title: Assessment of variation in bacterial composition among microhabitats in a mangrove environment using DGGE fingerprints and barcoded pyrosequencing.
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.
authors.affiliation: Department of Biology and CESAM, Universidade de Aveiro, Aveiro, Portugal.
authors.forename: Daniel F R
authors.initials: DF
authors.lastname: Cleary
authors.forename: Kornelia
authors.initials: K
authors.lastname: Smalla
authors.forename: Leda C S
authors.initials: LC
authors.lastname: Mendonça-Hagler
authors.forename: Newton C M
authors.initials: NC
authors.lastname: Gomes
mesh_terms: D020561:Alphaproteobacteria / Q000235:genetics / Q000302:isolation & purification*; D020562:Betaproteobacteria / Q000235:genetics / Q000302:isolation & purification*; D044822:Biodiversity; D058893:DNA Barcoding, Taxonomic; D016172:DNA Fingerprinting; D004269:DNA, Bacterial / Q000235:genetics; D058645:Denaturing Gradient Gel Electrophoresis; D017753:Ecosystem; D004784:Environmental Monitoring; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D043982:Rhizophoraceae / Q000382:microbiology*
chemical_list: D004269:DNA, Bacterial