EcologyVolume 104, Issue 5 e4030 THE SCIENTIFIC NATURALIST The Pharaoh's snakes of the teasel: New insights into Francis Darwin's observations Antoine Vergne, Antoine Vergne Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, FranceSearch for more papers by this authorEric Giraud, Eric Giraud Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), IRD, Université de Montpellier, CIRAD, INRAE, Institut Agro, TA-A82/J- Campus de Baillarguet, Montpellier, 34398 France Plant Health Institute, IRD, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, FranceSearch for more papers by this authorAlicia Camuel, Alicia Camuel Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), IRD, Université de Montpellier, CIRAD, INRAE, Institut Agro, TA-A82/J- Campus de Baillarguet, Montpellier, 34398 France Plant Health Institute, IRD, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, FranceSearch for more papers by this authorCorinne Bardot, Corinne Bardot Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, FranceSearch for more papers by this authorHermine Billard, Hermine Billard Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, FranceSearch for more papers by this authorClémentin Bouquet, Clémentin Bouquet Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, FranceSearch for more papers by this authorBruno Corbara, Bruno Corbara Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, FranceSearch for more papers by this authorDjamel Gully, Djamel Gully Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), IRD, Université de Montpellier, CIRAD, INRAE, Institut Agro, TA-A82/J- Campus de Baillarguet, Montpellier, 34398 France Plant Health Institute, IRD, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, FranceSearch for more papers by this authorFrédéric Mathonat, Frédéric Mathonat Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, FranceSearch for more papers by this authorChristian Jeanthon, Christian Jeanthon CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, FranceSearch for more papers by this authorIsabelle Mary, Isabelle Mary Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, FranceSearch for more papers by this authorJean-Claude Caissard, Jean-Claude Caissard Université de Lyon, UJM-Saint-Etienne, CNRS, LBVpam UMR 5079, 23 rue du Dr Paul Michelon, Saint-Etienne, F-42023 FranceSearch for more papers by this authorAnne-Catherine Lehours, Corresponding Author Anne-Catherine Lehours [email protected] Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, France Correspondence Anne-Catherine Lehours Email: [email protected]Search for more papers by this author Antoine Vergne, Antoine Vergne Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, FranceSearch for more papers by this authorEric Giraud, Eric Giraud Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), IRD, Université de Montpellier, CIRAD, INRAE, Institut Agro, TA-A82/J- Campus de Baillarguet, Montpellier, 34398 France Plant Health Institute, IRD, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, FranceSearch for more papers by this authorAlicia Camuel, Alicia Camuel Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), IRD, Université de Montpellier, CIRAD, INRAE, Institut Agro, TA-A82/J- Campus de Baillarguet, Montpellier, 34398 France Plant Health Institute, IRD, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, FranceSearch for more papers by this authorCorinne Bardot, Corinne Bardot Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, FranceSearch for more papers by this authorHermine Billard, Hermine Billard Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, FranceSearch for more papers by this authorClémentin Bouquet, Clémentin Bouquet Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, FranceSearch for more papers by this authorBruno Corbara, Bruno Corbara Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, FranceSearch for more papers by this authorDjamel Gully, Djamel Gully Laboratoire des Symbioses Tropicales et Méditerranéennes (LSTM), IRD, Université de Montpellier, CIRAD, INRAE, Institut Agro, TA-A82/J- Campus de Baillarguet, Montpellier, 34398 France Plant Health Institute, IRD, Université Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, FranceSearch for more papers by this authorFrédéric Mathonat, Frédéric Mathonat Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, FranceSearch for more papers by this authorChristian Jeanthon, Christian Jeanthon CNRS, Sorbonne Université, Station Biologique de Roscoff, Adaptation et Diversité en Milieu Marin, Roscoff, FranceSearch for more papers by this authorIsabelle Mary, Isabelle Mary Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, FranceSearch for more papers by this authorJean-Claude Caissard, Jean-Claude Caissard Université de Lyon, UJM-Saint-Etienne, CNRS, LBVpam UMR 5079, 23 rue du Dr Paul Michelon, Saint-Etienne, F-42023 FranceSearch for more papers by this authorAnne-Catherine Lehours, Corresponding Author Anne-Catherine Lehours [email protected] Université Clermont Auvergne, CNRS, LMGE, F-63000 Clermont-Ferrand, France Correspondence Anne-Catherine Lehours Email: [email protected]Search for more papers by this author First published: 13 March 2023 https://doi.org/10.1002/ecy.4030 Handling Editor: John Pastor Antoine Vergne and Eric Giraud have equally contributed to this work. Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL CONFLICT OF INTEREST STATEMENT The authors declare no conflicts of interest. Open Research DATA AVAILABILITY STATEMENT Video documenting the Pharaoh's snakes of the Teasel (Lehours et al., 2023) is available in Figshare at https://doi.org/10.6084/m9.figshare.21842163.v1. Values of nifH gene numbers and of acetylene reduction assays (Lehours, 2023) are available in Figshare at https://doi.org/10.6084/m9.figshare.21856494.v1. REFERENCES Abaurrea-Velasco, C., T. Auth, and G. Gompper. 2019. “Vesicles with Internal Active Filaments: Self-Organized Propulsion Controls Shape, Motility, and Dynamical Response.” New Journal of Physics 21: 123024. Baldotto, L. E., and F. L. Olivares. 2008. “Phylloepiphytic Interaction between Bacteria and Different Plant Species in a Tropical Agricultural System.” Canadian Journal of Microbioogyl 54: 918– 31. Chase, M. W., M. J. M. Christenhusz, D. Sanders, and M. F. Fay. 2009. “Murderous Plants: Victorian Gothic, Darwin and Modern Insights into Vegetable Carnivory.” Botanical Journal of the Linnean Society 161: 329– 56. Chodat, R., and R. Zollikofer. 