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http://hdl.handle.net/10773/26361
Title: | Assessment of variation in bacterial composition among microhabitats in a mangrove environment using DGGE fingerprints and barcoded pyrosequencing |
Author: | Cleary, Daniel F. R. Smalla, Kornelia Mendonça-Hagler, Leda C. S. Gomes, Newton C. M. |
Issue Date: | 2012 |
Publisher: | Public Library of Science |
Abstract: | Here, we use DGGE fingerprinting and barcoded pyrosequencing data, at six cut-off levels (85-100%), of all bacteria, Alphaproteobacteria and Betaproteobacteria to assess composition in the rhizosphere of nursery plants and nursery-raised transplants, native plants and bulk sediment in a mangrove habitat. When comparing compositional data based on DGGE fingerprinting and barcoded pyrosequencing at different cut-off levels, all revealed highly significant differences in composition among microhabitats. Procrustes superimposition revealed that ordination results using cut-off levels from 85-100% and DGGE fingerprint data were highly congruent with the standard 97% cut-off level. The various approaches revealed a primary gradient in composition from nursery to mangrove samples. The affinity between the nursery and transplants was greatest when using Betaproteobacteria followed by Alphaproteobacteria data. There was a distinct secondary gradient in composition from transplants to bulk sediment with native plants intermediate, which was most prevalent using all bacteria at intermediate cut-off levels (92-97%). Our results show that PCR-DGGE provides a robust and cost effective exploratory approach and is effective in distinguishing among a priori defined groups. |
Peer review: | yes |
URI: | http://hdl.handle.net/10773/26361 |
DOI: | 10.1371/journal.pone.0029380 |
ISSN: | 1932-6203 |
Appears in Collections: | CESAM - Artigos DBio - Artigos |
Files in This Item:
File | Description | Size | Format | |
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Cleary et al. - 2012 - Assessment of Variation in Bacterial Composition a.pdf | 971.6 kB | Adobe PDF | View/Open |
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