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Zeugner LE, Krüger K, Barrero-Canosa J, Amann RI, Fuchs BM. In situ visualization of glycoside hydrolase family 92 genes in marine flavobacteria. ISME COMMUNICATIONS 2021; 1:81. [PMID: 37938716 PMCID: PMC9723552 DOI: 10.1038/s43705-021-00082-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 11/24/2021] [Accepted: 12/02/2021] [Indexed: 11/09/2023]
Abstract
Gene clusters rich in carbohydrate-active enzymes within Flavobacteriia genera provide a competitiveness for their hosts to degrade diatom-derived polysaccharides. One such widely distributed polysaccharide is glucuronomannan, a main cell wall component of diatoms. A conserved gene cluster putatively degrading glucuronomannan was found previously among various flavobacterial taxa in marine metagenomes. Here, we aimed to visualize two glycoside hydrolase family 92 genes coding for α-mannosidases with fluorescently-labeled polynucleotide probes using direct-geneFISH. Reliable in situ localization of single-copy genes was achieved with an efficiency up to 74% not only in the flavobacterial strains Polaribacter Hel1_33_49 and Formosa Hel1_33_131 but also in planktonic samples from the North Sea. In combination with high-resolution microscopy, direct-geneFISH gave visual evidence of the contrasting lifestyles of closely related Polaribacter species in those samples and allowed for the determination of gene distribution among attached and free-living cells. We also detected highly similar GH92 genes in yet unidentified taxa by broadening probe specificities, enabling a visualization of the functional trait in subpopulations across the borders of species and genera. Such a quantitative insight into the niche separation of flavobacterial taxa complements our understanding of the ecology of polysaccharide-degrading bacteria beyond omics-based techniques on a single-cell level.
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Affiliation(s)
- Laura E Zeugner
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Karen Krüger
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Jimena Barrero-Canosa
- Technical University of Berlin, Institute of Environmental Technology, Environmental Microbiology, Berlin, Germany
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Bremen, Germany
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2
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Detection of an alkene monooxygenase in vinyl chloride-oxidizing bacteria with GeneFISH. J Microbiol Methods 2021; 181:106147. [PMID: 33493490 DOI: 10.1016/j.mimet.2021.106147] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 11/23/2022]
Abstract
Fluorescence in situ hybridization (FISH) can provide information on the morphology, spatial arrangement, and local environment of individual cells enabling the investigation of intact microbial communities. GeneFISH uses polynucleotide probes and enzymatic signal amplification to detect genes that are present in low copy numbers. Previously, this technique has only been applied in a small number of closely related organisms. However, many important functional genes, such as those involved in xenobiotic degradation or pathogenesis, are present in diverse microbial strains. Here, we present a geneFISH method for the detection of the functional gene etnC, which encodes the alpha subunit of an alkene monooxygenase used by aerobic ethene and vinyl chloride oxidizing bacteria (etheneotrophs). The probe concentration was optimized and found to be 100 pg/μl, similar to previous geneFISH reports. Permeabilization was necessary for successful geneFISH labeling of Mycobacteria; sequential treatment with lysozyme and achromopeptidase was the most effective treatment. This method was able to detect etnC in several organisms including Mycobacteria and Nocardioides, demonstrating for the first time that a single geneFISH probe can detect a variety of alleles (>80% sequence similarity) across multiple species. Detection of etnC with geneFISH has practical applications for bioremediation. This method can be readily adapted for other functional genes and has broad applications for investigating microbial communities in natural and engineered systems.
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Barrero-Canosa J, Moraru C. Linking Microbes to Their Genes at Single Cell Level with Direct-geneFISH. Methods Mol Biol 2021; 2246:169-205. [PMID: 33576990 DOI: 10.1007/978-1-0716-1115-9_12] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Direct-geneFISH is a Fluorescence In Situ Hybridization (FISH) method that directly links gene presence, and thus potential metabolic capabilities, to cell identity. The method uses rRNA-targeting oligonucleotide probes to identify cells and dsDNA polynucleotide probes carrying multiple molecules of the same fluorochrome to detect genes. In addition, direct-geneFISH allows quantification of the cell fraction carrying the targeted gene and the number of target genes per cell. It can be applied to laboratory cultures, for example, enrichments and phage infections, and to environmental samples. This book chapter describes the main steps of the direct-geneFISH protocol: probe design and synthesis, the "core" direct-geneFISH protocol and lastly, microscopy and data analysis.
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Affiliation(s)
- Jimena Barrero-Canosa
- Department of Environmental Technology, Technische Universität Berlin, Berlin, Germany
| | - Cristina Moraru
- Institute for Chemistry and Biology of the Marine Environment, Oldenburg, Germany.