1892. “Les Trichomes capités du Dipsacus et leurs filaments vibrants.” Communication de la Société de physique et d'histoire naturelle de Genève, Aubert-Schuchardt 4: 31– 52. Christy, M. 1923. “The Common Teasel as a Carnivorous Plant.” Journal of Botany 61: 33– 45. Cohn, F. J. 1878. “Über vibrirende Fäden in den Drüsenhaaren von Dipsacus.” Botanische Zeitung 36: 122– 4. Darwin, C. 1877b. “The Contractile Filaments of the Teasel.” Nature 16: 339– 9. Darwin, E. 1791. The Botanic Garden. A Poem, in Two Parts. Part I. Containing the Economy of Vegetation. Part II. The Loves of the Plants: With Philosophical Notes. New York: T. & J. Swords. Darwin, F. 1877a. “On the Protrusion of Protoplasmic Filaments from the Glandular Hairs on the Leaves of the Common Teasel (Dipsacus Sylvestris).” Quarterly Journal of Microscopical Science 2: 245– 72. Ellison, A. M. 2006. “Nutrient Limitation and Stoichiometry of Carnivorous Plants.” Plant Biology 8: 740– 7. Espenberg, M., M. Truu, Ü. Mander, K. Kasak, H. Nõlvak, T. Ligi, K. Oopkaup, M. Maddison, and J. Truu. 2018. “Differences in Microbial Community Structure and Nitrogen Cycling in Natural and Drained Tropical Peatland Soils.” Scientific Reports 8: 4742. Finzi-Hart, J. A., J. Pett-Ridge, P. K. Weber, R. Popa, S. J. Fallon, T. Gunderson, I. D. Hutcheon, K. H. Nealson, and D. G. Capone. 2009. “Fixation and Fate of C and N in the Cyanobacterium Trichodesmium Using Nanometer-Scale Secondary Ion Mass Spectrometry.” Proceedings of the National Academy of Sciences U.S.A. 106: 6345– 50. Gershenzon, J., and N. Dudareva. 2007. “The Function of Terpene Natural Products in the Natural World.” Nature Chemical Biology 3: 408– 14. Grassmann, J., S. Hippeli, and E. F. Elstner. 2002. “Plant's Defence and its Benefits for Animals and Medicine: Role of Phenolics and Terpenoids in Avoiding Oxygen Stress.” Plant Physiology Biochemistry 40: 471– 8. Hardy, R. W., R. D. Holsten, E. K. Jackson, and R. C. Burns. 1968. “The Acetylene-ethylene Assay for N2 fixation: Laboratory and Field Evaluation.” Plant Physiology 43: 1185– 207. Huang, A. C., T. Jiang, Y. X. Liu, Y. C. Bai, J. Reed, B. Qu, A. Goossens, H. W. Nützmann, Y. Bai, and A. Osbourn. 2019. “A Specialized Metabolic Network Selectively Modulates Arabidopsis Root Microbiota.” Science 364: eaau6389. Huchelmann, A., M. Boutry, and C. Hachez. 2017. “Plant Glandular Trichomes: Natural Cell Factories of High Biotechnological Interest.” Plant Physiology 175: 6– 22. Krupa, J. J., and J. M. Thomas. 2019. “Is the Common Teasel (Dipsacus Fullonum) Carnivorous or Was Francis Darwin Wrong?” Botany 97: 321– 8. Kusstatscher, P., W. A. Wicaksono, A. Bergna, T. Cernava, N. Bergau, A. Tissier, B. Hause, and G. Berg. 2020. “Trichomes Form Genotype-Specific Microbial Hotspots in the Phyllosphere of Tomato.” Environmental Microbiome 15: 17. Lehours, A.-C. 2023. “Data for ARA and qPCR Analyses.” Figshare. Dataset. https://doi.org/10.6084/m9.figshare.21856494.v1. Lehours, A.-C., A.-H. Le Jeune, J.-P. Aguer, R. Céréghino, B. Corbara, B. Kéraval, C. Leroy, F. Perrière, C. Jeanthon, and A.-C. Lehours. 2016. “Unexpectedly High Bacteriochlorophyll a Concentrations in Neotropical Tank Bromeliads.” Environmental Microbiology Reports 8: 689– 98. Lehours, A.-C., A. Vergne, E. Giraud, C. Bardot, A. Camuel, H. Billard, et al. 2023. “Video_1_ The Pharaoh's Snakes of Teasel: New Insights into Francis Darwin's Observations.” Figshare. Media. https://doi.org/10.6084/m9.figshare.21842163.v1. Ling, N., T. Wang, and Y. Kuzyakov. 2022. “Rhizosphere Bacteriome Structure and Functions.” Nature Communications 13: 836. Luo, Y. W., S. C. Doney, L. A. Anderson, M. Benavides, I. Berman-Frank, A. Bode, S. Bonnet, et al. 2012. “Database of Diazotrophs in Global Ocean: Abundance, Biomass and Nitrogen Fixation Rates.” Earth System Science Data 4: 47– 73. Mano, H., and M. Hasebe. 2021. “Rapid movements in plants.” Journal of Plant Research 134: 3– 17. Massalha, H., E. Korenblum, S. Malitsky, O. H. Shapiro, and A. Aharoni. 2017. “Live Imaging of Root-Bacteria Interactions in a Microfluidics Setup.” Proceedings of the National Academy of Sciences U.S.A. 114: 4549– 54. Muravnik, L. E. 2020. “ The Structural Peculiarities of the Leaf Glandular Trichomes: A Review.” In Plant Cell and Tissue Differentiation and Secondary Metabolites: Fundamentals and Applications, edited by K. G. Ramawat, H. M. Ekiert, and S. Goyal, 1– 35. Berlin: Springer. Paez-Garcia, A., J. A. Sparks, L. de Bang, and E. B. Blancaflor. 2018. “ Plant Actin Cytoskeleton: New Functions from Old Scaffold.” In Concepts in Cell Biology - History and Evolution. Plant Cell Monographs, Vol 23, edited by V. P. Sahi and F. Baluška, 103– 37. Berlin: Springer. Peddireddy, K., S. Čopar, K. V. Le, I. Muševič, C. Bahr, and V. S. R. Jampani. 2021. “Self-Shaping Liquid Crystal Droplets by Balancing Bulk Elasticity and Interfacial Tension.” Proceedings of the National Academy of Sciences U.S.A. 118: e2011174118. Rector, B. G., V. Harizanova, R. Sforza, T. Widmer, and R. N. Wiedenmann. 2006. “Prospects for Biological Control of Teasels, Dipsacus Spp., a New Target in the United States.” Biological Control 36: 1– 17. Rostock, R. 1904. “Ueber die biologische Bedeutung der Drüsenhaare von Dipsacus sylvestris.” Botanische Zeitung 62: 11– 20. Schaefer, J. R. 2021. “On Dipsacus and Drosera: Francis Darwin's Favorite Carnivores.” Carnivorous Plant Newsletter 50: 73– 80. Schuurink, R., and A. Tissier. 2020. “Glandular Trichomes: Micro-Organs with Model Status?” New Phytologist 225: 2251– 66. Shaw, P. J. A., and K. Shackleton. 2011. “Carnivory in the Teasel Dipsacus Fullonum - the Effect of Experimental Feeding on Growth and Seed Set.” PLoS One 6: e17935. The Angiosperm Phylogeny Group, M. W. Chase, M. J. M. Christenhusz, M. F. Fay, J. W. Byng, W. S. Judd, D. E. Soltis, et al. 2016. “Anupdate of the Angiosperm Phylogeny Group Classification for the Orders and Families of Flowering Plants: APG IV.” Botanical Journal of the Linnean Society 181: 1– 20. Vergne, A., V. Darbot, C. Bardot, F. Enault, A.-H. Le Jeune, J.-F. Carrias, B. Corbara, et al. 2021. “Assemblages of Anoxygenic Phototrophic Bacteria in Tank Bromeliads Exhibit a Host-Specific Signature.” Journal of Ecology 109: 2550– 65. Werner, P. A. 1975. “Predictions of Fate from Rosette Size in Teasel (Dipsacus Fullonum L.).” Œcologica 20: 197– 201. Whitman, W. B., D. C. Coleman, and W. J. Wiebe. 1998. “Prokaryotes: The Unseen Majority.” Proceedings of the National Academy of Sciences U.S.A. 95: 6578– 83. Supporting Information Filename Description ecy4030-sup-0001-AppendixS1.pdfPDF document, 52.6 MB Appendix S1. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article. Volume104, Issue5May 2023e4030 ReferencesRelatedInformation

