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Sørensen MES, Zlatogursky VV, Onuţ-Brännström I, Walraven A, Foster RA, Burki F. A novel kleptoplastidic symbiosis revealed in the marine centrohelid Meringosphaera with evidence of genetic integration. Curr Biol 2023; 33:3571-3584.e6. [PMID: 37536342 PMCID: PMC7615077 DOI: 10.1016/j.cub.2023.07.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 06/01/2023] [Accepted: 07/11/2023] [Indexed: 08/05/2023]
Abstract
Plastid symbioses between heterotrophic hosts and algae are widespread and abundant in surface oceans. They are critically important both for extant ecological systems and for understanding the evolution of plastids. Kleptoplastidy, where the plastids of prey are temporarily retained and continuously re-acquired, provides opportunities to study the transitional states of plastid establishment. Here, we investigated the poorly studied marine centrohelid Meringosphaera and its previously unidentified symbionts using culture-independent methods from environmental samples. Investigations of the 18S rDNA from single-cell assembled genomes (SAGs) revealed uncharacterized genetic diversity within Meringosphaera that likely represents multiple species. We found that Meringosphaera harbors plastids of Dictyochophyceae origin (stramenopiles), for which we recovered six full plastid genomes and found evidence of two distinct subgroups that are congruent with host identity. Environmental monitoring by qPCR and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) revealed seasonal dynamics of both host and plastid. In particular, we did not detect the plastids for 6 months of the year, which, combined with the lack of plastids in some SAGs, suggests that the plastids are temporary and the relationship is kleptoplastidic. Importantly, we found evidence of genetic integration of the kleptoplasts as we identified host-encoded plastid-associated genes, with evolutionary origins likely from the plastid source as well as from other alga sources. This is only the second case where host-encoded kleptoplast-targeted genes have been predicted in an ancestrally plastid-lacking group. Our results provide evidence for gene transfers and protein re-targeting as relatively early events in the evolution of plastid symbioses.
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Affiliation(s)
- Megan E S Sørensen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden; Institute of Microbial Cell Biology, Heinrich Heine University, 40225 Düsseldorf, Germany.
| | - Vasily V Zlatogursky
- Department of Botany, University of British Columbia, V6T 1Z4 Vancouver, BC, Canada; Department of Organismal Biology, Program in Systematic Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Ioana Onuţ-Brännström
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, 752 36 Uppsala, Sweden; Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden; Natural History Museum, University of Oslo, 0562 Oslo, Norway
| | - Anne Walraven
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Rachel A Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Fabien Burki
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, 752 36 Uppsala, Sweden; Science for Life Laboratory, Uppsala University, 752 37 Uppsala, Sweden.
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Zhang X, Bi L, Gentekaki E, Zhao J, Shen P, Zhang Q. Culture-Independent Single-Cell PacBio Sequencing Reveals Epibiotic Variovorax and Nucleus Associated Mycoplasma in the Microbiome of the Marine Benthic Protist Geleia sp. YT (Ciliophora, Karyorelictea). Microorganisms 2023; 11:1500. [PMID: 37375002 DOI: 10.3390/microorganisms11061500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/19/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
Microbes in marine sediments constitute up to five-sixths of the planet's total biomass, but their diversity is little explored, especially for those forming associations with unicellular protists. Heterotrophic ciliates are among the most dominant and diversified marine benthic protists and comprise hotspot niches of bacterial colonization. To date, studies using culture-independent single-cell approaches to explore microbiomes of marine benthic ciliates in nature are almost absent, even for the most ubiquitous species. Here, we characterize the major bacterial groups associated with a representative marine benthic ciliate, Geleia sp. YT, collected directly from the coastal zone of Yantai, China. PacBio sequencing of the nearly full-length 16Sr RNA genes was performed on single cells of Geleia. Fluorescence in situ hybridization (FISH) analysis with genus-specific probes was further applied to locate the dominant bacterial groups. We identified a Variovorax-like bacterium as the major epibiotic symbiont residing in the kineties of the ciliate host. We provide evidence of a nucleus-associated bacterium related to the human pathogen Mycoplasma, which appeared prevalently in the local populations of Geleia sp. YT for 4 months. The most abundant bacterial taxa associated with Geleia sp. YT likely represent its core microbiome, hinting at the important roles of the ciliate-bacteria consortium in the marine benthos. Overall, this work has contributed to the knowledge of the diversity of life in the enigmatic marine benthic ciliate and its symbioses.