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Moraru C. Gene-PROBER - a tool to design polynucleotide probes for targeting microbial genes. Syst Appl Microbiol 2020; 44:126173. [PMID: 33352459 DOI: 10.1016/j.syapm.2020.126173] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/06/2020] [Accepted: 11/26/2020] [Indexed: 11/27/2022]
Abstract
Recent developments in fluorescence in situ hybridization (FISH) methods allow the detection and visualization of the genes/genomic regions of bacteria, archaea and infecting viruses at the single cell level. These methods use mixtures of polynucleotides as probes to specifically detect the target of interest. Gene-PROBER enables the design of polynucleotide mixtures for targeting genes or genomic regions in microorganisms. It has four workflows, depending on the availability of non-target sequences and the choice of probe synthesis, either by chemical synthesis or by PCR. It outputs polynucleotides that are spread along the target sequence and have similar melting properties. Therefore, such a polynucleotide mixture can be used as a single probe, in a single hybridization reaction. Gene-PROBER is a freely available web service that can be accessed at http://gene-prober.icbm.de/, and is implemented in the R language using the Shiny package.
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Affiliation(s)
- Cristina Moraru
- Department of the Biology of Geological Processes, Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, 26111 Oldenburg, Germany.
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5
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Ansorge R, Romano S, Sayavedra L, Porras MÁG, Kupczok A, Tegetmeyer HE, Dubilier N, Petersen J. Functional diversity enables multiple symbiont strains to coexist in deep-sea mussels. Nat Microbiol 2019; 4:2487-2497. [DOI: 10.1038/s41564-019-0572-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 08/28/2019] [Indexed: 12/13/2022]
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Abstract
PhageFISH uses the power of fluorescence in situ hybridization to monitor intracellular phage infections at single cell level. It combines host cell identification via rRNA probes and phage identification via phage-specific gene probes, allowing for the quantification of the infected cell fraction and the discrimination between infection stages. This book chapter covers all aspects of the procedure, from phage probe design and synthesis, to the phageFISH protocol itself, to microscopy and image analysis.
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Sun C, Galicia C, Stenkamp DL. Transcripts within rod photoreceptors of the Zebrafish retina. BMC Genomics 2018; 19:127. [PMID: 29422031 PMCID: PMC5806438 DOI: 10.1186/s12864-018-4499-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 01/28/2018] [Indexed: 12/03/2022] Open
Abstract
Background The purpose of this study was to identify transcripts of retinal rod photoreceptors of the zebrafish. The zebrafish is an important animal model for vision science due to rapid and tractable development, persistent neurogenesis of rods throughout the lifespan, and capacity for functional retinal regeneration. Results Zebrafish rods, and non-rod retinal cells of the xops:eGFP transgenic line, were separated by cell dissociation and fluorescence-activated cell sorting (FACS), followed by RNA-seq. At a false discovery rate of < 0.01, 597 transcripts were upregulated (“enriched”) in rods vs. other retinal cells, and 1032 were downregulated (“depleted”). Thirteen thousand three hundred twenty four total transcripts were detected in rods, including many not previously known to be expressed by rods. Forty five transcripts were validated by qPCR in FACS-sorted rods vs. other retinal cells. Transcripts enriched in rods from adult retinas were also enriched in rods from larval and juvenile retinas, and were also enriched in rods sorted from retinas subjected to a neurotoxic lesion and allowed to regenerate. Many transcripts enriched in rods were upregulated in retinas of wildtype retinas vs. those of a zebrafish model for rod degeneration. Conclusions We report the generation and validation of an RNA-seq dataset describing the rod transcriptome of the zebrafish, which is now available as a resource for further studies of rod photoreceptor biology and comparative transcriptomics. Electronic supplementary material The online version of this article (10.1186/s12864-018-4499-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Chi Sun
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA
| | - Carlos Galicia
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA
| | - Deborah L Stenkamp
- Department of Biological Sciences, University of Idaho, 875 Perimeter Drive, MS 3051, Moscow, ID, 83844-3051, USA.