Coccolithophores have global ecological and biogeochemical significance as the most important calcifying marine phytoplankton group. The structure and selection of prokaryotic communities associated with the most abundant coccolithophore and bloom-forming species, Emiliania huxleyi, are still poorly known. In this study, we assessed the diversity of bacterial communities associated with an E. huxleyi bloom in the Celtic Sea, exposed axenic E. huxleyi cultures to prokaryotic communities derived from bloom and non-bloom conditions and followed the dynamics of their microbiome composition over one year. Bloom-associated prokaryotic communities were dominated by SAR11, Marine group II Euryarchaeota, Rhodobacterales and contained substantial proportions of known indicators of phytoplankton bloom demises such as Flavobacteriaceae and Pseudoalteromonadaceae. Taxonomic richness of replicated co-cultures resulting from natural communities with axenic E. huxleyi rapidly shifted and then stabilized over time, presumably by ecological selection favoring more beneficial populations. Recruited microbiomes from the environment were consistently dependent on the composition of the initial bacterioplankton community. Phycosphere-associated communities derived from the E. huxleyi bloom depth were highly similar to one another, suggesting deterministic processes, whereas cultures from non-bloom conditions show an effect of both deterministic processes and stochasticity. Overall, this work sheds new light on the importance of the initial inoculum composition in microbiome recruitment and elucidates the temporal dynamics of its composition and long-term stability.

