title: Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel. The International Society of Microbiologial Ecology Journal, 2020, 14 (8), pp.1966-1981. &#x27E8;10.1038/s41396-020-0659-6&#x27E9;. &#x27E8;hal-02888711&#x27E9;
text: Diversity and dynamics of relevant nanoplanktonic
  diatoms in the Western English Channel
  Laure Arsenieff, Florence Le Gall, Fabienne Rigaut-Jalabert, Frédéric Mahé,
  Diana Sarno, Léna Gouhier, Anne-Claire Baudoux, Nathalie Simon
  
  To cite this version:
  Laure Arsenieff, Florence Le Gall, Fabienne Rigaut-Jalabert, Frédéric Mahé, Diana Sarno, et al..
  Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel. The
  International Society of Microbiologial Ecology Journal, 2020, 14 (8), pp.1966-1981. �10.1038/s41396020-0659-6�. �hal-02888711�
  
  HAL Id: hal-02888711
  https://hal.sorbonne-universite.fr/hal-02888711
  Submitted on 3 Jul 2020
  
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  Table 1.
   Species
  
  Strains
  
  Isolation
  date
  
  RCC4660 26/05/2015
  RCC4661 26/05/2015
  RCC4662 26/05/2015
  
  Minidiscus
  comicus
  
  Minidiscus
  spinulatus
  
  RCC5839
  RCC5840
  RCC5841
  RCC5842
  RCC5843
  RCC5844
  RCC5845
  RCC5846
  RCC5847
  RCC5848
  RCC5849
  RCC5850
  RCC5851
  RCC5852
  RCC5853
  RCC5854
  RCC5855
  RCC5856
  RCC5857
  RCC5859
  
  20/11/2015
  04/12/2015
  04/12/2015
  04/12/2015
  04/12/2015
  04/01/2016
  04/01/2016
  02/02/2016
  02/02/2016
  02/02/2016
  04/03/2016
  04/03/2016
  04/03/2016
  01/04/2016
  01/04/2016
  01/04/2016
  01/04/2016
  15/04/2016
  15/04/2016
  13/05/2016
  
  Flow
  cytometry
  Flow
  cytometry
  Flow
  cytometry
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  
  Flow
  cytometry
  RCC5860 04/03/2016 Dilution
  RCC5861 04/03/2016 Dilution
  
  RCC4659 26/05/2015
  
  Flow
  cytometry
  Flow
  RCC4658 26/05/2015
  cytometry
  Flow
  RCC4665 26/05/2015
  cytometry
  Flow
  RCC4666 26/05/2015
  cytometry
  
  RCC4657 26/05/2015
  
  Minidiscus
  variabilis
  
  Isolation
  method
  
  Morphological
  identification
  
  SSU-18S
  
  ITS
  
  LSU-28S
  D1-D3
  region
  
  LM, SEM
  
  Complete Complete Complete
  
  LM, SEM
  
  Complete Complete Complete
  
  LM, SEM
  
  Complete Complete Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Partial
  Complete
  Complete
  Partial
  Complete
  Complete
  Partial
  Partial
  Partial
  Partial
  Complete
  
  LM, SEM
  
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  
  Complete Complete Complete
  Partial
  Partial
  
  Complete
  Complete
  
  LM, SEM
  
  Complete Complete Complete
  
  LM, SEM
  
  Complete Complete Complete
  
  LM, SEM
  
  Complete Complete Complete
  
  LM, SEM
  
  Complete Complete Complete
  
  RCC5862
  RCC5863
  RCC5864
  RCC5865
  RCC5866
  RCC5867
  RCC5868
  RCC5869
  RCC5870
  RCC5921
  RCC5871
  RCC5872
  RCC5873
  RCC5875
  RCC5876
  RCC5877
  RCC5878
  RCC5879
  RCC5880
  
  06/10/2015
  04/11/2015
  04/11/2015
  04/11/2015
  04/11/2015
  04/11/2015
  20/11/2015
  20/11/2015
  04/12/2015
  04/01/2016
  02/02/2016
  04/03/2016
  01/04/2016
  15/04/2016
  30/05/2016
  13/07/2016
  09/09/2016
  24/10/2016
  24/10/2016
  
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  
  Thalassiosira
  Flow
  RCC5154 26/05/2015
  curviseriata
  cytometry
  RCC4663 26/05/2015
  RCC5881
  Thalassiosira RCC5882
  cf. profunda RCC5883
  RCC5884
  RCC5885
  RCC5886
  