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Barrero‐Canosa J, Moraru C, Zeugner L, Fuchs BM, Amann R. Direct‐geneFISH: a simplified protocol for the simultaneous detection and quantification of genes and rRNA in microorganisms. Environ Microbiol 2016; 19:70-82. [DOI: 10.1111/1462-2920.13432] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Jimena Barrero‐Canosa
- Department of Molecular EcologyMax Planck Institute for Marine MicrobiologyCelsiusstr. 1BremenD‐28359 Germany
| | - Cristina Moraru
- Department of Biology of Geological ProcessesInstitute for Chemistry and Biology of the Marine environment (ICBM)Carl‐von‐Ossietzky‐Straße 9‐11OldenburgD‐26111 Germany
| | - Laura Zeugner
- Department of Molecular EcologyMax Planck Institute for Marine MicrobiologyCelsiusstr. 1BremenD‐28359 Germany
| | - Bernhard M. Fuchs
- Department of Molecular EcologyMax Planck Institute for Marine MicrobiologyCelsiusstr. 1BremenD‐28359 Germany
| | - Rudolf Amann
- Department of Molecular EcologyMax Planck Institute for Marine MicrobiologyCelsiusstr. 1BremenD‐28359 Germany
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Acidianus Tailed Spindle Virus: a New Archaeal Large Tailed Spindle Virus Discovered by Culture-Independent Methods. J Virol 2016; 90:3458-68. [PMID: 26763997 DOI: 10.1128/jvi.03098-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2015] [Accepted: 01/07/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The field of viral metagenomics has expanded our understanding of viral diversity from all three domains of life (Archaea, Bacteria, and Eukarya). Traditionally, viral metagenomic studies provide information about viral gene content but rarely provide knowledge about virion morphology and/or cellular host identity. Here we describe a new virus, Acidianus tailed spindle virus (ATSV), initially identified by bioinformatic analysis of viral metagenomic data sets from a high-temperature (80°C) acidic (pH 2) hot spring located in Yellowstone National Park, followed by more detailed characterization using only environmental samples without dependency on culturing. Characterization included the identification of the large tailed spindle virion morphology, determination of the complete 70.8-kb circular double-stranded DNA (dsDNA) viral genome content, and identification of its cellular host. Annotation of the ATSV genome revealed a potential three-domain gene product containing an N-terminal leucine-rich repeat domain, followed by a likely posttranslation regulatory region consisting of high serine and threonine content, and a C-terminal ESCRT-III domain, suggesting interplay with the host ESCRT system. The host of ATSV, which is most closely related to Acidianus hospitalis, was determined by a combination of analysis of cellular clustered regularly interspaced short palindromic repeat (CRISPR)/Cas loci and dual viral and cellular fluorescence in situ hybridization (viral FISH) analysis of environmental samples and confirmed by culture-based infection studies. This work provides an expanded pathway for the discovery, isolation, and characterization of new viruses using culture-independent approaches and provides a platform for predicting and confirming virus hosts. IMPORTANCE Virus discovery and characterization have been traditionally accomplished by using culture-based methods. While a valuable approach, it is limited by the availability of culturable hosts. In this research, we report a virus-centered approach to virus discovery and characterization, linking viral metagenomic sequences to a virus particle, its sequenced genome, and its host directly in environmental samples, without using culture-dependent methods. This approach provides a pathway for the discovery, isolation, and characterization of new viruses. While this study used an acidic hot spring environment to characterize a new archaeal virus, Acidianus tailed spindle virus (ATSV), the approach can be generally applied to any environment to expand knowledge of virus diversity in all three domains of life.
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Stagars MH, Ruff SE, Amann R, Knittel K. High Diversity of Anaerobic Alkane-Degrading Microbial Communities in Marine Seep Sediments Based on (1-methylalkyl)succinate Synthase Genes. Front Microbiol 2016; 6:1511. [PMID: 26779166 PMCID: PMC4703814 DOI: 10.3389/fmicb.2015.01511] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 12/14/2015] [Indexed: 11/13/2022] Open
Abstract
Alkanes comprise a substantial fraction of crude oil and are prevalent at marine seeps. These environments are typically anoxic and host diverse microbial communities that grow on alkanes. The most widely distributed mechanism of anaerobic alkane activation is the addition of alkanes to fumarate by (1-methylalkyl)succinate synthase (Mas). Here we studied the diversity of MasD, the catalytic subunit of the enzyme, in 12 marine sediments sampled at seven seeps. We aimed to identify cosmopolitan species as well as to identify factors structuring the alkane-degrading community. Using next generation sequencing we obtained a total of 420 MasD species-level operational taxonomic units (OTU0.96) at 96% amino acid identity. Diversity analysis shows a high richness and evenness of alkane-degrading bacteria. Sites with similar hydrocarbon composition harbored similar alkane-degrading communities based on MasD genes; the MasD community structure is clearly driven by the hydrocarbon source available at the various seeps. Two of the detected OTU0.96 were cosmopolitan and abundant while 75% were locally restricted, suggesting the presence of few abundant and globally distributed alkane degraders as well as specialized variants that have developed under specific conditions at the diverse seep environments. Of the three MasD clades identified, the most diverse was affiliated with Deltaproteobacteria. A second clade was affiliated with both Deltaproteobacteria and Firmicutes likely indicating lateral gene transfer events. The third clade was only distantly related to known alkane-degrading organisms and comprises new divergent lineages of MasD homologs, which might belong to an overlooked phylum of alkane-degrading bacteria. In addition, masD geneFISH allowed for the in situ identification and quantification of the target guild in alkane-degrading enrichment cultures. Altogether, these findings suggest an unexpectedly high number of yet unknown groups of anaerobic alkane degraders and underline the need for comprehensive surveys of microbial diversity based on metabolic genes in addition to ribosomal genes.