The MALINA oceanographic campaign was conducted during summer 2009 to investigate the carbon stocks and the processes controlling the carbon fluxes in the Mackenzie River estuary and the Beaufort Sea. During the campaign, an extensive suite of physical, chemical and biological variables were measured across seven shelf–basin transects (south–north) to capture the meridional gradient between the estuary and the open ocean. Key variables such as temperature, absolute salinity, radiance, irradiance, nutrient concentrations, chlorophyll a concentration, bacteria, phytoplankton and zooplankton abundance and taxonomy, and carbon stocks and fluxes were routinely measured onboard the Canadian research icebreaker CCGS Amundsen and from a barge in shallow coastal areas or for sampling within broken ice fields. Here, we present the results of a joint effort to compile and standardize the collected data sets that will facilitate their reuse in further studies of the changing Arctic Ocean. The data set is available at https://doi.org/10.17882/75345 (Massicotte et al., 2020).

Anoxygenic phototrophic bacteria (APB) are a very significant metabolic functional group in the phytotelmata of tank‐forming Bromeliaceae plants. Considering the close relationships existing between the bromeliad and its tank microbiota, the dominance of APB raises the question of their role in the ecology and evolution of these plants. Here, using pufM gene sequencing for taxonomic profiling, we investigated the structure of APB communities in the tanks of five bromeliad species exhibiting different habitat characteristics (i.e. physicochemical factors associated with the host), and occurring in different localities of French Guiana. We found that APB assemblages were specific to plant species and were less dependent on location or on bromeliad habitat characteristics. This convergence suggests that the identity of the bromeliad species per se is more important than habitat filtering or dispersal to control specific assembly rules for APB. The pufM OTUs were affiliated with five orders of Alpha‐ and Beta‐proteobacteria (Rhodobacterales, Sphingomonadales, Rhizobiales, Burkholderiales and Rhodospirillales), and we assume that they may be major components of the core microbiota of plant‐held waters. Our findings also revealed that up to 79% of the sequences were affiliated with APB clades possessing nitrogen‐fixing genes suggesting that this metabolic capability is widespread within the APB community inhabiting tank bromeliads. We hypothesized that bromeliads may benefit nutritionally from associations with free‐living APB capable to fix atmospheric nitrogen. Synthesis. Understanding the dominance of APB in tank bromeliads and determining whether a potential interplay exists between these partners is an intriguing aspect of possible mutualistic and coevolving interactions between the two existing forms of chlorophototrophy (i.e. bacteriochlorophyll‐based anoxygenic and chlorophyll‐based oxygenic phototrophy). In the present study, we found that bromeliad species was the main factor that explained variance in APB community composition. These findings suggest that APB and tank bromeliads may have a close, mutualistic relationship and we hypothesize according to our genomic analyses that APB may promote the bromeliad growth by provisioning essential nutrients like nitrogen.

