Culture-dependent and -independent methods capture different microbial community fractions in hydrocarbon-contaminated soils

Franck O.P. Stefani, Terrence Bell, Charlotte Marchand, Ivan E. De La Providencia, Abdel El Yassimi, Marc St-Arnaud, Mohamed Hijri

Research output: Contribution to journalArticle

49 Citations (Scopus)

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.

Original languageEnglish (US)
Article numbere0128272
JournalPloS one
Volume10
Issue number6
DOIs
StatePublished - Jun 8 2015

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Otus
Hydrocarbons
polluted soils
microbial communities
hydrocarbons
bioremediation
Soil
Soils
Environmental Biodegradation
Bioremediation
Fungi
fungi
fungal communities
bacteria
Bacteria
methodology
bacterial communities
soil
culture media
microorganisms

All Science Journal Classification (ASJC) codes

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Stefani, F. O. P., Bell, T., Marchand, C., De La Providencia, I. E., El Yassimi, A., St-Arnaud, M., & Hijri, M. (2015). Culture-dependent and -independent methods capture different microbial community fractions in hydrocarbon-contaminated soils. PloS one, 10(6), [e0128272]. https://doi.org/10.1371/journal.pone.0128272
Stefani, Franck O.P. ; Bell, Terrence ; Marchand, Charlotte ; De La Providencia, Ivan E. ; El Yassimi, Abdel ; St-Arnaud, Marc ; Hijri, Mohamed. / Culture-dependent and -independent methods capture different microbial community fractions in hydrocarbon-contaminated soils. In: PloS one. 2015 ; Vol. 10, No. 6.
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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.",
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Stefani, FOP, Bell, T, Marchand, C, De La Providencia, IE, El Yassimi, A, St-Arnaud, M & Hijri, M 2015, 'Culture-dependent and -independent methods capture different microbial community fractions in hydrocarbon-contaminated soils', PloS one, vol. 10, no. 6, e0128272. https://doi.org/10.1371/journal.pone.0128272

Culture-dependent and -independent methods capture different microbial community fractions in hydrocarbon-contaminated soils. / Stefani, Franck O.P.; Bell, Terrence; Marchand, Charlotte; De La Providencia, Ivan E.; El Yassimi, Abdel; St-Arnaud, Marc; Hijri, Mohamed.

In: PloS one, Vol. 10, No. 6, e0128272, 08.06.2015.

Research output: Contribution to journalArticle

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