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Affiliation(s)
- Xiaoxin Zhang
- School of Ocean, Yantai University, Yantai 264003, China
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Luping Bi
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Eleni Gentekaki
- School of Science, Mae Fah Luang University, Chiang Rai 57100, Thailand
- Gut Microbiome Research Group, Mae Fah Luang University, Chiang Rai 57100, Thailand
| | - Jianmin Zhao
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Pingping Shen
- School of Ocean, Yantai University, Yantai 264003, China
| | - Qianqian Zhang
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
- Muping Coastal Environment Research Station, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
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Cao Z, Zuo W, Wang L, Chen J, Qu Z, Jin F, Dai L. Spatial profiling of microbial communities by sequential FISH with error-robust encoding. Nat Commun 2023; 14:1477. [PMID: 36932092 PMCID: PMC10023729 DOI: 10.1038/s41467-023-37188-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
Spatial analysis of microbiomes at single cell resolution with high multiplexity and accuracy has remained challenging. Here we present spatial profiling of a microbiome using sequential error-robust fluorescence in situ hybridization (SEER-FISH), a highly multiplexed and accurate imaging method that allows mapping of microbial communities at micron-scale. We show that multiplexity of RNA profiling in microbiomes can be increased significantly by sequential rounds of probe hybridization and dissociation. Combined with error-correction strategies, we demonstrate that SEER-FISH enables accurate taxonomic identification in complex microbial communities. Using microbial communities composed of diverse bacterial taxa isolated from plant rhizospheres, we apply SEER-FISH to quantify the abundance of each taxon and map microbial biogeography on roots. At micron-scale, we identify clustering of microbial cells from multiple species on the rhizoplane. Under treatment of plant metabolites, we find spatial re-organization of microbial colonization along the root and alterations in spatial association among microbial taxa. Taken together, SEER-FISH provides a useful method for profiling the spatial ecology of complex microbial communities in situ.
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Affiliation(s)
- Zhaohui Cao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenlong Zuo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Lanxiang Wang
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Junyu Chen
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zepeng Qu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Fan Jin
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Visualization of Lokiarchaeia and Heimdallarchaeia (Asgardarchaeota) by Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition (CARD-FISH). mSphere 2020; 5:5/4/e00686-20. [PMID: 32727863 PMCID: PMC7392546 DOI: 10.1128/msphere.00686-20] [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: 11/20/2022] Open
Abstract
Asgardarchaeota are considered to be the closest relatives to modern eukaryotes. These enigmatic microbes have been mainly studied using metagenome-assembled genomes (MAGs). Only very recently, a first member of Lokiarchaeia was isolated and characterized in detail; it featured a striking morphology with long, branching protrusions. In order to visualize additional members of the phylum Asgardarchaeota, we applied a fluorescence in situ hybridization technique and epifluorescence microscopy on coastal hypersaline sediment samples, using specifically designed probes for Heimdallarchaeia and Lokiarchaeia lineages. We provide the first visual evidence for Heimdallarchaeia that are characterized by a uniform cellular morphology typified by an apparently centralized DNA localization. Further, we provide new images of a lineage of Lokiarchaeia that is different from the cultured representative and with multiple morphologies, ranging from small ovoid cells to long filaments. This diversity in observed cell shapes is likely owing to the large phylogenetic diversity within Asgardarchaeota, the vast majority of which remain uncultured. Metagenome-assembled genomes (MAGs) of Asgardarchaeota have been recovered from a variety of habitats, broadening their environmental distribution and providing access to the genetic makeup of this archaeal lineage. The recent success in cultivating the first representative of Lokiarchaeia was a breakthrough in science at large and gave rise to new hypotheses about the evolution of eukaryotes. Despite their singular phylogenetic position at the base of the eukaryotic tree of life, the morphology of these bewildering organisms remains a mystery, except for the report of an unusual morphology with long, branching protrusions of the cultivated Lokiarchaeion strain “Candidatus Prometheoarchaeum syntrophicum” MK-D1. In order to visualize this elusive group, we applied a combination of fluorescence in situ hybridization and catalyzed reporter deposition (CARD-FISH) and epifluorescence microscopy on coastal hypersaline sediment samples, using specifically designed CARD-FISH probes for Heimdallarchaeia and Lokiarchaeia lineages, and provide the first visual evidence for Heimdallarchaeia and new images of a lineage of Lokiarchaeia that is different from the cultured representative. Here, we show that while Heimdallarchaeia are characterized by a uniform cellular morphology typified by a centralized DNA localization, Lokiarchaeia display a plethora of shapes and sizes that likely reflect their broad phylogenetic diversity and ecological distribution. IMPORTANCE Asgardarchaeota are considered to be the closest relatives to modern eukaryotes. These enigmatic microbes have been mainly studied using metagenome-assembled genomes (MAGs). Only very recently, a first member of Lokiarchaeia was isolated and characterized in detail; it featured a striking morphology with long, branching protrusions. In order to visualize additional members of the phylum Asgardarchaeota, we applied a fluorescence in situ hybridization technique and epifluorescence microscopy on coastal hypersaline sediment samples, using specifically designed probes for Heimdallarchaeia and Lokiarchaeia lineages. We provide the first visual evidence for Heimdallarchaeia that are characterized by a uniform cellular morphology typified by an apparently centralized DNA localization. Further, we provide new images of a lineage of Lokiarchaeia that is different from the cultured representative and with multiple morphologies, ranging from small ovoid cells to long filaments. This diversity in observed cell shapes is likely owing to the large phylogenetic diversity within Asgardarchaeota, the vast majority of which remain uncultured.
