The phylogenetic and ecological context of cultured and whole genome-sequenced planktonic bacteria from the coastal NW Mediterranean Sea.
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.
Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain.
Itziar
I
Lekunberri
Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain. Electronic address: pepgasol@icm.csic.es.
Josep M
JM
Gasol
Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain.
Silvia G
SG
Acinas
Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain; Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Barlastgatan 11, SE-39182 Kalmar, Sweden.
Laura
L
Gómez-Consarnau
Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain.
Bibiana G
BG
Crespo
Centre d'Estudis Avançats de Blanes - CSIC, Accés a la cala Sant Francesc 14, 17300 Blanes, Catalunya, Spain.
Emilio O
EO
Casamayor
Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain.
Ramon
R
Massana
Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta 37-49, 08003 Barcelona, Catalunya, Spain.
Carlos
C
Pedrós-Alió
Centre for Ecology and Evolution in Microbial Model Systems - EEMiS, Linnaeus University, Barlastgatan 11, SE-39182 Kalmar, Sweden. Electronic address: jarone.pinhassi@lnu.se.
Jarone
J
Pinhassi
D020561:Alphaproteobacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D041963:Bacteroidetes / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D058448:Biota; D016000:Cluster Analysis; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D004275:DNA, Ribosomal / Q000737:chemistry / Q000235:genetics; D020563:Gammaproteobacteria / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification; D016680:Genome, Bacterial; D008522:Mediterranean Sea; D008969:Molecular Sequence Data; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA
D004269:DNA, Bacterial; D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S
Alphaproteobacteria; Bacterial isolates; Bacteroidetes; Blanes Bay Microbial Observatory; Diversity; Gammaproteobacteria; Microdiversity; Phylogeny