Journal ArticleDOI
Changes in archaeal, bacterial and eukaryal assemblages along a salinity gradient by comparison of genetic fingerprinting methods in a multipond solar saltern.
Emilio O. Casamayor,Ramon Massana,Susana Benlloch,Lise Øvreås,Beatriz Díez,Victoria Goddard,Josep M. Gasol,Ian Joint,Francisco Rodriguez-Valera,Carlos Pedrós-Alió +9 more
TLDR
Although the particular taxonomic composition of microbial communities inhabiting a multipond solar saltern could vary among protocols, the general structure of the microbial assemblages was maintained.Abstract:
Summary
Microbial communities inhabiting a multipond solar saltern were analysed and compared using SSU rRNA polymerase chain reaction (PCR)-based fingerprintings carried out in parallel by four laboratories. A salinity gradient from seawater (3.7%) to NaCl precipitation (37%) was studied for Bacteria, Archaea and Eukarya, and laboratories applied their own techniques and protocols on the same set of samples. Members of all three domains were retrieved from all salt concentrations. Three fingerprinting techniques were used: denaturing gradient gel electrophoresis (DGGE), ribosomal internal spacer analysis (RISA), and terminal-restriction fragments length polymorphism (T-RFLP). In addition, each laboratory used its own biomass collection method and DNA extraction protocols. Prokaryotes were addressed using DGGE and RISA with different ‘domain-specific’ primers sets. Eukaryotes were analysed by one laboratory using DGGE and T-RFLP, but targeting the same 18S rDNA site. Fingerprints were compared through cluster analysis and non-metric multidimensional scaling plots. This exercise allowed fast comparison of microbial assemblages and determined to what extent the picture provided by each laboratory was similar to those of others. Formation of two main, salinity-based groups of samples in prokaryotes (4–15% and 22–37% salinity) was consistent for all the laboratories. When other clusters appeared, this was a result of the particular technique and the protocol used in each case, but more affected by the primers set used. Eukaryotic microorganisms changed more from pond to pond; 4–5% and 8–37% salinity were but the two main groups detected. Archaea showed the lowest number of bands whereas Eukarya showed the highest number of operational taxonomic units (OTUs) in the initial ponds. Artefacts appeared in the DGGE from ponds with extremely low microbial richness. On the other hand, different 16S rDNA fragments with the same restriction or internal transcribed spacer (ITS) length were the main limitations for T-RFLP and RISA analyses, respectively, in ponds with the highest OTUs richness. However, although the particular taxonomic composition could vary among protocols, the general structure of the microbial assemblages was maintained.read more
Citations
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Journal ArticleDOI
Microbial biogeography : putting microorganisms on the map
Jennifer B. H. Martiny,Brendan J. M. Bohannan,James H. Brown,Robert K. Colwell,Jed A. Fuhrman,Jessica L. Green,M. Claire Horner-Devine,Matthew D. Kane,Jennifer Adams Krumins,Cheryl R. Kuske,Peter J. Morin,Shahid Naeem,Lise Øvreås,Anna-Louise Reysenbach,Val H. Smith,James T. Staley +15 more
TL;DR: Current evidence confirms that, as proposed by the Baas-Becking hypothesis, 'the environment selects' and is, in part, responsible for spatial variation in microbial diversity, but recent studies also dispute the idea that 'everything is everywhere'.
Journal ArticleDOI
Review and re-analysis of domain-specific 16S primers
TL;DR: This work re-assess the specificity of commonly used 16S rRNA gene primers and presents these data in tabular form designed as a tool to aid simple analysis, selection and implementation.
Journal ArticleDOI
Multivariate analyses in microbial ecology.
TL;DR: Here, well-established exploratory and hypothesis-driven approaches are reviewed, so as to foster their addition to the microbial ecologist toolbox.
Review and re-analysis of domain-specific 16S primers (Review article)
TL;DR: In this article, the specificity of commonly used 16S rRNA gene primers was evaluated and two new primers were designed for effective 'universal' Archaeal16S rDNA sequence amplification.
Journal ArticleDOI
A global perspective on wetland salinization: ecological consequences of a growing threat to freshwater wetlands
Ellen R. Herbert,Paul I. Boon,Amy J. Burgin,Scott C. Neubauer,Rima B. Franklin,Marcelo Ardón,Kristine N. Hopfensperger,Leon P. M. Lamers,Peter Gell +8 more
TL;DR: Salinization, a widespread threat to the structure and ecological functioning of inland and coastal wetlands, is currently occurring at an unprecedented rate and geographic scale as discussed by the authors, and the causes of salinization are diverse and include alterations to freshwater flows, land-clearance, irrigation, disposal of wastewater effluent, sea level rise, storm surges, and applications of de-icing salts.
References
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Distribution of bacterioplankton in meromictic Lake Saelenvannet, as determined by denaturing gradient gel electrophoresis of PCR-amplified gene fragments coding for 16S rRNA.
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