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Can F, Ökten HE, Ergön-Can T, Ergenekon P, Özkan M, Erhan E. Thermodynamically designed target-specific DNA probe as an electrochemical hybridization biosensor. Bioelectrochemistry 2020; 135:107553. [PMID: 32442773 DOI: 10.1016/j.bioelechem.2020.107553] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Revised: 05/07/2020] [Accepted: 05/08/2020] [Indexed: 01/28/2023]
Abstract
Applications of molecular techniques to elucidate identity or function using biomarkers still remain highly empirical and biosensors are no exception. In the present study, target-specific oligonucleotide probes for E. coli K12 were designed thermodynamically and applied in an electrochemical DNA biosensor setup. Biosensor was prepared by immobilization of a stem-loop structured probe, modified with a thiol functional group at its 5' end and a biotin molecule at its 3' end, on a gold electrode through self-assembly. Mercaptopropionic acid (MPA) was used to optimize the surface probe density of the electrode. Hybridization between the immobilized probe and the target DNA was detected via the electrochemical response of streptavidin-horseradish peroxidase in the presence of the substrate. The amperometric response showed a linear relationship with the target DNA concentration, ranging from 10 and 400 nM, with a correlation coefficient of 0.989. High selectivity and good repeatability of the biosensor showed that the thermodynamic approach to oligonucleotide probe design can be used in development of electrochemical DNA biosensors.
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Affiliation(s)
- Faruk Can
- Gebze Technical University, Department of Environmental Engineering, 41400 Gebze, Kocaeli, Turkey
| | - Hatice Eser Ökten
- Izmir Institute of Technology, Department of Environmental Engineering, 35430 Urla, İzmir, Turkey
| | - Tülay Ergön-Can
- Atatürk University, Department of Biology, Faculty of Science, 25240 Erzurum, Turkey
| | - Pınar Ergenekon
- Gebze Technical University, Department of Environmental Engineering, 41400 Gebze, Kocaeli, Turkey
| | - Melek Özkan
- Gebze Technical University, Department of Environmental Engineering, 41400 Gebze, Kocaeli, Turkey
| | - Elif Erhan
- Uskudar University, Department of Bioengineering, 34662 Uskudar, Istanbul, Turkey.
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Speirs LBM, Rice DTF, Petrovski S, Seviour RJ. The Phylogeny, Biodiversity, and Ecology of the Chloroflexi in Activated Sludge. Front Microbiol 2019; 10:2015. [PMID: 31572309 PMCID: PMC6753630 DOI: 10.3389/fmicb.2019.02015] [Citation(s) in RCA: 124] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 08/16/2019] [Indexed: 02/01/2023] Open
Abstract
It is now clear that several of the filamentous bacteria in activated sludge wastewater treatment plants globally, are members of the phylum Chloroflexi. They appear to be more commonly found in treatment plants designed to remove nitrogen (N) and phosphorus (P), most of which operate at long sludge ages and expose the biomass to anaerobic conditions. The Chloroflexi seem to play an important beneficial role in providing the filamentous scaffolding around which flocs are formed, to feed on the debris from lysed bacterial cells, to ferment carbohydrates and to degrade other complex polymeric organic compounds to low molecular weight substrates to support their growth and that of other bacterial populations. A few commonly extend beyond the floc surface, while others can align in bundles, which may facilitate interfloc bridging and hence generate a bulking sludge. Although several recent papers have examined the phylogeny and in situ physiology of Chloroflexi in activated sludge plants in Denmark, this review takes a wider look at what we now know about these filaments, especially their global distribution in activated sludge plants, and what their functional roles there might be. It also attempts to outline why such information might provide us with clues as to how their population levels may be manipulated, and the main research questions that need addressing to achieve these outcomes.
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Affiliation(s)
- Lachlan B. M. Speirs
- La Trobe Institute for Molecular Sciences, La Trobe University, Bendigo, VIC, Australia
| | - Daniel T. F. Rice
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Steve Petrovski
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
| | - Robert J. Seviour
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, VIC, Australia
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Rubin-Blum M, Antony CP, Sayavedra L, Martínez-Pérez C, Birgel D, Peckmann J, Wu YC, Cardenas P, MacDonald I, Marcon Y, Sahling H, Hentschel U, Dubilier N. Fueled by methane: deep-sea sponges from asphalt seeps gain their nutrition from methane-oxidizing symbionts. THE ISME JOURNAL 2019; 13:1209-1225. [PMID: 30647460 PMCID: PMC6474228 DOI: 10.1038/s41396-019-0346-7] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 12/16/2018] [Accepted: 12/20/2018] [Indexed: 01/26/2023]
Abstract
Sponges host a remarkable diversity of microbial symbionts, however, the benefit their microbes provide is rarely understood. Here, we describe two new sponge species from deep-sea asphalt seeps and show that they live in a nutritional symbiosis with methane-oxidizing (MOX) bacteria. Metagenomics and imaging analyses revealed unusually high amounts of MOX symbionts in hosts from a group previously assumed to have low microbial abundances. These symbionts belonged to the Marine Methylotrophic Group 2 clade. They are host-specific and likely vertically transmitted, based on their presence in sponge embryos and streamlined genomes, which lacked genes typical of related free-living MOX. Moreover, genes known to play a role in host-symbiont interactions, such as those that encode eukaryote-like proteins, were abundant and expressed. Methane assimilation by the symbionts was one of the most highly expressed metabolic pathways in the sponges. Molecular and stable carbon isotope patterns of lipids confirmed that methane-derived carbon was incorporated into the hosts. Our results revealed that two species of sponges, although distantly related, independently established highly specific, nutritional symbioses with two closely related methanotrophs. This convergence in symbiont acquisition underscores the strong selective advantage for these sponges in harboring MOX bacteria in the food-limited deep sea.