As critical primary producers and recyclers of organic matter, the diversity of marine protists has been extensively explored by high-throughput barcode sequencing. However, classification of short metabarcoding sequences into traditional taxonomic units is not trivial, especially for lineages mainly known by their genetic fingerprints. This is the case for the widespread Amoebophrya ceratii species complex, parasites of their dinoflagellate congeners. We used genetic and phenotypic characters, applied to 119 Amoebophrya individuals sampled from the same geographic area, to construct practical guidelines for species delineation that could be applied in DNA/RNA based diversity analyses. Based on the internal transcribed spacer (ITS) regions, ITS2 compensatory base changes (CBC) and genome k -mer comparisons, we unambiguously defined eight cryptic species among closely related ribotypes that differed by less than 97% sequence identity in their SSU rDNA. We then followed the genetic signatures of these parasitic species during a three-year survey of Alexandrium minutum blooms. We showed that these cryptic Amoebophrya species co-occurred and shared the same ecological niche. We also observed a maximal ecological fitness for parasites having narrow to intermediate host ranges, reflecting a high cost for infecting a broader host range. This study suggests that a complete taxonomic revision of these parasitic dinoflagellates is long overdue to understand their diversity and ecological role in the marine plankton.

Silicimonas algicola strain KC90BT is an alphaproteobacterium of the Roseobacter clade that was isolated from a culture of the marine diatom Thalassiosira delicatula. Here, we report the complete genome sequence of this type strain, which is 4,351,658 bp in size with 4,272 coding sequences and an average G+C content of 65.2%.

In marine environments, aerobic anoxygenic phototrophic (AAP) bacterial assemblages vary in space and along environmental gradients but the factors shaping their diversity and distribution at different taxonomic levels remain poorly identified. Using sets of sequences encoding the M sub-unit of the photosynthetic apparatus from different oceanic regions, we prioritized the processes underlying AAP bacterial biogeographical patterns. The present analysis offers novel insights into the ecological distribution of marine AAP bacteria and highlights that physiological constraints play a key role in structuring AAP bacterial assemblages at a global scale. Salinity especially seems to favor lineage-specific adaptations. Moreover, by inferring the evolutionary history of habitat transitions, a substantial congruence between habitat and evolutionary relatedness was highlighted. The identification of ecological cohesive clades for AAP bacteria suggests that prediction of AAP bacterial assemblages is possible from marine habitat properties.

Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. The cosmopolitan diatoms Thalassiosira and Chaetoceros often dominate phytoplankton communities in marine systems. Past studies of diatom-bacterial associations have employed community-level methods and culture-based or natural diatom populations. Although bacterial assemblages attached to individual diatoms represents tight associations little is known on their makeup or interactions. Here, we examined the epibiotic bacteria of 436 Thalassiosira and 329 Chaetoceros single cells isolated from natural samples and collection cultures, regarded here as short- and long-term associations, respectively. Epibiotic microbiota of single diatom hosts was analyzed by cultivation and by cloning-sequencing of 16S rRNA genes obtained from whole-genome amplification products. The prevalence of epibiotic bacteria was higher in cultures and dependent of the host species. Culture approaches demonstrated that both diatoms carry distinct bacterial communities in short- and long-term associations. Bacterial epibonts, commonly associated with phytoplankton, were repeatedly isolated from cells of diatom collection cultures but were not recovered from environmental cells. Our results suggest that in controlled laboratory culture conditions bacterial-diatom and bacterial-bacterial interactions select for a simplified, but specific, epibiotic microbiota shaped and adapted for long-term associations.

We report for the first time the in situ dynamics of a vampyrellid in a marine system. A high sampling frequency (twice-weekly) was applied in a tropical eutrophic lagoon (Rio de Janeiro, Brazil) for 5 years (2012–2016). The vampyrellid Hyalodiscus sp. specifically fed on the diatom Chaetoceros minimus during a short time window (~3 months), although the prey was intermittently detected as the dominant phytoplanktonic species over a longer period (~1 year). A classic Lotka–Volterra predator–prey dynamic was observed between the two partners, with a significant modification of the short-term oscillations of the prey. Specific abiotic preferences (i.e., relatively low temperature, intermediate salinity, and stratified conditions) associated with prey availability seemed to define this narrow temporal window of occurrence. Our results suggest that vampyrellids can be ecologically relevant in marine pelagic systems, with their impact on planktonic dynamics strongly depending on complex interactions between both biotic and abiotic factors.

Coastal areas form the major habitat of brown macroalgae, photosynthetic multicellular eukaryotes that have great ecological value and industrial potential. Macroalgal growth, development, and physiology are influenced by the microbial community they accommodate. Studying the algal microbiome should thus increase our fundamental understanding of algal biology and may help to improve culturing efforts. Currently, a freshwater strain of the brown macroalga Ectocarpus subulatus is being developed as a model organism for brown macroalgal physiology and algal microbiome studies. It can grow in high and low salinities depending on which microbes it hosts. However, the molecular mechanisms involved in this process are still unclear. Cultivation of Ectocarpus-associated bacteria is the first step toward the development of a model system for in vitro functional studies of brown macroalgal–bacterial interactions during abiotic stress. The main aim of the present study is thus to provide an extensive collection of cultivable E. subulatus-associated bacteria. To meet the variety of metabolic demands of Ectocarpus-associated bacteria, several isolation techniques were applied, i.e., direct plating and dilution-to-extinction cultivation techniques, each with chemically defined and undefined bacterial growth media. Algal tissue and algal growth media were directly used as inoculum, or they were pretreated with antibiotics, by filtration, or by digestion of algal cell walls. In total, 388 isolates were identified falling into 33 genera (46 distinct strains), of which Halomonas (Gammaproteobacteria), Bosea (Alphaproteobacteria), and Limnobacter (Betaproteobacteria) were the most abundant. Comparisons with 16S rRNA gene metabarcoding data showed that culturability in this study was remarkably high (∼50%), although several cultivable strains were not detected or only present in extremely low abundance in the libraries. These undetected bacteria could be considered as part of the rare biosphere and they may form the basis for the temporal changes in the Ectocarpus microbiome.

