Diversity and Dynamics of Relevant Nanoplanktonic Diatoms in The

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, etal.. Diversity and dynamics of relevant nanoplanktonic diatoms in the Western English Channel. ISME Journal, Nature Publishing Group, 2020, 14 (8), pp.1966-1981. 10.1038/s41396-020-0659-6. hal- 02888711

HAL Id: hal-02888711 https://hal.sorbonne-universite.fr/hal-02888711 Submitted on 3 Jul 2020

HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés.

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Table 1.

LSU-28S Isolation Isolation Morphological Species Strains SSU-18S ITS D1-D3 date method identification region Flow RCC4660 26/05/2015 LM, SEM Complete Complete Complete cytometry Flow RCC4661 26/05/2015 LM, SEM Complete Complete Complete cytometry Flow RCC4662 26/05/2015 LM, SEM Complete Complete Complete cytometry RCC5839 20/11/2015 Dilution Complete Complete RCC5840 04/12/2015 Dilution Complete Complete RCC5841 04/12/2015 Dilution Complete Complete RCC5842 04/12/2015 Dilution Complete Complete RCC5843 04/12/2015 Dilution Complete RCC5844 04/01/2016 Dilution Complete Complete Minidiscus RCC5845 04/01/2016 Dilution Complete Complete comicus RCC5846 02/02/2016 Dilution Complete RCC5847 02/02/2016 Dilution Complete Complete RCC5848 02/02/2016 Dilution Partial Complete RCC5849 04/03/2016 Dilution Complete RCC5850 04/03/2016 Dilution Complete Complete RCC5851 04/03/2016 Dilution Partial Complete RCC5852 01/04/2016 Dilution Complete Complete RCC5853 01/04/2016 Dilution Complete Complete RCC5854 01/04/2016 Dilution Partial Complete RCC5855 01/04/2016 Dilution Partial Complete RCC5856 15/04/2016 Dilution Partial Complete RCC5857 15/04/2016 Dilution Partial Complete RCC5859 13/05/2016 Dilution Complete Complete Flow RCC4659 26/05/2015 LM, SEM Complete Complete Complete Minidiscus cytometry spinulatus RCC5860 04/03/2016 Dilution Partial Complete RCC5861 04/03/2016 Dilution Partial Complete Flow RCC4657 26/05/2015 LM, SEM Complete Complete Complete cytometry Flow RCC4658 26/05/2015 LM, SEM Complete Complete Complete Minidiscus cytometry variabilis Flow RCC4665 26/05/2015 LM, SEM Complete Complete Complete cytometry Flow RCC4666 26/05/2015 LM, SEM Complete Complete Complete cytometry RCC5862 06/10/2015 Dilution Complete RCC5863 04/11/2015 Dilution Complete Complete RCC5864 04/11/2015 Dilution Partial RCC5865 04/11/2015 Dilution Complete RCC5866 04/11/2015 Dilution Complete RCC5867 04/11/2015 Dilution Complete Complete RCC5868 20/11/2015 Dilution Complete Complete RCC5869 20/11/2015 Dilution Complete Complete RCC5870 04/12/2015 Dilution Complete Complete RCC5921 04/01/2016 Dilution Complete Complete RCC5871 02/02/2016 Dilution Complete Complete RCC5872 04/03/2016 Dilution Partial Complete RCC5873 01/04/2016 Dilution Partial Complete RCC5875 15/04/2016 Dilution Partial Complete RCC5876 30/05/2016 Dilution Complete Complete RCC5877 13/07/2016 Dilution Complete Complete RCC5878 09/09/2016 Dilution Partial Complete RCC5879 24/10/2016 Dilution Complete RCC5880 24/10/2016 Dilution Complete Thalassiosira Flow RCC5154 26/05/2015 LM, SEM Complete Complete Complete curviseriata cytometry Flow RCC4663 26/05/2015 LM, SEM Complete Complete Complete cytometry RCC5881 20/11/2015 Dilution Partial Thalassiosira RCC5882 02/02/2016 Dilution Partial cf. profunda RCC5883 04/03/2016 Dilution Complete Complete RCC5884 29/04/2016 Dilution Partial Complete RCC5885 13/05/2016 Dilution Partial Complete RCC5886 13/07/2016 Dilution Partial Complete Flow Thalassiosira RCC4664 26/05/2015 LM, SEM Complete Complete Complete cytometry sp. RCC5887 02/02/2016 Dilution Partial Complete

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Table S1.