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Affiliation(s)
- Maxim Rubin-Blum
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany.
- Israel Limnology and Oceanography Research, Tel Shikmona, 3108000, Haifa, Israel.
| | - Chakkiath Paul Antony
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
| | - Lizbeth Sayavedra
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Clara Martínez-Pérez
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany
| | - Daniel Birgel
- Institute for Geology, Center for Earth System Research and Sustainability, University of Hamburg, 20146, Hamburg, Germany
| | - Jörn Peckmann
- Institute for Geology, Center for Earth System Research and Sustainability, University of Hamburg, 20146, Hamburg, Germany
| | - Yu-Chen Wu
- GEOMAR Helmholtz Centre for Ocean Research, RD3 Marine Microbiology and Christian-Albrechts University of Kiel, Düsternbrooker Weg 20, D-24105, Kiel, Germany
| | - Paco Cardenas
- Department of Medicinal Chemistry, Pharmacognosy, BioMedical Centre, Uppsala University, Husargatan 3, 751 23, Uppsala, Sweden
| | - Ian MacDonald
- Florida State University, POB 3064326, Tallahassee, FL, 32306, USA
| | - Yann Marcon
- Wegener Institute Helmholtz Centre for Polar and Marine Research, HGF-MPG Group for Deep Sea Ecology and Technology, Am Handelshafen 12, 27570, Bremerhaven, Germany
| | - Heiko Sahling
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany
| | - Ute Hentschel
- GEOMAR Helmholtz Centre for Ocean Research, RD3 Marine Microbiology and Christian-Albrechts University of Kiel, Düsternbrooker Weg 20, D-24105, Kiel, Germany
| | - Nicole Dubilier
- Max Planck Institute for Marine Microbiology, Celsiusstrasse 1, 28359, Bremen, Germany.
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359, Bremen, Germany.
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Fluorescence in situ hybridization (FISH): History, limitations and what to expect from micro-scale FISH? MICRO AND NANO ENGINEERING 2018. [DOI: 10.1016/j.mne.2018.10.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Ostromohov N, Huber D, Bercovici M, Kaigala GV. Real-Time Monitoring of Fluorescence in Situ Hybridization Kinetics. Anal Chem 2018; 90:11470-11477. [DOI: 10.1021/acs.analchem.8b02630] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Nadya Ostromohov
- IBM Research—Zurich, Säumerstrasse 4, 8803 Rüschlikon, Zurich, Switzerland
- Faculty of Mechanical Engineering, Technion—Israel Institute of Technology, Haifa 3200003, Israel
| | - Deborah Huber
- IBM Research—Zurich, Säumerstrasse 4, 8803 Rüschlikon, Zurich, Switzerland
| | - Moran Bercovici
- Faculty of Mechanical Engineering, Technion—Israel Institute of Technology, Haifa 3200003, Israel
| | - Govind V. Kaigala
- IBM Research—Zurich, Säumerstrasse 4, 8803 Rüschlikon, Zurich, Switzerland
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10
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Frickmann H, Zautner AE, Moter A, Kikhney J, Hagen RM, Stender H, Poppert S. Fluorescence in situ hybridization (FISH) in the microbiological diagnostic routine laboratory: a review. Crit Rev Microbiol 2017; 43:263-293. [PMID: 28129707 DOI: 10.3109/1040841x.2016.1169990] [Citation(s) in RCA: 126] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Early identification of microbial pathogens is essential for rational and conservative antibiotic use especially in the case of known regional resistance patterns. Here, we describe fluorescence in situ hybridization (FISH) as one of the rapid methods for easy identification of microbial pathogens, and its advantages and disadvantages for the diagnosis of pathogens in human infections in the laboratory diagnostic routine. Binding of short fluorescence-labeled DNA or nucleic acid-mimicking PNA probes to ribosomes of infectious agents with consecutive analysis by fluorescence microscopy allows identification of bacterial and eukaryotic pathogens at genus or species level. FISH analysis leads to immediate differentiation of infectious agents without delay due to the need for microbial culture. As a microscopic technique, FISH has the unique potential to provide information about spatial resolution, morphology and identification of key pathogens in mixed species samples. On-going automation and commercialization of the FISH procedure has led to significant shortening of the time-to-result and increased test reliability. FISH is a useful tool for the rapid initial identification of microbial pathogens, even from primary materials. Among the rapidly developing alternative techniques, FISH serves as a bridging technology between microscopy, microbial culture, biochemical identification and molecular diagnostic procedures.
