title: Validation of a new catalysed reporter deposition-fluorescence in situ hybridization probe for the accurate quantification of marine Bacteroidetes populations.
abstract: Catalysed reporter deposition-fluorescence in situ hybridization (CARD-FISH) is a powerful approach to quantify bacterial taxa. In this study, we compare the performance of the widely used Bacteroidetes CF319a probe with the new CF968 probe. In silico analyses and tests with isolates demonstrate that CF319a hybridizes with non-Bacteroidetes sequences from the Rhodobacteraceae and Alteromonadaceae families. We test the probes' accuracy in 37 globally distributed marine samples and over two consecutive years at the Blanes Bay Microbial Observatory (NW Mediterranean). We also compared the CARD-FISH data with the Bacteroidetes 16S rRNA gene sequences retrieved from 27 marine metagenomes from the TARA Oceans expedition. We find no significant differences in abundances between both approaches, although CF319a targeted some unspecific sequences and both probes displayed different abundances of specific Bacteroidetes phylotypes. Our results demonstrate that quantitative estimations by using both probes are significantly different in certain oceanographic regions (Mediterranean Sea, Red Sea and Arabian Sea) and that CF968 shows seasonality within marine Bacteroidetes, notably large differences between summer and winter that is overlooked by CF319a. We propose CF968 as an alternative to CF319a for targeting the whole Bacteroidetes phylum since it has better coverage, greater specificity and overall better quantifies marine Bacteroidetes.
authors.affiliation: Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain.
authors.forename: Silvia G
authors.initials: SG
authors.lastname: Acinas
authors.affiliation: Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain.
authors.forename: Isabel
authors.initials: I
authors.lastname: Ferrera
authors.affiliation: Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain.|Department of Hydrobiology, Federal University of São Carlos, São Carlos, São Paulo, Brazil.
authors.forename: Hugo
authors.initials: H
authors.lastname: Sarmento
authors.affiliation: Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain.
authors.forename: Cristina
authors.initials: C
authors.lastname: Díez-Vives
authors.affiliation: Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain.
authors.forename: Irene
authors.initials: I
authors.lastname: Forn
authors.affiliation: Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain.|Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, QC, Canada.
authors.forename: Clara
authors.initials: C
authors.lastname: Ruiz-González
authors.affiliation: Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain.
authors.forename: Francisco M
authors.initials: FM
authors.lastname: Cornejo-Castillo
authors.affiliation: Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain.
authors.forename: Guillem
authors.initials: G
authors.lastname: Salazar
authors.affiliation: Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (ICM), CSIC, Barcelona, Catalunya, E-08003, Spain.
authors.forename: Josep M
authors.initials: JM
authors.lastname: Gasol
mesh_terms: D034241:Alteromonadaceae / Q000235:genetics; D041963:Bacteroidetes / Q000145:classification* / Q000235:genetics; D015342:DNA Probes / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics*; D017404:In Situ Hybridization, Fluorescence / Q000379:methods*; D008522:Mediterranean Sea; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D041902:Rhodobacteraceae / Q000235:genetics; D012621:Seasons; D012623:Seawater / Q000382:microbiology; D017422:Sequence Analysis, DNA
chemical_list: D015342:DNA Probes; D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S