Mass blooms of purple sulfur bacteria growing seasonally on green stranded macroalgae have a major impact on the microbial composition and functionality of intertidal mats. To explore the active anoxygenic phototrophic community in purple bacterial mats from the Roscoff Aber Bay (Brittany, France), we conducted a combined approach including molecular and high-resolution secondary ion mass spectrometry (NanoSIMS) analyses. To investigate the dynamics of carbon and nitrogen assimilation activities, NanoSIMS was coupled with a stable isotope probing (SIP) experiment and a compound specific isotope analysis (CSIA) of fatty acid methyl ester (FAME). Sediment samples were incubated with 13C- and/or 15N-labeled acetate, pyruvate, bicarbonate and ammonium. NanoSIMS analysis of 13C - and 15N -incubated samples showed elevated incorporations of 13C - and 15N in the light and of 13C -acetate in the dark into dense populations of spherical cells that unambiguously dominated the mats. These results confirmed CSIA data that ranked vaccenic acid, an unambiguous marker of purple sulfur bacteria, as the most strongly enriched in the light after 13C -acetate amendment and indicated that acetate uptake, the most active in the mat, was not light-dependent. Analysis of DNA- and cDNA-derived pufM gene sequences revealed that Thiohalocapsa-related clones dominated both libraries and were the most photosynthetically active members of the mat samples. This study provides novel insights into the contribution of purple sulfur bacteria to the carbon cycle during their seasonal developments at the sediment surface in the intertidal zone.

Proteorhodopsins (PR) are phylogenetically diverse and highly expressed proton pumps in marine bacterial communities. The phylogenetic diversity and in situ expression of the main PR groups in polar off-shore, coastal and estuarine waters is poorly known and their abundance has not yet been reported. Here, we show that PR gene sequences of the southern Beaufort Sea including MacKenzie shelf and estuary are mainly affiliated to Gammaproteobacteria, Alphaproteobacteria and Bacteroidetes. Substantial overlap (78%) between DNA- and cDNA-based librairies indicated in situ PR transcription within a large fraction of PR-containing community. Sets of specific qPCR primers were designed to measure the absolute abundances of the major PR types. Spatial and depth profiles showed that PR-containing bacteria were abundant throughout the photic zone, comprising up to 45% of total bacteria. Although their abundance varied greatly with location and depth, Alphaproteobacteria predominated in the PR community in all water masses, with SAR11 as the major PR type. Low nutrient concentrations rather than light were the environmental drivers that best explained the abundance and distribution of arctic PR types. Together, our data suggests that PR-based phototrophy could be the major phototrophic prokaryotic process during the Arctic Ocean summer.

The contribution of bacteriochlorophyll a (BChl a) to photosynthetically driven electron transport is generally low in aquatic and terrestrial systems. Here, we provide evidence that anoxygenic bacterial phototrophy is widespread and substantial in water retained by tank bromeliads of a primary rainforest in French Guiana. An analysis of the water extracted from 104 randomly selected tank bromeliads using infrared fluorimetry suggested the overall presence of abundant anoxygenic phototrophic bacterial populations. We found that purple bacteria dominated these populations responsible for unusually high BChl a/chlorophyll a ratios (>50%). Our data suggest that BChl a-based phototrophy in tank bromeliads can have significant effects on the ecology of tank-bromeliad ecosystems and on the carbon and energy fluxes in Neotropical forests.