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Affiliation(s)
- Hagen Frickmann
- a German Armed Forces Hospital of Hamburg, Department of Tropical Medicine at the Bernhard Nocht Institute , Hamburg , Germany
| | - Andreas Erich Zautner
- b Department of Medical Microbiology, University Medical Center Göttingen , Göttingen , Germany
| | - Annette Moter
- c University Medical Center Berlin, Biofilmcenter at the German Heart Institute Berlin , Berlin , Germany
| | - Judith Kikhney
- c University Medical Center Berlin, Biofilmcenter at the German Heart Institute Berlin , Berlin , Germany
| | - Ralf Matthias Hagen
- a German Armed Forces Hospital of Hamburg, Department of Tropical Medicine at the Bernhard Nocht Institute , Hamburg , Germany
| | | | - Sven Poppert
- e Institute for Medical Microbiology, Justus-Liebig-University Giessen , Giessen , Germany
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11
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Trojan D, Schreiber L, Bjerg JT, Bøggild A, Yang T, Kjeldsen KU, Schramm A. A taxonomic framework for cable bacteria and proposal of the candidate genera Electrothrix and Electronema. Syst Appl Microbiol 2016; 39:297-306. [PMID: 27324572 PMCID: PMC4958695 DOI: 10.1016/j.syapm.2016.05.006] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Revised: 05/06/2016] [Accepted: 05/09/2016] [Indexed: 11/29/2022]
Abstract
Cable bacteria are long, multicellular filaments that can conduct electric currents over centimeter-scale distances. All cable bacteria identified to date belong to the deltaproteobacterial family Desulfobulbaceae and have not been isolated in pure culture yet. Their taxonomic delineation and exact phylogeny is uncertain, as most studies so far have reported only short partial 16S rRNA sequences or have relied on identification by a combination of filament morphology and 16S rRNA-targeted fluorescence in situ hybridization with a Desulfobulbaceae-specific probe. In this study, nearly full-length 16S rRNA gene sequences of 16 individual cable bacteria filaments from freshwater, salt marsh, and marine sites of four geographic locations are presented. These sequences formed a distinct, monophyletic sister clade to the genus Desulfobulbus and could be divided into six coherent, species-level clusters, arranged as two genus-level groups. The same grouping was retrieved by phylogenetic analysis of full or partial dsrAB genes encoding the dissimilatory sulfite reductase. Based on these results, it is proposed to accommodate cable bacteria within two novel candidate genera: the mostly marine “Candidatus Electrothrix”, with four candidate species, and the mostly freshwater “Candidatus Electronema”, with two candidate species. This taxonomic framework can be used to assign environmental sequences confidently to the cable bacteria clade, even without morphological information. Database searches revealed 185 16S rRNA gene sequences that affiliated within the clade formed by the proposed cable bacteria genera, of which 120 sequences could be assigned to one of the six candidate species, while the remaining 65 sequences indicated the existence of up to five additional species.
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Affiliation(s)
- Daniela Trojan
- Section for Microbiology & Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark.
| | - Lars Schreiber
- Section for Microbiology & Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Jesper T Bjerg
- Section for Microbiology & Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Andreas Bøggild
- Section for Microbiology & Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Tingting Yang
- Section for Microbiology & Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Kasper U Kjeldsen
- Section for Microbiology & Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark
| | - Andreas Schramm
- Section for Microbiology & Center for Geomicrobiology, Department of Bioscience, Aarhus University, Ny Munkegade 114, 8000 Aarhus C, Denmark.
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Silvia F, Joana B, Pedro M, Céu F, Jesper W, Filipe AN. Mismatch discrimination in fluorescent in situ hybridization using different types of nucleic acids. Appl Microbiol Biotechnol 2015; 99:3961-9. [DOI: 10.1007/s00253-015-6389-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2014] [Revised: 11/07/2014] [Accepted: 11/08/2014] [Indexed: 10/24/2022]
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13
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Fontenete S, Guimarães N, Wengel J, Azevedo NF. Prediction of melting temperatures in fluorescence in situ hybridization (FISH) procedures using thermodynamic models. Crit Rev Biotechnol 2015; 36:566-77. [PMID: 25586037 DOI: 10.3109/07388551.2014.993589] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
The thermodynamics and kinetics of DNA hybridization, i.e. the process of self-assembly of one, two or more complementary nucleic acid strands, has been studied for many years. The appearance of the nearest-neighbor model led to several theoretical and experimental papers on DNA thermodynamics that provide reasonably accurate thermodynamic information on nucleic acid duplexes and allow estimation of the melting temperature. Because there are no thermodynamic models specifically developed to predict the hybridization temperature of a probe used in a fluorescence in situ hybridization (FISH) procedure, the melting temperature is used as a reference, together with corrections for certain compounds that are used during FISH. However, the quantitative relation between melting and experimental FISH temperatures is poorly described. In this review, various models used to predict the melting temperature for rRNA targets, for DNA oligonucleotides and for nucleic acid mimics (chemically modified oligonucleotides), will be addressed in detail, together with a critical assessment of how this information should be used in FISH.
