confocal laser scanning microscopy and a specific probe, MCYA, targeting the mcyA mRNA we have labelled M. aeruginosa PCC 7806, which produces microcystins. Microcystis aeruginosa PCC 7005 which does not produce microcystins is not labelled by this probe. Furthermore, we show here that this specific mRNA labelling in M. aeruginosa PCC 7806 is enhanced in cells illuminated for 1 h just after a dark period of cultivation of 24 h, conditions in which the mcyA gene is up regulated. The data presented here might be applicable to the monitoring of toxic Microcystis strains in the environment. SIGNIFICANCE AND IMPACT OF THE STUDY Cyanobacteria producing toxic compounds (cyanotoxins) are present in the environment and in water bodies. Their presence poses a threat on human and animal health. It is thus important to detect, identify and enumerate these toxic Cyanobacteria. Using tyramide signal amplification fluorescence in situ hybridization (TSA-FISH) and specific probes, with confocal laser scanning microscopy, we have specifically detected Microcystis strains producing microcystin toxins. The data presented here might be applied to the monitoring of water bodies at early stages and all along the formation of Microcystis blooms.
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Affiliation(s)
| | - A Méjean
- Laboratoire des Energies de Demain, LIED, UMR 8236 CNRS, Université Paris Diderot-Paris 7, Paris, France.
| | - I Biegala
- CNRS/INSU, Université de Toulon, IRD, Mediterranean Institute of Oceanography (MIO) UM110, Aix-Marseille Université, Marseille, France
| | - V Contremoulins
- Institut Jacques Monod, CNRS UMR 7592, Sorbonne Paris Cité, Université Paris Diderot, Paris Cedex, France.,ImagoSeine, Institut Jacques Monod, CNRS UMR 7592, Sorbonne Paris Cité, Université Paris Diderot, Paris Cedex, France
| | - O Ploux
- Chimie ParisTech, Paris, France. .,Laboratoire des Energies de Demain, LIED, UMR 8236 CNRS, Université Paris Diderot-Paris 7, Paris, France.
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Nuñez H, Covarrubias PC, Moya-Beltrán A, Issotta F, Atavales J, Acuña LG, Johnson DB, Quatrini R. Detection, identification and typing of Acidithiobacillus species and strains: a review. Res Microbiol 2016; 167:555-67. [DOI: 10.1016/j.resmic.2016.05.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 05/19/2016] [Accepted: 05/23/2016] [Indexed: 01/10/2023]
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Frossard A, Hammes F, Gessner MO. Flow Cytometric Assessment of Bacterial Abundance in Soils, Sediments and Sludge. Front Microbiol 2016; 7:903. [PMID: 27379043 PMCID: PMC4905975 DOI: 10.3389/fmicb.2016.00903] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 05/26/2016] [Indexed: 11/13/2022] Open
Abstract
Bacterial abundance is a fundamental measure in microbiology, but its assessment is often tedious, especially for soil, and sediment samples. To overcome this limitation, we adopted a time-efficient flow-cytometric (FCM) counting method involving cell detachment and separation from matrix particles by centrifugation in tubes receiving sample suspensions and Histodenz® solution. We used this approach to assess bacterial abundances in diverse soils (natural and agricultural), sediments (streams and lakes) and sludge from sand-filters in a drinking water treatment plant and compared the results to bacterial abundances determined by two established methods, epifluorescence microscopy (EM) and adenosine triphosphate (ATP) quantification. Cell abundances determined by FCM and EM correlated fairly well, although absolute cell abundances were generally lower when determined by FCM. FCM also showed significant relations with cell counts converted from ATP concentrations, although estimates derived from ATP determinations were typically higher, indicating the presence of ATP sources other than bacteria. Soil and sediment organic matter (OM) content influenced the goodness of fit between counts obtained with EM and FCM. In particular, bacterial abundance determined by FCM in samples containing less than 10% OM, such as stream sediment, was particularly well correlated with the cell counts assessed by EM. Overall, these results suggest that FCM following cell detachment and purification is a useful approach to increase sample throughput for determining bacterial abundances in soils, sediments and sludge. However, notable scatter and only partial concordance among the FCM and reference methods suggests that protocols require further improvement for assessments requiring high precision, especially when OM contents in samples are high.