ABSTRACT Aerobic anoxygenic phototrophic bacteria (AAPB) are thought to be important players in oceanic carbon and energy cycling in the euphotic zone of the ocean. The genus Citromicrobium , widely found in oligotrophic oceans, is a member of marine alphaproteobacterial AAPB. Nine Citromicrobium strains isolated from the South China Sea, the Mediterranean Sea, or the tropical South Atlantic Ocean were found to harbor identical 16S rRNA sequences. The sequencing of their genomes revealed high synteny in major regions. Nine genetic islands (GIs) involved mainly in type IV secretion systems, flagellar biosynthesis, prophage, and integrative conjugative elements, were identified by a fine-scale comparative genomics analysis. These GIs played significant roles in genomic evolution and divergence. Interestingly, the coexistence of two different photosynthetic gene clusters (PGCs) was not only found in the analyzed genomes but also confirmed, for the first time, to our knowledge, in environmental samples. The prevalence of the coexistence of two different PGCs may suggest an adaptation mechanism for Citromicrobium members to survive in the oceans. Comparison of genomic characteristics (e.g., GIs, average nucleotide identity [ANI], single-nucleotide polymorphisms [SNPs], and phylogeny) revealed that strains within a marine region shared a similar evolutionary history that was distinct from that of strains isolated from other regions (South China Sea versus Mediterranean Sea). Geographic differences are partly responsible for driving the observed genomic divergences and allow microbes to evolve through local adaptation. Three Citromicrobium strains isolated from the Mediterranean Sea diverged millions of years ago from other strains and evolved into a novel group. IMPORTANCE Aerobic anoxygenic phototrophic bacteria are a widespread functional group in the upper ocean, and their abundance could be up to 15% of the total heterotrophic bacteria. To date, a great number of studies display AAPB biogeographic distribution patterns in the ocean; however, little is understood about the geographic isolation impact on the genome divergence of marine AAPB. In this study, we compare nine Citromicrobium genomes of strains that have identical 16S rRNA sequences but different ocean origins. Our results reveal that strains isolated from the same marine region share a similar evolutionary history that is distinct from that of strains isolated from other regions. These Citromicrobium strains diverged millions of years ago. In addition, the coexistence of two different PGCs is prevalent in the analyzed genomes and in environmental samples.

A Gram-negative, aerobic, non-motile bacterium, designated strain KC90BT, was isolated from the surface of a cell of the marine diatom Thalassiosira delicatula. The bacterial cells were pleomorphic and formed very small, beige colonies on marine agar. Optimal growth was obtained at 25 °C, at pH 6.5-7.5 and in the presence of 1.5-2.0 % (w/v) NaCl. Phylogenetic analyses based on its 16S rRNA gene sequence revealed that strain KC90BT belonged to the Roseobacter clade and formed a monophyletic cluster with the sequences of Boseongicola aestuarii, Profundibacterium mesophilum, Hwanghaeicola aestuarii, Maribius pelagius and M. salinus, showing 91.4-95.7 % sequence similarities. Ubiquinone Q-10 was the predominant lipoquinone but a significant amount of ubiquinone Q-9 was also detected. The major cellular fatty acids were C18 : 1ω7c, 11-methyl C18 : 1ω7c and C18 : 0. Strain KC90BT also contained specific fatty acids (C17 : 0, anteiso-C15 : 0 and anteiso-C17 : 0) that were not detected in its closest described relatives. The major polar lipids of strain KC90BT comprised phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol and an unidentified aminolipid. The DNA G+C content of strain KC90BT was 65.2 mol%. The phylogenetic analysis of strain KC90BT, together with the differential phenotypic and chemotaxonomic properties demonstrate that strain KC90BT is distinct from type strains of B. aestuarii, P. mesophilum, H. aestuarii, M. pelagius and M. salinus. Based on the data presented in this study, strain KC90BT represents a novel genus and species within the family Rhodobacteraceae, for which the name Silicimonas algicola gen. nov., sp. nov. is proposed. The type strain is KC90BT (=DSM 103371T=RCC 4681T).

The aim of this paper was to study the effects of temperature and irradiance on the photodegradation state of killed phytoplankton cells. For this purpose, killed cells of the diatom Chaetoceros neogracilis RCC2022 were irradiated (photosynthetically active radiation) at 36 and 446 J · s−1 · m−2 (for the same cumulative dose of irradiation energy) and at two temperatures (7°C and 17°C). Analyses of specific lipid tracers (fatty acids and sterols) revealed that low temperatures and irradiances increased photooxidative damages of monounsaturated lipids (i.e., palmitoleic acid, cholesterol and campesterol). The high efficiency of type II photosensitized degradation processes was attributed to: (i) the relative preservation of the sensitizer (chlorophyll) at low irradiances allowing a longer production of singlet oxygen and (ii) the slow diffusion rate of singlet oxygen through membranes at low temperatures inducing more damages. Conversely, high temperatures and irradiances induced (i) a rapid degradation of the photosensitizer and a loss of singlet oxygen by diffusion outside the membranes (limiting type II photosensitized oxidation), and (ii) intense autoxidation processes degrading unsaturated cell lipids and oxidation products used as photodegradation tracers. Our results may explain the paradoxical relationship observed in situ between latitude and photodegradation state of phytoplankton cells.