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Affiliation(s)
- Sílvia Fontenete
- a Department of Chemical Engineering, Faculty of Engineering, LEPABE , University of Porto , Porto , Portugal .,b Institute of Molecular Pathology and Immunology of the University of Porto , Porto , Portugal .,c Department of Physics, Chemistry and Pharmacy , Nucleic Acid Center, University of Southern Denmark , Odense M , Denmark , and.,d ICBAS, Institute of Biomedical Sciences Abel Salazar, University of Porto , Porto , Portugal
| | - Nuno Guimarães
- a Department of Chemical Engineering, Faculty of Engineering, LEPABE , University of Porto , Porto , Portugal .,b Institute of Molecular Pathology and Immunology of the University of Porto , Porto , Portugal .,c Department of Physics, Chemistry and Pharmacy , Nucleic Acid Center, University of Southern Denmark , Odense M , Denmark , and
| | - Jesper Wengel
- c Department of Physics, Chemistry and Pharmacy , Nucleic Acid Center, University of Southern Denmark , Odense M , Denmark , and
| | - Nuno Filipe Azevedo
- a Department of Chemical Engineering, Faculty of Engineering, LEPABE , University of Porto , Porto , Portugal
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14
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Mathematical tools to optimize the design of oligonucleotide probes and primers. Appl Microbiol Biotechnol 2014; 98:9595-608. [PMID: 25359473 DOI: 10.1007/s00253-014-6165-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Revised: 10/12/2014] [Accepted: 10/14/2014] [Indexed: 12/11/2022]
Abstract
The identification and quantification of specific organisms in mixed microbial communities often relies on the ability to design oligonucleotide probes and primers with high specificity and sensitivity. The design of these oligonucleotides (or "oligos" for short) shares many of the same principles in spite of their widely divergent applications. Three common molecular biology technologies that require oligonucleotide design are polymerase chain reaction (PCR), fluorescence in situ hybridization (FISH), and DNA microarrays. This article reviews techniques and software available for the design and optimization of oligos with the goal of targeting a specific group of organisms within mixed microbial communities. Strategies for enhancing specificity without compromising sensitivity are described, as well as design tools well suited for this purpose.
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15
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Automated design of probes for rRNA-targeted fluorescence in situ hybridization reveals the advantages of using dual probes for accurate identification. Appl Environ Microbiol 2014; 80:5124-33. [PMID: 24928876 DOI: 10.1128/aem.01685-14] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) is a common technique for identifying cells in their natural environment and is often used to complement next-generation sequencing approaches as an integral part of the full-cycle rRNA approach. A major challenge in FISH is the design of oligonucleotide probes with high sensitivity and specificity to their target group. The rapidly expanding number of rRNA sequences has increased awareness of the number of potential nontargets for every FISH probe, making the design of new FISH probes challenging using traditional methods. In this study, we conducted a systematic analysis of published probes that revealed that many have insufficient coverage or specificity for their intended target group. Therefore, we developed an improved thermodynamic model of FISH that can be applied at any taxonomic level, used the model to systematically design probes for all recognized genera of bacteria and archaea, and identified potential cross-hybridizations for the selected probes. This analysis resulted in high-specificity probes for 35.6% of the genera when a single probe was used in the absence of competitor probes and for 60.9% when up to two competitor probes were used. Requiring the hybridization of two independent probes for positive identification further increased specificity. In this case, we could design highly specific probe sets for up to 68.5% of the genera without the use of competitor probes and 87.7% when up to two competitor probes were used. The probes designed in this study, as well as tools for designing new probes, are available online (http://DECIPHER.cee.wisc.edu).
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Okten HE, Yilmaz LS, Noguera DR. Exploring the in situ accessibility of small subunit ribosomal RNA of members of the domains Bacteria and Eukarya to oligonucleotide probes. Syst Appl Microbiol 2012; 35:485-95. [DOI: 10.1016/j.syapm.2011.11.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2011] [Revised: 11/04/2011] [Accepted: 11/09/2011] [Indexed: 10/14/2022]
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17
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Yilmaz LS, Loy A, Wright ES, Wagner M, Noguera DR. Modeling formamide denaturation of probe-target hybrids for improved microarray probe design in microbial diagnostics. PLoS One 2012; 7:e43862. [PMID: 22952791 PMCID: PMC3428302 DOI: 10.1371/journal.pone.0043862] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2011] [Accepted: 07/30/2012] [Indexed: 02/01/2023] Open
Abstract
Application of high-density microarrays to the diagnostic analysis of microbial communities is challenged by the optimization of oligonucleotide probe sensitivity and specificity, as it is generally unfeasible to experimentally test thousands of probes. This study investigated the adjustment of hybridization stringency using formamide with the idea that sensitivity and specificity can be optimized during probe design if the hybridization efficiency of oligonucleotides with target and non-target molecules can be predicted as a function of formamide concentration. Sigmoidal denaturation profiles were obtained using fluorescently labeled and fragmented 16S rRNA gene amplicon of Escherichia coli as the target with increasing concentrations of formamide in the hybridization buffer. A linear free energy model (LFEM) was developed and microarray-specific nearest neighbor rules were derived. The model simulated formamide melting with a denaturant m-value that increased hybridization free energy (ΔG°) by 0.173 kcal/mol per percent of formamide added (v/v). Using the LFEM and specific probe sets, free energy rules were systematically established to predict the stability of single and double mismatches, including bulged and tandem mismatches. The absolute error in predicting the position of experimental denaturation profiles was less than 5% formamide for more than 90 percent of probes, enabling a practical level of accuracy in probe design. The potential of the modeling approach for probe design and optimization is demonstrated using a dataset including the 16S rRNA gene of Rhodobacter sphaeroides as an additional target molecule. The LFEM and thermodynamic databases were incorporated into a computational tool (ProbeMelt) that is freely available at http://DECIPHER.cee.wisc.edu.