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Affiliation(s)
- Aline Frossard
- Forest Soils and Biogeochemistry, Swiss Federal Institute for Forest, Snow and Landscape Research (WSL)Birmensdorf Switzerland; Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag)Dübendorf Switzerland; Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), StechlinGermany; Institute of Integrative Biology (IBZ), ETH ZürichZürich Switzerland
| | - Frederik Hammes
- Department of Environmental Microbiology, Swiss Federal Institute of Aquatic Science and Technology (Eawag) Dübendorf Switzerland
| | - Mark O Gessner
- Department of Aquatic Ecology, Swiss Federal Institute of Aquatic Science and Technology (Eawag)Dübendorf Switzerland; Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), StechlinGermany; Institute of Integrative Biology (IBZ), ETH ZürichZürich Switzerland; Department of Ecology, Berlin Institute of Technology (TU Berlin)Berlin Germany
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Recent analysis of status and outcomes of peritoneal dialysis in the Tokai area of Japan: the second report of the Tokai peritoneal dialysis registry. Clin Exp Nephrol 2016; 20:960-971. [PMID: 26951303 DOI: 10.1007/s10157-016-1249-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2015] [Accepted: 02/10/2016] [Indexed: 10/22/2022]
Abstract
BACKGROUND Early withdrawal within 3 years after starting peritoneal dialysis (PD) and PD-related peritonitis have been major obstacles preventing increases in the population of PD patients. To address these problems, we implemented education programs for medical staff. This study analyzed the recent status and outcomes of PD therapy, focusing on findings such as the incidence and prognosis of peritonitis as of 5 years after our last study. METHODS We investigated background, laboratory data and status of PD therapy, reasons for withdrawal from PD and incidental statements on peritonitis from 2010 to 2012 (R2), and compared findings with those from our last study of 2005-2007 (R1). RESULTS Early PD therapy withdrawal in R2 clearly improved to 44.7 %, compared with 50.9 % in R1. Peritonitis incidence improved slightly from once per 42.8 months/patient in R1 to once per 47.3 months/patient in R2. Notably, PD-related peritonitis as a cause of mortality improved markedly in R2, but outcomes of PD-related peritonitis did not change significantly between R1 and R2. In contrast, social problems increased as a reason for withdrawal from PD therapy. CONCLUSION Our efforts at education might have been useful for improving early withdrawal from PD and deaths attributable to PD-related peritonitis. However, since improvements to incidence of PD-related peritonitis were limited by education, further improvement in PD-related peritonitis incidence requires development of new sterilized connecting systems during PD-bag exchanges to decrease PD-related peritonitis opportunities. Construction of medical support systems to address social problems is required to maintain long-term PD therapy.
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Methodological Studies on Estimates of Abundance and Diversity of Heterotrophic Flagellates from the Deep-Sea Floor. JOURNAL OF MARINE SCIENCE AND ENGINEERING 2016. [DOI: 10.3390/jmse4010022] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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Affiliation(s)
- Koji Mori
- NITE Biological Resource Center (NBRC), National Institute of Technology and Evaluation (NITE)
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Rapid and sensitive identification of marine bacteria by an improved in situ DNA hybridization chain reaction (quickHCR-FISH). Syst Appl Microbiol 2015. [PMID: 26215142 DOI: 10.1016/j.syapm.2015.06.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) with rRNA-targeted oligonucleotide probes has significantly improved the identification of microorganisms in various environmental samples. However, one of the major constraints of CARD-FISH is the low probe penetration due to the high molecular weight of the horseradish peroxidase (HRP) label. Recently, this limitation has been overcome by a novel signal amplification approach termed in situ DNA-hybridization chain reaction (in situ DNA-HCR). In this study, we present an improved and accelerated in situ DNA-HCR protocol (quickHCR-FISH) with increased signal intensity, which was approximately 2 times higher than that of standard in situ DNA-HCR. In addition, the amplification time was only 15 min for the extension of amplifier probes from the initiator probe compared to 2h in the original protocol. The quickHCR-FISH was successfully tested for the quantification of marine bacteria with low rRNA contents in both seawater and sediment samples. It was possible to detect the same number of marine bacteria with quickHCR-FISH compared to CARD-FISH within only 3h. Thus, this newly developed protocol could be an attractive alternative to CARD-FISH for the detection and visualization of microorganisms in their environmental context.
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Almeida C, Constante D, Ferreira A, Cerqueira L, Vieira MJ, Azevedo NF. A new colorimetric peptide nucleic acid-based assay for the specific detection of bacteria. Future Microbiol 2015; 9:1131-42. [PMID: 25405883 DOI: 10.2217/fmb.14.68] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM Developments on synthetic molecules, such as peptide nucleic acid (PNA), make FISH procedures more robust for microbial identification. Fluorochromes use might hinder a broader implementation of PNA-FISH, but colorimetric applications are inexistent so far. METHODS A biotin-labeled eubacteria probe was used to develop a colorimetric PNA-in situ hybridization (ISH) assay. An enzymatic-conjugate, targeting biotin, was introduced. The procedure was optimized and evaluated regarding sensitivity, specificity and detection limit. RESULTS RESULTS have shown strong ISH signals. The method was specific, but permeabilization problems were observed for Gram-positive bacteria. Detection limit was 5 × 10(7) CFU/ml, limiting current applications to pre-enriched samples. CONCLUSION The PNA-ISH procedure described here is a simple alternative to other detection methods, and is also the base for the development of other PNA colorimetric systems.