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Affiliation(s)
- Marion H Stagars
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - S Emil Ruff
- Department of Molecular Ecology, Max Planck Institute for Marine MicrobiologyBremen, Germany; HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine MicrobiologyBremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology Bremen, Germany
| | - Katrin Knittel
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology Bremen, Germany
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Matturro B, Rossetti S. GeneCARD-FISH: Detection of tceA and vcrA reductive dehalogenase genes in Dehalococcoides mccartyi by fluorescence in situ hybridization. J Microbiol Methods 2015; 110:27-32. [DOI: 10.1016/j.mimet.2015.01.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/12/2015] [Accepted: 01/12/2015] [Indexed: 11/26/2022]
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12
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Allers E, Moraru C, Duhaime MB, Beneze E, Solonenko N, Barrero-Canosa J, Amann R, Sullivan MB. Single-cell and population level viral infection dynamics revealed by phageFISH, a method to visualize intracellular and free viruses. Environ Microbiol 2013; 15:2306-18. [PMID: 23489642 PMCID: PMC3884771 DOI: 10.1111/1462-2920.12100] [Citation(s) in RCA: 104] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 01/18/2013] [Accepted: 01/19/2013] [Indexed: 11/29/2022]
Abstract
Microbes drive the biogeochemical cycles that fuel planet Earth, and their viruses (phages) alter microbial population structure, genome repertoire, and metabolic capacity. However, our ability to understand and quantify phage–host interactions is technique-limited. Here, we introduce phageFISH – a markedly improved geneFISH protocol that increases gene detection efficiency from 40% to > 92% and is optimized for detection and visualization of intra- and extracellular phage DNA. The application of phageFISH to characterize infection dynamics in a marine podovirus–gammaproteobacterial host model system corroborated classical metrics (qPCR, plaque assay, FVIC, DAPI) and outperformed most of them to reveal new biology. PhageFISH detected both replicating and encapsidated (intracellular and extracellular) phage DNA, while simultaneously identifying and quantifying host cells during all stages of infection. Additionally, phageFISH allowed per-cell relative measurements of phage DNA, enabling single-cell documentation of infection status (e.g. early vs late stage infections). Further, it discriminated between two waves of infection, which no other measurement could due to population-averaged signals. Together, these findings richly characterize the infection dynamics of a novel model phage–host system, and debut phageFISH as a much-needed tool for studying phage–host interactions in the laboratory, with great promise for environmental surveys and lineage-specific population ecology of free phages.
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Affiliation(s)
- Elke Allers
- Department of Ecology and Evolutionary Biology, University of Arizona, Life Sciences South, 1007 East Lowell Street, Tucson, AZ 85721, USA
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Lenk S, Moraru C, Hahnke S, Arnds J, Richter M, Kube M, Reinhardt R, Brinkhoff T, Harder J, Amann R, Mußmann M. Roseobacter clade bacteria are abundant in coastal sediments and encode a novel combination of sulfur oxidation genes. THE ISME JOURNAL 2012; 6:2178-87. [PMID: 22739490 PMCID: PMC3504970 DOI: 10.1038/ismej.2012.66] [Citation(s) in RCA: 95] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2012] [Revised: 05/01/2012] [Accepted: 05/03/2012] [Indexed: 11/09/2022]
Abstract
Roseobacter clade bacteria (RCB) are abundant in marine bacterioplankton worldwide and central to pelagic sulfur cycling. Very little is known about their abundance and function in marine sediments. We investigated the abundance, diversity and sulfur oxidation potential of RCB in surface sediments of two tidal flats. Here, RCB accounted for up to 9.6% of all cells and exceeded abundances commonly known for pelagic RCB by 1000-fold as revealed by fluorescence in situ hybridization (FISH). Phylogenetic analysis of 16S rRNA and sulfate thiohydrolase (SoxB) genes indicated diverse, possibly sulfur-oxidizing RCB related to sequences known from bacterioplankton and marine biofilms. To investigate the sulfur oxidation potential of RCB in sediments in more detail, we analyzed a metagenomic fragment from a RCB. This fragment encoded the reverse dissimilatory sulfite reductase (rDSR) pathway, which was not yet found in RCB, a novel type of sulfite dehydrogenase (SoeABC) and the Sox multi-enzyme complex including the SoxCD subunits. This was unexpected as soxCD and dsr genes were presumed to be mutually exclusive in sulfur-oxidizing prokaryotes. This unique gene arrangement would allow a metabolic flexibility beyond known sulfur-oxidizing pathways. We confirmed the presence of dsrA by geneFISH in closely related RCB from an enrichment culture. Our results show that RCB are an integral part of the microbial community in marine sediments, where they possibly oxidize inorganic and organic sulfur compounds in oxic and suboxic sediment layers.