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Affiliation(s)
- L Safak Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States of America.
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18
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Lawson TS, Connally RE, Vemulpad S, Piper JA. In Silico Evaluation and Testing of Fluorescence In Situ Hybridization 16S rRNA Probes forStaphylococcus aureus. Lab Med 2011. [DOI: 10.1309/lmi4l6cf6hgfbgya] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/15/2022] Open
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19
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mathFISH, a web tool that uses thermodynamics-based mathematical models for in silico evaluation of oligonucleotide probes for fluorescence in situ hybridization. Appl Environ Microbiol 2010; 77:1118-22. [PMID: 21148691 DOI: 10.1128/aem.01733-10] [Citation(s) in RCA: 133] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Mathematical models of RNA-targeted fluorescence in situ hybridization (FISH) for perfectly matched and mismatched probe/target pairs are organized and automated in web-based mathFISH (http://mathfish.cee.wisc.edu). Offering the users up-to-date knowledge of hybridization thermodynamics within a theoretical framework, mathFISH is expected to maximize the probability of success during oligonucleotide probe design.
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20
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McIlroy SJ, Tillett D, Petrovski S, Seviour RJ. Non-target sites with single nucleotide insertions or deletions are frequently found in 16S rRNA sequences and can lead to false positives in fluorescencein situhybridization (FISH). Environ Microbiol 2010; 13:33-47. [DOI: 10.1111/j.1462-2920.2010.02306.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Flowers JJ, He S, Yilmaz S, Noguera DR, McMahon KD. Denitrification capabilities of two biological phosphorus removal sludges dominated by different "Candidatus Accumulibacter" clades. ENVIRONMENTAL MICROBIOLOGY REPORTS 2009; 1:583-588. [PMID: 20808723 PMCID: PMC2929836 DOI: 10.1111/j.1758-2229.2009.00090.x] [Citation(s) in RCA: 158] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The capability of "Candidatus Accumulibacter" to use nitrate as an electron acceptor for phosphorus uptake was investigated using two activated sludge communities. The two communities were enriched in Accumulibacter clade IA and clade IIA, respectively. By performing a series of batch experiments, we found that clade IA was able to couple nitrate reduction with phosphorus uptake, but clade IIA could not. These results agree with a previously proposed hypothesis that different populations of Accumulibacter have different nitrate reduction capabilities, and they will help to understand the ecological roles that these two clades provide.
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Affiliation(s)
- Jason J. Flowers
- Department of Civil and Environmental Engineering, University of Wisconsin at Madison, Madison, WI, 53706, USA
| | - Shaomei He
- Department of Civil and Environmental Engineering, University of Wisconsin at Madison, Madison, WI, 53706, USA
| | - Safak Yilmaz
- Department of Civil and Environmental Engineering, University of Wisconsin at Madison, Madison, WI, 53706, USA
| | - Daniel R. Noguera
- Department of Civil and Environmental Engineering, University of Wisconsin at Madison, Madison, WI, 53706, USA
| | - Katherine D. McMahon
- Department of Civil and Environmental Engineering, University of Wisconsin at Madison, Madison, WI, 53706, USA
- Department of Bacteriology, University of Wisconsin at Madison, Madison, WI, 53706, USA
- corresponding author: Address: 5525 Microbial Science Building, 1550 Linden Dr., Madison, WI 53925, Tel: (608) 263-3137, Fax: (608) 262-5199,
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Yilmaz LS, Bergsven LI, Noguera DR. Systematic evaluation of single mismatch stability predictors for fluorescence in situ hybridization. Environ Microbiol 2008; 10:2872-85. [PMID: 18707615 DOI: 10.1111/j.1462-2920.2008.01719.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The mismatch discrimination potential of probes in fluorescence in situ hybridization can be defined as the difference between the melting formamide points of perfect complementary and mismatched duplexes (Delta[FA](m)). Using a combined experimental and theoretical approach, Delta[FA](m) was determined for a set of 35 mismatched probes targeting seven locations in the 16S rRNA of Escherichia coli. The mismatches were created by changing single nucleotides on the probes, while maintaining the target unmodified. Estimated Delta[FA](m) values were used to systematically evaluate four predictors of mismatch stability: weighted mismatch (WM) scores from the software arb, published statistical summary of microarray hybridizations, free energy of mismatch stability (DeltaDeltaG degrees (1)) and theoretical Delta[FA](m) estimations obtained with a thermodynamic model. Based on the predictors' ability to explain variability in Delta[FA](m) and to discriminate weak mismatches from strong ones, DeltaDeltaG degrees (1) and WM scores from arb (with an updated set of relative strength parameters) were demonstrated to be adequate estimators of mismatch stability, with DeltaDeltaG degrees (1) offering the benefit of capturing the variability associated with nearest-neighbour effects and being compatible with thermodynamic models of in situ hybridization. The use of DeltaDeltaG degrees (1) and WM in probe design was illustrated as a tool that complements experimental design approaches.