SSU LSU Culture Species accession accession Reference strain number number Bacterosira bathyomphala NB04_B6 DQ514894 DQ512444 Alverson et al. , 2007 Bacterosira constricta Alverson et al. , 2007 CCMP991 DQ514877 DQ512426 (formerly Thalassiosira minima ) Luddington et al. , 2012 Bacterosira constricta SMDC01286 KT692951 KT692948 Park et al. , 2016 (formerly T. constricta ) Thalassiosira angulata BEN02_35 DQ514867 DQ512416 Alverson et al. , 2007 Thalassiosira anguste lineata BEN02_30 DQ514865 DQ512414 Alverson et al. , 2007 Thalassiosira antarctica CCMP982 DQ514874 DQ512423 Alverson et al. , 2007 Thalassiosira cf pacifica FB02_35 DQ514888 DQ512438 Alverson et al. , 2007 Direct submission by Thalassiosira curviseriata - HM991690 HM991675 Park et al. , 2010 Thalassiosira eccentrica BER02_09 DQ514868 DQ512417 Alverson et al. , 2007 Thalassiosira gessneri ANO2_08 DQ514864 DQ512413 Alverson et al. , 2007 Thalassiosira minima CCMP990 DQ514876 DQ512425 Alverson et al. , 2007 Thalassiosira minuscula CCMP1093 DQ514882 DQ512431 Alverson et al. , 2007 Thalassiosira nodulolineata BEN02_33 DQ514866 DQ512415 Alverson et al. , 2007 Thalassiosira nordenskioeldii FB02_19 DQ514886 DQ512436 Alverson et al. , 2007 Not Thalassiosira profunda X9lll12 KC284713 Alverson, 2014 available Thalassiosira pseudonana CCMP1057 DQ514880 DQ512429 Alverson et al. , 2007 Thalassiosira punctigera FB02_06 DQ514885 DQ512435 Alverson et al. , 2007 Thalassiosira rotula CCMP1812 DQ514884 DQ512433 Alverson et al. , 2007 Thalassiosira sp. CCMP1065 DQ514881 DQ512430 Alverson et al. , 2007 Thalassiosira sp. CCMP353 DQ514871 DQ512420 Alverson et al. , 2007 Thalassiosira tumida CCMP1469 DQ514883 DQ512432 Alverson et al. , 2007 Not Minidiscus comicus SC72 JQ657759 Gu et al. , 2012 available Not Minidiscus comicus MCXM01 JQ657758 Gu et al. , 2012 available Minidiscus proschkinae SMDC305 KY912618 KY912621 Park et al. , 2017 Minidiscus spinulatus SMDC050 Too short KY912619 Park et al. , 2017 Minidiscus spinulatus SMDC303 KY912617 KY912620 Park et al. , 2017 Not Minidiscus spinulosus SSND12 JQ657760 Gu et al. , 2012 available Not Minidiscus trioculatus CCMP496 FJ590768 Kaczmarska et al. , 2009 available Not M. trioculatus var . monoculatus MiniNova FJ590769 Kaczmarska et al. , 2009 available Minidiscus variabilis Alverson et al. , 2007 CCMP495 FJ590770 DQ512421 (formerly M. trioculatus ) Kaczmarska et al. , 2009 Skeletonema grethae (Labeled in Alverson and Kolnick, CCAP1077/3 AY684941 DQ512445 GenBank as S. costatum ) 2005 Skeletonema grevillei CCMP1685 DQ396512 DQ396495 Sarno et al. , 2007 Skeletonema japonicum (Labeled Alverson and Kolnick, NB02_45 AY684968 DQ512450 in GenBank as S. costatum ) 2005 Alverson and Kolnick, Skeletonema menzelii CCMP787 DQ011161 DQ512449 2005 Direct submission by Skeletonema potamos AJA010_19 KJ081747 KJ081744 Alverson (2014) Alverson and Kolnick, Skeletonema pseudocostatum CCAP1077/7 AY684952 DQ512447 2005 Alverson and Kolnick, Skeletonema subsalsum CCAP1077/8 AY684962 DQ512448 2005 Outgroups Lithodesmium undulatum CCMP1806 DQ514846 DQ512393 Alverson et al. , 2007 Porosira pseudodenticulata CCMP1433 DQ514848 DQ512396 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.