  20/11/2015
  02/02/2016
  04/03/2016
  29/04/2016
  13/05/2016
  13/07/2016
  
  Flow
  cytometry
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  Dilution
  
  Flow
  Thalassiosira RCC4664 26/05/2015
  cytometry
  sp.
   RCC5887 02/02/2016 Dilution
  
  Complete
  Complete
  Partial
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Partial
  Partial
  Partial
  Complete
  Complete
  Partial
  Complete
  Complete
  
  Complete
  
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  Complete
  
  LM, SEM
  
  Complete Complete Complete
  
  LM, SEM
  
  Complete Complete Complete
  Partial
  Partial
  Complete
  Partial
  Partial
  Partial
  
  LM, SEM
  
  Complete
  Complete
  Complete
  Complete
  
  Complete Complete Complete
  Partial
  
  Complete
  
  !
  
  !
  
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  Table S1.
  Species
  Bacterosira bathyomphala
  Bacterosira constricta
  (formerly Thalassiosira minima)
  Bacterosira constricta
  (formerly T. constricta)
  Thalassiosira angulata
  Thalassiosira anguste lineata
  Thalassiosira antarctica
  Thalassiosira cf pacifica
  
  NB04_B6
  
  SSU
  accession
  number
  DQ514894
  
  CCMP991
  
  DQ514877
  
  SMDC01286
  
  KT692951
  
  KT692948
  
  Park et al., 2016
  
  BEN02_35
  BEN02_30
  CCMP982
  FB02_35
  
  DQ514867
  DQ514865
  DQ514874
  DQ514888
  
  DQ512416
  DQ512414
  DQ512423
  DQ512438
  
  Alverson et al., 2007
  Alverson et al., 2007
  Alverson et al., 2007
  Alverson et al., 2007
  Direct submission by
  Park et al., 2010
  Alverson et al., 2007
  Alverson et al., 2007
  Alverson et al., 2007
  Alverson et al., 2007
  Alverson et al., 2007
  Alverson et al., 2007
  
  Culture
  strain
  
  Thalassiosira curviseriata
  
  -
  
  Thalassiosira eccentrica
  Thalassiosira gessneri
  Thalassiosira minima
  Thalassiosira minuscula
  Thalassiosira nodulolineata
  Thalassiosira nordenskioeldii
  
  BER02_09
  ANO2_08
  CCMP990
  CCMP1093
  BEN02_33
  FB02_19
  
  DQ514868
  DQ514864
  DQ514876
  DQ514882
  DQ514866
  DQ514886
  
  Thalassiosira profunda
  
  X9lll12
  
  KC284713
  
  Thalassiosira pseudonana
  Thalassiosira punctigera
  Thalassiosira rotula
  Thalassiosira sp.
  Thalassiosira sp.
   Thalassiosira tumida
  
  CCMP1057
  FB02_06
  CCMP1812
  CCMP1065
  CCMP353
  CCMP1469
  
  Minidiscus comicus
  
  SC72
  
  Minidiscus comicus
  
  MCXM01
  
  Minidiscus proschkinae
  Minidiscus spinulatus
  Minidiscus spinulatus
  
  SMDC305
  SMDC050
  SMDC303
  
  Minidiscus spinulosus
  
  SSND12
  
  DQ514880
  DQ514885
  DQ514884
  DQ514881
  DQ514871
  DQ514883
  Not
  available
  Not
  available
  KY912618
  Too short
  KY912617
  Not
  available
  
  Minidiscus trioculatus
  
  CCMP496
  
  FJ590768
  
  M. trioculatus var. monoculatus
  
  MiniNova
  
  FJ590769
  
  LSU
  accession
  number
  DQ512444
  
  Alverson et al., 2007
  Alverson et al., 2007
  DQ512426
  Luddington et al., 2012
  
  HM991690 HM991675
  
  Minidiscus variabilis
  CCMP495
  FJ590770
  (formerly M. trioculatus)
  Skeletonema grethae (Labeled in
  CCAP1077/3 AY684941
  GenBank as S. costatum)
  Skeletonema grevillei
  CCMP1685 DQ396512
  
  Reference
  
  DQ512417
  DQ512413
  DQ512425
  DQ512431
  DQ512415
  DQ512436
  Not
  available
  DQ512429
  DQ512435
  DQ512433
  DQ512430
  DQ512420
  DQ512432
  
