Seasonality in bacterial diversity in north-west Mediterranean coastal waters: assessment through clone libraries, fingerprinting and FISH.
We combined denaturing gradient gel electrophoresis (DGGE), catalysed reporter deposition-FISH (CARD-FISH) and clone libraries to investigate the seasonality of the bacterial assemblage composition in north-west Mediterranean coastal waters. DGGE analysis indicated that bacterial diversity changed gradually throughout the year, although with a clear distinction of the summer period. Alphaproteobacteria were the dominant group on an annual basis [29% of the DAPI (4',6-diamidino-2-phenylindole) counts by CARD-FISH, and 70% of the bacterial clones]. The SAR11 clade was most abundant during spring and summer (>20% of DAPI counts), while the Roseobacter clade was abundant primarily in winter and spring (up to 7% of DAPI counts). The phylum Bacteroidetes constituted the second most important group and was quantitatively uniform throughout the year (average 11% of the DAPI counts). Gammaproteobacteria showed a peak during summer (8% of DAPI counts), when most of them belonged to the NOR5 cluster. Clone libraries and CARD-FISH showed reasonable agreement in the quantitative proportions of Bacteroidetes and Gammaproteobacteria, but Alphaproteobacteria were overrepresented in clone libraries. Sequencing of the most predominant DGGE bands failed to detect the SAR11 group despite their high abundance. The combination of the three molecular approaches allowed a comprehensive assessment of seasonal changes in bacterial diversity.
Alonso-Sáez
Laura
L
Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar CSIC, 08003-Barcelona, Catalunya, Spain. lalonso@icm.csic.edu
Balagué
Vanessa
V
Sà
Elisabet L
EL
Sánchez
Olga
O
González
José M
JM
Pinhassi
Jarone
J
Massana
Ramon
R
Pernthaler
Jakob
J
Pedrós-Alió
Carlos
C
Gasol
Josep M
JM
D020561:Alphaproteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D041963:Bacteroidetes / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D003001:Cloning, Molecular; D016172:DNA Fingerprinting / Q000379:methods; D004269:DNA, Bacterial / Q000032:analysis / Q000302:isolation & purification; D020563:Gammaproteobacteria / Q000145:classification / Q000235:genetics / Q000302:isolation & purification; D015723:Gene Library; D014644:Genetic Variation; D006090:Gram-Negative Bacteria / Q000145:classification* / Q000235:genetics / Q000254:growth & development / Q000302:isolation & purification; D017404:In Situ Hybridization, Fluorescence; D008522:Mediterranean Sea; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D012621:Seasons; D012623:Seawater / Q000382:microbiology*; D017422:Sequence Analysis, DNA
D004269:DNA, Bacterial