PMID- 27235440
OWN - NLM
STAT- MEDLINE
DCOM- 20170922
LR  - 20240325
IS  - 1098-5336 (Electronic)
IS  - 0099-2240 (Print)
IS  - 0099-2240 (Linking)
VI  - 82
IP  - 15
DP  - 2016 Aug 1
TI  - Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance 
      of Specific Picoeukaryotes.
PG  - 4757-4766
LID - 10.1128/AEM.00560-16 [doi]
AB  - High-throughput sequencing (HTS) is revolutionizing environmental surveys of 
      microbial diversity in the three domains of life by providing detailed 
      information on which taxa are present in microbial assemblages. However, it is 
      still unclear how the relative abundance of specific taxa gathered by HTS 
      correlates with cell abundances. Here, we quantified the relative cell abundance 
      of 6 picoeukaryotic taxa in 13 planktonic samples from 6 European coastal sites 
      using epifluorescence microscopy on tyramide signal amplification-fluorescence in 
      situ hybridization preparations. These relative abundance values were then 
      compared with HTS data obtained in three separate molecular surveys: 454 
      sequencing of the V4 region of the 18S ribosomal DNA (rDNA) using DNA and RNA 
      extracts (DNA-V4 and cDNA-V4) and Illumina sequencing of the V9 region (cDNA-V9). 
      The microscopic and molecular signals were generally correlated, indicating that 
      a relative increase in specific 18S rDNA was the result of a large proportion of 
      cells in the given taxa. Despite these positive correlations, the slopes often 
      deviated from 1, precluding a direct translation of sequences to cells. Our data 
      highlighted clear differences depending on the nucleic acid template or the 18S 
      rDNA region targeted. Thus, the molecular signal obtained using cDNA templates 
      was always closer to relative cell abundances, while the V4 and V9 regions gave 
      better results depending on the taxa. Our data support the quantitative use of 
      HTS data but warn about considering it as a direct proxy of cell abundances. 
      IMPORTANCE: Direct studies on marine picoeukaryotes by epifluorescence microscopy 
      are problematic due to the lack of morphological features and due to the limited 
      number and poor resolution of specific phylogenetic probes used in fluorescence 
      in situ hybridization (FISH) routines. As a consequence, there is an increasing 
      use of molecular methods, including high-throughput sequencing (HTS), to study 
      marine microbial diversity. HTS can provide a detailed picture of the taxa 
      present in a community and can reveal diversity not evident using other methods, 
      but it is still unclear what the meaning of the sequence abundance in a given 
      taxon is. Our aim is to investigate the correspondence between the relative HTS 
      signal and relative cell abundances in selected picoeukaryotic taxa. 
      Environmental sequencing provides reasonable estimates of the relative abundance 
      of specific taxa. Better results are obtained when using RNA extracts as the 
      templates, while the region of 18S ribosomal DNA had different influences 
      depending on the taxa assayed.
CI  - Copyright (c) 2016, American Society for Microbiology. All Rights Reserved.
FAU - Giner, Caterina R
AU  - Giner CR
AD  - Department of Marine Biology and Oceanography, Institut de Ciencies del Mar 
      (CSIC), Barcelona, Spain caterina@icm.csic.es ramonm@icm.csic.es.
FAU - Forn, Irene
AU  - Forn I
AD  - Department of Marine Biology and Oceanography, Institut de Ciencies del Mar 
      (CSIC), Barcelona, Spain.
FAU - Romac, Sarah
AU  - Romac S
AD  - CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France.
AD  - Universite Pierre et Marie Curie Paris 06, UMR 7144, Station Biologique de 
      Roscoff, Roscoff, France.
FAU - Logares, Ramiro
AU  - Logares R
AD  - Department of Marine Biology and Oceanography, Institut de Ciencies del Mar 
      (CSIC), Barcelona, Spain.
FAU - de Vargas, Colomban
AU  - de Vargas C
AD  - CNRS, UMR 7144, Station Biologique de Roscoff, Roscoff, France.
AD  - Universite Pierre et Marie Curie Paris 06, UMR 7144, Station Biologique de 
      Roscoff, Roscoff, France.
FAU - Massana, Ramon
AU  - Massana R
AD  - Department of Marine Biology and Oceanography, Institut de Ciencies del Mar 
      (CSIC), Barcelona, Spain caterina@icm.csic.es ramonm@icm.csic.es.
LA  - eng
PT  - Evaluation Study
PT  - Journal Article
DEP - 20160715
PL  - United States
TA  - Appl Environ Microbiol
JT  - Applied and environmental microbiology
JID - 7605801
SB  - IM
MH  - Biodiversity
MH  - Eukaryota/classification/genetics/*isolation & purification
MH  - High-Throughput Nucleotide Sequencing/*methods
MH  - In Situ Hybridization, Fluorescence
MH  - Seawater/*parasitology
PMC - PMC4984273
EDAT- 2016/05/29 06:00
MHDA- 2017/09/25 06:00
PMCR- 2017/01/15
CRDT- 2016/05/29 06:00
PHST- 2016/02/19 00:00 [received]
PHST- 2016/05/23 00:00 [accepted]
PHST- 2016/05/29 06:00 [entrez]
PHST- 2016/05/29 06:00 [pubmed]
PHST- 2017/09/25 06:00 [medline]
PHST- 2017/01/15 00:00 [pmc-release]
AID - AEM.00560-16 [pii]
AID - 00560-16 [pii]
AID - 10.1128/AEM.00560-16 [doi]
PST - epublish
SO  - Appl Environ Microbiol. 2016 Jul 15;82(15):4757-4766. doi: 10.1128/AEM.00560-16. 
      Print 2016 Aug 1.