2024-03-28T15:35:19Zhttp://digital.csic.es/dspace-oai/requestoai:digital.csic.es:10261/975582020-12-09T17:46:21Zcom_10261_123com_10261_8com_10261_88col_10261_376col_10261_341
The phylogenetic and ecological context of cultured and whole genome-sequenced planktonic bacteria from the coastal NW Mediterranean Sea
Lekunberri, Itziar
Gasol, Josep M.
Acinas, Silvia G.
Gómez-Consarnau, Laura
Crespo, B. G.
Casamayor, Emilio O.
Massana, Ramon
Pedrós-Alió, Carlos
Pinhassi, Jarone
Gammaproteobacteria
Blanes Bay Microbial Observatory
Bacteroidetes
Alphaproteobacteria
Microdiversity
Bacterial isolates
Phylogeny
Diversity
13 pages, 6 figures, 3 tables
Microbial isolates are useful models for physiological and ecological studies and can also be used to reassemble genomes from metagenomic analyses. However, the phylogenetic diversity that can be found among cultured marine bacteria may vary significantly depending on the isolation. Therefore, this study describes a set of 136 bacterial isolates obtained by traditional isolation techniques from the Blanes Bay Microbial Observatory, of which seven strains have had the whole genome sequenced. The complete set was compared to a series of environmental sequences obtained by culture-independent techniques (60 DGGE sequences and 303 clone library sequences) previously obtained by molecular methods. In this way, each isolate was placed in both its >ecological> (time of year, nutrient limitation, chlorophyll and temperature values) context or setting, and its >phylogenetic> landscape (i.e. similar organisms that were found by culture-independent techniques, when they were relevant, and when they appeared). Nearly all isolates belonged to the Gammaproteobacteria, Alphaproteobacteria, or the Bacteroidetes (70, 40 and 20 isolates, respectively). Rarefaction analyses showed similar diversity patterns for sequences from isolates and molecular approaches, except for Alphaproteobacteria where cultivation retrieved a higher diversity per unit effort. Approximately 30% of the environmental clones and isolates formed microdiversity clusters constrained at 99% 16S rRNA gene sequence identity, but the pattern was different in Bacteroidetes (less microdiversity) than in the other main groups. Seventeen cases (12.5%) of nearly complete (98-100%) rRNA sequence identity between isolates and environmental sequences were found: nine in the Alphaproteobacteria, five in the Gammaproteobacteria, and three in the Bacteroidetes, indicating that cultivation could be used to obtain at least some organisms representative of the various taxa detected by molecular methods. Collectively, these results illustrated the largely unexplored potential of culturing on standard media for complementing the study of microbial diversity by culture-independent techniques and for obtaining phylogenetically distinct model organisms from natural seawater. © 2014 Elsevier GmbH.
This work was supported by theEU project BASICS (CTM2005-04795/MAR), Spanish MEC projects GEMMA (CTM2007-63753-C02-01/MAR) and STORM (CTM2009-09352/MAR), as well as the Swedish research program EcoChangeand the Swedish Research Council (Grant 621-2011-4369 to J.P.)
Peer Reviewed
2014-06-02T11:11:43Z
2014-06-02T11:11:43Z
2014-05
2014-06-02T11:11:43Z
artículo
http://purl.org/coar/resource_type/c_6501
doi: 10.1016/j.syapm.2013.11.005
issn: 0723-2020
e-issn: 1618-0984
Systematic and Applied Microbiology 37(3): 216-228 (2014)
http://hdl.handle.net/10261/97558
10.1016/j.syapm.2013.11.005
https://doi.org/10.1016/j.syapm.2013.11.005
none
Urban and Fischer