Ecological coherence of diversity patterns derived from classical fingerprinting and Next Generation Sequencing techniques

Gobet, Angélique; Boetius, Antje; Ramette, Alban Nicolas (2013). Ecological coherence of diversity patterns derived from classical fingerprinting and Next Generation Sequencing techniques. Environmental microbiology, 16(9), pp. 2672-2681. Wiley-Blackwell 10.1111/1462-2920.12308

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Changes in richness and bacterial community structure obtained via 454 Massively Parallel Tag Sequencing (MPTS) and Automated Ribosomal Intergenic Analysis (ARISA) were systematically compared to determine whether and how the ecological knowledge obtained from both molecular techniques could be combined. We evaluated community changes over time and depth in marine coastal sands at different levels of taxonomic resolutions, sequence corrections and sequence abundances. Although richness over depth layers or sampling dates greatly varied [∼ 30% and 70–80% new operational taxonomic units (OTU) between two samples with ARISA and MPTS respectively], overall patterns of community variations were similar with both approaches. Alpha-diversity estimated by ARISA-derived OTU was most similar to that obtained from MPTS-derived OTU defined at the order level. Similar patterns of OTU replacement were also found with MPTS at the family level and with 20–25% rare types removed. Using ARISA or MPTS datasets with lower resolution, such as those containing only resident OTU, yielded a similar set of significant contextual variables explaining bacterial community changes. Hence, ARISA as a rapid and low-cost fingerprinting technique represents a valid starting point for more in-depth exploration of community composition when complemented by the detailed taxonomic description offered by MPTS.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Service Sector > Institute for Infectious Diseases
04 Faculty of Medicine > Pre-clinic Human Medicine > Institute of Social and Preventive Medicine (ISPM)

UniBE Contributor:

Ramette, Alban Nicolas

Subjects:

500 Science > 570 Life sciences; biology
300 Social sciences, sociology & anthropology > 360 Social problems & social services
600 Technology > 610 Medicine & health

ISSN:

1462-2912

Publisher:

Wiley-Blackwell

Language:

English

Submitter:

Alban Nicolas Ramette

Date Deposited:

14 Feb 2017 10:00

Last Modified:

21 Feb 2017 16:58

Publisher DOI:

10.1111/1462-2920.12308

PubMed ID:

24147993

BORIS DOI:

10.7892/boris.91367

URI:

https://boris.unibe.ch/id/eprint/91367

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