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

Type Article
Date 2014-09
Language English
Author(s) Gobet AngeliqueORCID1, 2, Boetius AntjeORCID1, 3, Ramette AlbanORCID1
Affiliation(s) 1 : Max Planck Inst Marine Microbiol, HGF MPG Grp Deep Sea Ecol & Technol, Bremen, Germany.
2 : Jacobs Univ Bremen GmbH, Bremen, Germany.
3 : Alfred Wegener Inst Polar & Marine Res, Bremerhaven, Germany.
Source Environmental Microbiology (1462-2912) (Wiley-blackwell), 2014-09 , Vol. 16 , N. 9 , P. 2672-2681
DOI 10.1111/1462-2920.12308
WOS© Times Cited 46
Note Special Issue: Metagenomics, and Biomes in Health and Disease
Abstract

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 [approximate to 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.

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