title: Culture-Dependent and -Independent Methods Capture Different Microbial Community Fractions in Hydrocarbon-Contaminated Soils.
abstract: Bioremediation is a cost-effective and sustainable approach for treating polluted soils, but our ability to improve on current bioremediation strategies depends on our ability to isolate microorganisms from these soils. Although culturing is widely used in bioremediation research and applications, it is unknown whether the composition of cultured isolates closely mirrors the indigenous microbial community from contaminated soils. To assess this, we paired culture-independent (454-pyrosequencing of total soil DNA) with culture-dependent (isolation using seven different growth media) techniques to analyse the bacterial and fungal communities from hydrocarbon-contaminated soils. Although bacterial and fungal rarefaction curves were saturated for both methods, only 2.4% and 8.2% of the bacterial and fungal OTUs, respectively, were shared between datasets. Isolated taxa increased the total recovered species richness by only 2% for bacteria and 5% for fungi. Interestingly, none of the bacteria that we isolated were representative of the major bacterial OTUs recovered by 454-pyrosequencing. Isolation of fungi was moderately more effective at capturing the dominant OTUs observed by culture-independent analysis, as 3 of 31 cultured fungal strains ranked among the 20 most abundant fungal OTUs in the 454-pyrosequencing dataset. This study is one of the most comprehensive comparisons of microbial communities from hydrocarbon-contaminated soils using both isolation and high-throughput sequencing methods.
authors.affiliation: Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada.
authors.forename: Franck O P
authors.initials: FO
authors.lastname: Stefani
authors.affiliation: Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada.
authors.forename: Terrence H
authors.initials: TH
authors.lastname: Bell
authors.affiliation: Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada.
authors.forename: Charlotte
authors.initials: C
authors.lastname: Marchand
authors.affiliation: Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada.
authors.forename: Ivan E
authors.initials: IE
authors.lastname: de la Providencia
authors.affiliation: Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada.
authors.forename: Abdel
authors.initials: A
authors.lastname: El Yassimi
authors.affiliation: Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada.
authors.forename: Marc
authors.initials: M
authors.lastname: St-Arnaud
authors.affiliation: Department of Biological Sciences, Centre sur la biodiversité, Université de Montréal, Montréal, Québec, Canada.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Hijri
mesh_terms: D001419:Bacteria / Q000302:isolation & purification; D044822:Biodiversity; D018929:Cell Culture Techniques / Q000379:methods*; D004787:Environmental Pollution / Q000032:analysis*; D005658:Fungi / Q000302:isolation & purification; D006838:Hydrocarbons / Q000032:analysis*; D064307:Microbiota; D008969:Molecular Sequence Data; D012988:Soil Microbiology
chemical_list: D006838:Hydrocarbons