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Affiliation(s)
- Sabine Lenk
- Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Cristina Moraru
- Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Sarah Hahnke
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Julia Arnds
- Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Michael Richter
- Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Michael Kube
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | | | - Thorsten Brinkhoff
- Institute for Chemistry and Biology of the Marine Environment, University of Oldenburg, Oldenburg, Germany
| | - Jens Harder
- Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marc Mußmann
- Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
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Kubota K. CARD-FISH for environmental microorganisms: technical advancement and future applications. Microbes Environ 2012; 28:3-12. [PMID: 23124765 PMCID: PMC4070690 DOI: 10.1264/jsme2.me12107] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Fluorescence in situ hybridization (FISH) has become a standard technique in environmental microbiology. More than 20 years have passed since this technique was first described, and it is currently used for the detection of ribosomal RNA, messenger RNA, and functional genes encoded on chromosomes. This review focuses on the advancement and applications of FISH combined with catalyzed reporter deposition (CARD, also known as tyramide signal amplification or TSA), in the detection of environmental microorganisms. Significant methodological improvements have been made in CARD-FISH technology, including its combination with other techniques and instruments.
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Affiliation(s)
- Kengo Kubota
- Department of Civil and Environmental Engineering, Tohoku University, Miyagi, Japan.
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15
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Wagner M, Haider S. New trends in fluorescence in situ hybridization for identification and functional analyses of microbes. Curr Opin Biotechnol 2011; 23:96-102. [PMID: 22079351 DOI: 10.1016/j.copbio.2011.10.010] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 10/22/2011] [Indexed: 11/16/2022]
Abstract
Fluorescence in situ hybridization (FISH) has become an indispensable tool for rapid and direct single-cell identification of microbes by detecting signature regions in their rRNA molecules. Recent advances in this field include new web-based tools for assisting probe design and optimization of experimental conditions, easy-to-implement signal amplification strategies, innovative multiplexing approaches, and the combination of FISH with transmission electron microscopy or extracellular staining techniques. Further emerging developments focus on sorting FISH-identified cells for subsequent single-cell genomics and on the direct detection of specific genes within single microbial cells by advanced FISH techniques employing various strategies for massive signal amplification.
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Affiliation(s)
- Michael Wagner
- Department of Microbial Ecology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.
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Hydrogen is an energy source for hydrothermal vent symbioses. Nature 2011; 476:176-80. [PMID: 21833083 DOI: 10.1038/nature10325] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Accepted: 06/20/2011] [Indexed: 11/08/2022]
Abstract
The discovery of deep-sea hydrothermal vents in 1977 revolutionized our understanding of the energy sources that fuel primary productivity on Earth. Hydrothermal vent ecosystems are dominated by animals that live in symbiosis with chemosynthetic bacteria. So far, only two energy sources have been shown to power chemosynthetic symbioses: reduced sulphur compounds and methane. Using metagenome sequencing, single-gene fluorescence in situ hybridization, immunohistochemistry, shipboard incubations and in situ mass spectrometry, we show here that the symbionts of the hydrothermal vent mussel Bathymodiolus from the Mid-Atlantic Ridge use hydrogen to power primary production. In addition, we show that the symbionts of Bathymodiolus mussels from Pacific vents have hupL, the key gene for hydrogen oxidation. Furthermore, the symbionts of other vent animals such as the tubeworm Riftia pachyptila and the shrimp Rimicaris exoculata also have hupL. We propose that the ability to use hydrogen as an energy source is widespread in hydrothermal vent symbioses, particularly at sites where hydrogen is abundant.
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