GeneFISH--an in situ technique for linking gene presence and cell identity in environmental microorganisms

Environmental Microbiology
Cristina MoraruRudolf Amann

Abstract

Our knowledge concerning the metabolic potentials of as yet to be cultured microorganisms has increased tremendously with the advance of sequencing technologies and the consequent discoveries of novel genes. On the other hand, it is often difficult to reliably assign a particular gene to a phylogenetic clade, because these sequences are usually found on genomic fragments that carry no direct marker of cell identity, such as rRNA genes. Therefore, the aim of the present study was to develop geneFISH - a protocol for linking gene presence with cell identity in environmental samples, the signals of which can be visualized at a single cell level. This protocol combines rRNA-targeted catalysed reporter deposition - fluorescence in situ hybridization and in situ gene detection. To test the protocol, it was applied to seawater samples from the Benguela upwelling system. For gene detection, a polynucleotide probe mix was used, which was designed based on crenarchaeotal amoA clone libraries prepared from each seawater sample. Each probe in the mix was selected to bind to targets with up to 5% mismatches. To determine the hybridization parameters, the T(m) of probes, targets and hybrids was estimated based on theoretical calculations and...Continue Reading

References

Oct 11, 1992·Nucleic Acids Research·R Kierzek
Jan 1, 1991·Critical Reviews in Biochemistry and Molecular Biology·J G Wetmur
Mar 1, 1989·Applied and Environmental Microbiology·C C SomervilleR R Colwell
Dec 5, 1973·Journal of Molecular Biology·T I BonnerR J Britten
Jan 14, 1972·Journal of Molecular Biology·M L BirnstielI F Purdom
Jul 1, 1971·Journal of Bacteriology·H E Kubitschek, M L Freedman
Feb 14, 1968·Journal of Molecular Biology·J G Wetmur, N Davidson
Jan 25, 1984·Journal of Molecular Biology·N WatsonD Apirion
Aug 11, 1994·Nucleic Acids Research·H YuA S Waggoner
Mar 12, 1998·FEMS Microbiology Letters·M WagnerK H Schleifer
Sep 15, 1999·Proceedings of the National Academy of Sciences of the United States of America·R B Jensen, L Shapiro
Sep 28, 2001·Journal of Molecular Endocrinology·N J PavlosM H Zheng
Jun 1, 2002·Applied and Environmental Microbiology·Annelie PernthalerRudolf Amann
Apr 1, 2003·IUBMB Life·Chaitanya Jain
Jun 10, 2003·Microbiology and Molecular Biology Reviews : MMBR·Ciarán Condon
Aug 7, 2003·Applied and Environmental Microbiology·Fumito MaruyamaMasao Nasu
Feb 27, 2004·Nucleic Acids Research·Wolfgang LudwigKarl-Heinz Schleifer
Apr 7, 2004·Science·J Craig VenterHamilton O Smith
Jun 5, 2004·Proceedings of the National Academy of Sciences of the United States of America·Patrick H ViollierLucy Shapiro
Sep 4, 2004·Applied and Environmental Microbiology·Annelie Pernthaler, Rudolf Amann
Mar 5, 2005·Applied and Environmental Microbiology·Patrick D Schloss, Jo Handelsman
Jun 3, 2005·Nature Reviews. Microbiology·Christa SchleperMelanie Jonuscheit
Sep 24, 2005·Nature·Martin KönnekeDavid A Stahl
Sep 28, 2005·Proceedings of the National Academy of Sciences of the United States of America·Christopher A FrancisBrian B Oakley
Nov 5, 2005·Applied and Environmental Microbiology·Takehiko KenzakaMasao Nasu
Dec 8, 2005·Applied and Environmental Microbiology·Fumito MaruyamaMasao Nasu
Feb 3, 2006·Nucleic Acids Research·Murray P Deutscher
Dec 22, 2006·PloS One·Sebastian BreuertJörg Soppa
Apr 11, 2007·Proceedings of the National Academy of Sciences of the United States of America·Phyllis LamMarcel M M Kuypers

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Citations

Dec 29, 2011·Microbial Ecology·Sonja OberbeckmannGunnar Gerdts
Apr 9, 2011·Applied Microbiology and Biotechnology·Meng Li, Ji-Dong Gu
Dec 17, 2011·Journal of Microbiological Methods·Shuji KawakamiKengo Kubota
Dec 3, 2011·The ISME Journal·Joan M BernhardDavid J Beaudoin
May 31, 2011·Applied and Environmental Microbiology·Graham M PumphreyJim C Spain
Jul 15, 2015·The ISME Journal·Martin KaltenpothAleš Svatoš
Apr 2, 2013·Systematic and Applied Microbiology·Andreas KrupkeRachel A Foster
Apr 17, 2012·Systematic and Applied Microbiology·Cecilia Alonso
Feb 1, 2011·Environmental Microbiology Reports·Cristina MoraruRudolf Amann
Feb 28, 2015·Environmental Microbiology Reports·Ricardo Amils
Nov 19, 2011·FEMS Microbiology Reviews·Niculina MusatMarcel M M Kuypers
Nov 15, 2011·Current Opinion in Biotechnology·Michael Wagner, Susanne Haider
Jan 8, 2015·Frontiers in Microbiology·Vinh T Dang, Matthew B Sullivan
Jun 19, 2016·Marine Pollution Bulletin·Bruna MatturroSimona Rossetti
May 19, 2016·PloS One·Yunjun MeiXiangdong Chen
Jan 26, 2018·Scientific Reports·Cristina EscuderoRicardo Amils
Aug 13, 2011·Nature·Jillian M PetersenNicole Dubilier
Nov 5, 2011·Environmental Microbiology·Benjamin J TullyJohn F Heidelberg
Feb 28, 2019·International Microbiology : the Official Journal of the Spanish Society for Microbiology·Cristina EscuderoRicardo Amils
May 18, 2020·The Science of the Total Environment·Sara GallegoN L Fahrenfeld
Jan 26, 2021·Journal of Microbiological Methods·Patrick M Richards, Timothy E Mattes
Dec 23, 2020·Systematic and Applied Microbiology·Cristina Moraru
Mar 23, 2021·Frontiers in Microbiology·Kasia PiwoszKarel Šimek
Jun 22, 2021·Current Opinion in Biomedical Engineering·Hao ShiIwijn De Vlaminck

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