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Affiliation(s)
- L Safak Yilmaz
- Department of Civil and Environmental Engineering, University of Wisconsin-Madison, 1415 Engineering Drive, Madison, WI 53706-1691, USA
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Loy A, Arnold R, Tischler P, Rattei T, Wagner M, Horn M. probeCheck--a central resource for evaluating oligonucleotide probe coverage and specificity. Environ Microbiol 2008; 10:2894-8. [PMID: 18647333 PMCID: PMC2613240 DOI: 10.1111/j.1462-2920.2008.01706.x] [Citation(s) in RCA: 162] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The web server probeCheck, freely accessible at http://www.microbial-ecology.net/probecheck, provides a pivotal forum for rapid specificity and coverage evaluations of probes and primers against selected databases of phylogenetic and functional marker genes. Currently, 24 widely used sequence collections including the Ribosomal Database Project (RDP) II, Greengenes, SILVA and the Functional Gene Pipeline/Repository can be queried. For this purpose, probeCheck integrates a new online version of the popular ARB probe match tool with free energy (ΔG) calculations for each perfectly matched and mismatched probe-target hybrid, allowing assessment of the theoretical binding stabilities of oligo-target and non-target hybrids. For each output sequence, the accession number, the GenBank taxonomy and a link to the respective entry at GenBank, EMBL and, if applicable, the query database are displayed. Filtering options allow customizing results on the output page. In addition, probeCheck is linked with probe match tools of RDP II and Greengenes, NCBI blast, the Oligonucleotide Properties Calculator, the two-state folding tool of the DINAMelt server and the rRNA-targeted probe database probeBase. Taken together, these features provide a multifunctional platform with maximal flexibility for the user in the choice of databases and options for the evaluation of published and newly developed probes and primers.
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Affiliation(s)
- Alexander Loy
- Department of Microbial Ecology, Universität Wien, Althanstrasse 14, A-1090 Wien, Austria
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Quantification of target molecules needed to detect microorganisms by fluorescence in situ hybridization (FISH) and catalyzed reporter deposition-FISH. Appl Environ Microbiol 2008; 74:5068-77. [PMID: 18552182 DOI: 10.1128/aem.00208-08] [Citation(s) in RCA: 100] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) with rRNA-targeted oligonucleotide probes is a method that is widely used to detect and quantify microorganisms in environmental samples and medical specimens by fluorescence microscopy. Difficulties with FISH arise if the rRNA content of the probe target organisms is low, causing dim fluorescence signals that are not detectable against the background fluorescence. This limitation is ameliorated by technical modifications such as catalyzed reporter deposition (CARD)-FISH, but the minimal numbers of rRNA copies needed to obtain a visible signal of a microbial cell after FISH or CARD-FISH have not been determined previously. In this study, a novel competitive FISH approach was developed and used to determine, based on a thermodynamic model of probe competition, the numbers of 16S rRNA copies per cell required to detect bacteria by FISH and CARD-FISH with oligonucleotide probes in mixed pure cultures and in activated sludge. The detection limits of conventional FISH with Cy3-labeled probe EUB338-I were found to be 370 +/- 45 16S rRNA molecules per cell for Escherichia coli hybridized on glass microscope slides and 1,400 +/- 170 16S rRNA copies per E. coli cell in activated sludge. For CARD-FISH the values ranged from 8.9 +/- 1.5 to 14 +/- 2 and from 36 +/- 6 to 54 +/- 7 16S rRNA molecules per cell, respectively, indicating that the sensitivity of CARD-FISH was 26- to 41-fold higher than that of conventional FISH. These results suggest that optimized FISH protocols using oligonucleotide probes could be suitable for more recent applications of FISH (for example, to detect mRNA in situ in microbial cells).
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25
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Single-cell identification in microbial communities by improved fluorescence in situ hybridization techniques. Nat Rev Microbiol 2008; 6:339-48. [PMID: 18414500 DOI: 10.1038/nrmicro1888] [Citation(s) in RCA: 428] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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