Culture-dependent and culture-independent diversity surveys target different bacteria: a case study in a freshwater sample

• Type: Article in International Scientific Journal
• Date: 2011

Authors

Ivone Vaz Moreira (Author) FEUP; Conceição Egas (Author) Other; Olga C. Nunes (Author) FEUP; Célia M. Manaia (Author) Other

Journal

Title: Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Vol. 100 No. 2

Pages: 245-257

ISSN: 0003-6072

Publisher: Springer Nature

Indexing

ISI Web of Knowledge - 66 Citations

ISI Web of Science

Scopus - 89 Citations

Scientific classification

FOS: Natural sciences > Biological sciences

CORDIS: Natural sciences > Biological sciences > Biology > Microbiology

Other information

Authenticus ID: P-002-PE4

DOI: 10.1007/s10482-011-9583-0

Abstract (EN): Compared with culture-independent approaches, traditionally used culture-dependent methods have a limited capacity to characterize water microbiota. Nevertheless, for almost a century the latter have been optimized to detect and quantify relevant bacteria. A pertinent question is if culture-independent diversity surveys give merely an extended perspective of the bacterial diversity or if, even with a higher coverage, focus on a different set of organisms. We compared the diversity and phylogeny of bacteria in a freshwater sample recovered by currently used culture-dependent and culture-independent methods (DGGE and 454 pyrosequencing). The culture-dependent diversity survey presented lower coverage than the other methods. However, it allowed bacterial identifications to the species level, in contrast with the other procedures that rarely produced identifications below the order. Although the predominant bacterial phyla detected by both approaches were the same (Proteobacteria, Actinobacteria, Bacteroidetes), sequence similarity analysis showed that, in general, different operational taxonomical units were targeted by each method. The observation that culture-dependent and independent approaches target different organisms has implications for the use of the latter for studies in which taxonomic identification has a predictive value. In comparison to DGGE, 454 pyrosequencing method had a higher capacity to explore the bacterial richness and to detect cultured organisms, being also less laborious.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 13