  Alverson, 2014
  Alverson et al., 2007
  Alverson et al., 2007
  Alverson et al., 2007
  Alverson et al., 2007
  Alverson et al., 2007
  Alverson et al., 2007
  
  JQ657759
  
  Gu et al., 2012
  
  JQ657758
  
  Gu et al., 2012
  
  KY912621
  KY912619
  KY912620
  
  Park et al., 2017
  Park et al., 2017
  Park et al., 2017
  
  JQ657760
  
  Gu et al., 2012
  
  Not
  available
  Not
  available
  
  Kaczmarska et al., 2009
  Kaczmarska et al., 2009
  
  Alverson et al., 2007
  Kaczmarska et al., 2009
  Alverson and Kolnick,
  DQ512445
  2005
  DQ396495
  Sarno et al., 2007
  
  DQ512421
  
  Skeletonema japonicum (Labeled
  in GenBank as S. costatum)
  
  NB02_45
  
  AY684968
  
  DQ512450
  
  Skeletonema menzelii
  
  CCMP787
  
  DQ011161
  
  DQ512449
  
  Skeletonema potamos
  
  AJA010_19
  
  KJ081747
  
  KJ081744
  
  Skeletonema pseudocostatum
  
  CCAP1077/7
  
  AY684952
  
  DQ512447
  
  Skeletonema subsalsum
  
  CCAP1077/8
  
  AY684962
  
  DQ512448
  
  Outgroups
  Lithodesmium undulatum
  Porosira pseudodenticulata
  
  CCMP1806
  CCMP1433
  
  DQ514846
  DQ514848
  
  DQ512393
  DQ512396
  
  Alverson and Kolnick,
  2005
  Alverson and Kolnick,
  2005
  Direct submission by
  Alverson (2014)
  Alverson and Kolnick,
  2005
  Alverson and Kolnick,
  2005
  Alverson et al., 2007
  Alverson et al., 2007
  
  References:
  Alverson AJ (2014) Timing marine–freshwater transitions in the diatom order Thalassiosirales.
  Paleobiology 40:91–101.
   Alverson AJ, Jansen RK, Theriot EC (2007) Bridging the Rubicon: Phylogenetic analysis reveals
  repeated colonizations of marine and fresh waters by thalassiosiroid diatoms. Mol
  Phylogenet Evol 45:193–210.
  Alverson AJ, Kolnick L (2005) Intragenomic nucleotide polymorphism among small subunit
  (18S) rDNA paralogs in the diatom genus Skeletonema (Bacillariophyta). J Phycol
  41:1248–1257.
  Gu H, Zhang X, Sun J, Luo Z (2012) Diversity and Seasonal Occurrence of Skeletonema
  (Bacillariophyta) Species in Xiamen Harbour and Surrounding Seas, China. Cryptogam
  Algol 33:245–263.
  Kaczmarska I, Lovejoy C, Potvin M, Macgillivary M (2009) Morphological and molecular
  characteristics of selected species of Minidiscus (Bacillariophyta, Thalassiosiraceae). Eur
  J Phycol 44:461–475.
  Luddington IA, Kaczmarska I, Lovejoy C (2012) Distance and character-based evaluation of the
  V4 region of the 18S rRNA gene for the identification of diatoms (Bacillariophyceae). PLoS
  One 7(9):e45664
  Park JS, Alverson AJ, Lee JH (2016) A phylogenetic re-definition of the diatom genus
  Bacterosira (Thalassiosirales, Bacillariophyta), with the transfer of Thalassiosira
  constricta based on morphological and molecular characters. Phytotaxa 245:1–16.
  Park JS, Jung SW, Ki JS, Guo R, Kim HJ, Lee KW, et al (2017) Transfer of the small diatoms
  Thalassiosira proschkinae and T. spinulata to the genus Minidiscus and their taxonomic
  re-description. PLoS One 12(9):e0181980.
  Sarno D, Kooistra WHCF, Balzano S, Hargraves PE, Zingone A (2007) Diversity in the genus
  Skeletonema (Bacillariophyceae): III. Phylogenetic position and morphological variability
  of Skeletonema costatum and Skeletonema grevillea, with the description of
  Skeletonema ardens sp. nov. J Phycol 43:156–170.
  