FN Archimer Export Format
PT J
TI Evaluation of sequential filtration and centrifugation to capture environmental DNA and survey microbial eukaryotic communities in aquatic environments
BT 
AF Atteia, Ariane
   Bec, Beatrice
   Gianaroli, Camille
   Serais, Ophelie
   Quétel, Isaure
   Lagarde, Franck
   Gobet, Angélique
AS 1:3;2:2;3:1;4:1;5:1;6:1;7:1;
FF 1:;2:;3:PDG-ODE-LITTORAL-LERLR;4:PDG-ODE-LITTORAL-LERLR;5:;6:PDG-ODE-LITTORAL-LERLR;7:PDG-RBE-MARBEC-LAAAS;
C1 MARBEC Univ Montpellier, CNRS, Ifremer, IRD Sète, France
   MARBEC Univ Montpellier, CNRS, Ifremer, IRD Montpellier, France
   MARBEC Univ Montpellier, CNRS, Ifremer, IRD Sète, France
C2 IFREMER, FRANCE
   UNIV MONTPELLIER, FRANCE
   CNRS, FRANCE
SI SETE
   PALAVAS
SE PDG-ODE-LITTORAL-LERLR
   PDG-RBE-MARBEC-LAAAS
UM MARBEC
IN WOS Ifremer UMR
   WOS Cotutelle UMR
   copubli-france
   copubli-univ-france
IF 7.7
TC 0
UR https://archimer.ifremer.fr/doc/00859/97061/105813.pdf
   https://archimer.ifremer.fr/doc/00859/97061/105814.xlsx
   https://archimer.ifremer.fr/doc/00859/97061/105815.docx
LA English
DT Article
DE ;biomonitoring;eDNA capture;metabarcoding;microbial community ecology;phytoplankton;protists
AB Sequential membrane filtration of water samples is commonly used to monitor the diversity of aquatic microbial eukaryotes. This capture method is efficient to focus on specific taxonomic groups within a size fraction, but it is time‐consuming. Centrifugation, often used to collect microorganisms from pure culture, could be seen as an alternative to capture microbial eukaryotic communities from environmental samples. Here, we compared the two capture methods to assess diversity and ecological patterns of eukaryotic communities in the Thau lagoon, France. Water samples were taken twice a month over a full year and sequential filtration targeting the picoplankton (0.2–3 μm) and larger organisms (>3 μm) was used in parallel to centrifugation. The microbial eukaryotic community in the samples was described using an environmental DNA approach targeting the V4 region of the 18S rRNA gene. The most abundant divisions in the filtration fractions and the centrifugation pellet were Dinoflagellata, Metazoa, Ochrophyta, Cryptophyta. Chlorophyta were dominant in the centrifugation pellet and the picoplankton fraction but not in the larger fraction. Diversity indices and structuring patterns of the community in the two size fractions and the centrifugation pellet were comparable. Twenty amplicon sequence variants were significantly differentially abundant between the two size fractions and the centrifugation pellet, and their temporal patterns of abundance in the two fractions combined were similar to those obtained with centrifugation. Overall, centrifugation led to similar ecological conclusions as the two filtrated fractions combined, thus making it an attractive time‐efficient alternative to sequential filtration. 
PY 2024
PD JAN
SO Molecular Ecology Resources
SN 1755-098X
PU Wiley
VL 24
IS 1
UT 001093457700001
DI 10.1111/1755-0998.13887
ID 97061
ER

EF