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Affiliation(s)
- Carina Almeida
- LEPABE, Department of Chemical Engineering, Faculty of Engineering, University of Porto, Porto, Portugal
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High-resolution and specific detection of bacteria on complex surfaces using nanoparticle probes and electron microscopy. PLoS One 2015; 10:e0126404. [PMID: 26018431 PMCID: PMC4446341 DOI: 10.1371/journal.pone.0126404] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 04/01/2015] [Indexed: 11/21/2022] Open
Abstract
The study of the interaction of bacteria with surfaces requires the detection of specific bacterial groups with high spatial resolution. Here, we describe a method to rapidly and efficiently add nanogold particles to oligonucleotide probes, which target bacterial ribosomal RNA. These nanogold-labeled probes are then used in an in situ hybridization procedure that ensures both cellular integrity and high specificity. Electron microscopy subsequently enables the visualization of specific cells with high local precision on complex surface structures. This method will contribute to an increased understanding of how bacteria interact with surface structures on a sub-micron scale.
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Yamaguchi T, Kawakami S, Hatamoto M, Imachi H, Takahashi M, Araki N, Yamaguchi T, Kubota K. In situ DNA-hybridization chain reaction (HCR): a facilitated in situ HCR system for the detection of environmental microorganisms. Environ Microbiol 2015; 17:2532-41. [DOI: 10.1111/1462-2920.12745] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Revised: 11/22/2014] [Accepted: 12/06/2014] [Indexed: 11/28/2022]
Affiliation(s)
- Tsuyoshi Yamaguchi
- Department of Environmental Systems Engineering; Nagaoka University of Technology; 1603-1 Kamitomioka Nagaoka Niigata 940-2188 Japan
| | - Shuji Kawakami
- Department of Environmental Systems Engineering; Nagaoka University of Technology; 1603-1 Kamitomioka Nagaoka Niigata 940-2188 Japan
- Department of Construction Systems Engineering; Anan National College of Technology; 265 Aoki Minobayashi Anan Tokushima 774-0017 Japan
| | - Masashi Hatamoto
- Department of Environmental Systems Engineering; Nagaoka University of Technology; 1603-1 Kamitomioka Nagaoka Niigata 940-2188 Japan
| | - Hiroyuki Imachi
- Department of Subsurface Geobiology Analysis and Research (D-SUGAR); Japan Agency for Marine-Earth Science & Technology (JAMSTEC); Yokosuka Kanagawa 237-0061 Japan
| | - Masanobu Takahashi
- Department of Environmental Systems Engineering; Nagaoka University of Technology; 1603-1 Kamitomioka Nagaoka Niigata 940-2188 Japan
- Department of Civil and Environmental Engineering; Tohoku University; 6-6-06 Aoba Sendai Miyagi 980-8579 Japan
| | - Nobuo Araki
- Department of Civil Engineering; Nagaoka National College of Technology; 888 Nishikatagai Nagaoka Niigata 940-8532 Japan
| | - Takashi Yamaguchi
- Department of Environmental Systems Engineering; Nagaoka University of Technology; 1603-1 Kamitomioka Nagaoka Niigata 940-2188 Japan
| | - Kengo Kubota
- Department of Civil and Environmental Engineering; Tohoku University; 6-6-06 Aoba Sendai Miyagi 980-8579 Japan
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Metaproteomic identification of diazotrophic methanotrophs and their localization in root tissues of field-grown rice plants. Appl Environ Microbiol 2014; 80:5043-52. [PMID: 24928870 DOI: 10.1128/aem.00969-14] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In a previous study by our group, CH4 oxidation and N2 fixation were simultaneously activated in the roots of wild-type rice plants in a paddy field with no N input; both processes are likely controlled by a rice gene for microbial symbiosis. The present study examined which microorganisms in rice roots were responsible for CH4 oxidation and N2 fixation under the field conditions. Metaproteomic analysis of root-associated bacteria from field-grown rice (Oryza sativa Nipponbare) revealed that nitrogenase complex-containing nitrogenase reductase (NifH) and the alpha subunit (NifD) and beta subunit (NifK) of dinitrogenase were mainly derived from type II methanotrophic bacteria of the family Methylocystaceae, including Methylosinus spp. Minor nitrogenase proteins such as Methylocella, Bradyrhizobium, Rhodopseudomonas, and Anaeromyxobacter were also detected. Methane monooxygenase proteins (PmoCBA and MmoXYZCBG) were detected in the same bacterial group of the Methylocystaceae. Because these results indicated that Methylocystaceae members mediate both CH4 oxidation and N2 fixation, we examined their localization in rice tissues by using catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). The methanotrophs were localized around the epidermal cells and vascular cylinder in the root tissues of the field-grown rice plants. Our metaproteomics and CARD-FISH results suggest that CH4 oxidation and N2 fixation are performed mainly by type II methanotrophs of the Methylocystaceae, including Methylosinus spp., inhabiting the vascular bundles and epidermal cells of rice roots.
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