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Maire Y, Schmitt FG, Kormas K, Vasileiadis S, Caruana A, Skouroliakou DI, Bampouris V, Courcot L, Hervé F, Crouvoisier M, Christaki U. Effects of turbulence on diatoms of the genus Pseudo-nitzschia spp. and associated bacteria. FEMS Microbiol Ecol 2024; 100:fiae094. [PMID: 38986513 PMCID: PMC11264304 DOI: 10.1093/femsec/fiae094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Revised: 04/30/2024] [Accepted: 07/09/2024] [Indexed: 07/12/2024] Open
Abstract
Turbulence is one of the least investigated environmental factors impacting the ecophysiology of phytoplankton, both at the community and individual species level. Here, we investigated, for the first time, the effect of a turbulence gradient (Reynolds number, from Reλ = 0 to Reλ = 360) on two species of the marine diatom Pseudo-nitzschia and their associated bacterial communities under laboratory conditions. Cell abundance, domoic acid (DA) production, chain formation, and Chl a content of P. fraudulenta and P. multiseries were higher for intermediate turbulence (Reλ = 160 or 240). DA was detectable only in P. multiseries samples. These observations were supported by transcriptomic analyses results, which suggested the turbulence related induction of the expression of the DA production locus, with a linkage to an increased photosynthetic activity of the total metatranscriptome. This study also highlighted a higher richness of the bacterial community associated with the nontoxic strain of P. fraudulenta in comparison to the toxic strain of P. multiseries. Bacillus was an important genus in P. multiseries cultures (relative abundance 15.5%) and its highest abundances coincided with the highest DA levels. However, associated bacterial communities of both Pseudo-nitzschia species did not show clear patterns relative to turbulence intensity.
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Affiliation(s)
- Yanis Maire
- Université du Littoral Côte d'Opale, CNRS, Université de Lille, UMR 8187 LOG, 32 Ave. Foch, F-62930 Wimereux, France
| | - François G Schmitt
- Université du Littoral Côte d'Opale, CNRS, Université de Lille, UMR 8187 LOG, 32 Ave. Foch, F-62930 Wimereux, France
| | - Konstantinos Kormas
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, Fitoko st. 1, 38446 Volos, Greece
- Agricultural Development Institute, University Research and Innovation Centre “IASON”, Argonafton & Filellinon, 38221, Greece
| | - Sotirios Vasileiadis
- Agricultural Development Institute, University Research and Innovation Centre “IASON”, Argonafton & Filellinon, 38221, Greece
- Department of Biochemistry and Biotechnology, Viopolis 41500, University of Thessaly, Larissa, Greece
| | - Amandine Caruana
- IFREMER, PHYTOX, Laboratoire PHYSALG, BP21105, Rue de l'Ile d'Yeu, F-44300 Nantes, France
| | - Dimitra-Ioli Skouroliakou
- Université du Littoral Côte d'Opale, CNRS, Université de Lille, UMR 8187 LOG, 32 Ave. Foch, F-62930 Wimereux, France
| | - Vasileios Bampouris
- Université du Littoral Côte d'Opale, CNRS, Université de Lille, UMR 8187 LOG, 32 Ave. Foch, F-62930 Wimereux, France
- Department of Ichthyology and Aquatic Environment, School of Agricultural Sciences, Fitoko st. 1, 38446 Volos, Greece
| | - Lucie Courcot
- Université du Littoral Côte d'Opale, CNRS, Université de Lille, UMR 8187 LOG, 32 Ave. Foch, F-62930 Wimereux, France
| | - Fabienne Hervé
- IFREMER, PHYTOX, Laboratoire PHYSALG, BP21105, Rue de l'Ile d'Yeu, F-44300 Nantes, France
| | - Muriel Crouvoisier
- Université du Littoral Côte d'Opale, CNRS, Université de Lille, UMR 8187 LOG, 32 Ave. Foch, F-62930 Wimereux, France
| | - Urania Christaki
- Université du Littoral Côte d'Opale, CNRS, Université de Lille, UMR 8187 LOG, 32 Ave. Foch, F-62930 Wimereux, France
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2
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Stenow R, Robertson EK, Whitehouse MJ, Ploug H. Single cell dynamics and nitrogen transformations in the chain forming diatom Chaetoceros affinis. THE ISME JOURNAL 2023; 17:2070-2078. [PMID: 37723340 PMCID: PMC10579250 DOI: 10.1038/s41396-023-01511-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/20/2023]
Abstract
Colony formation in phytoplankton is often considered a disadvantage during nutrient limitation in aquatic systems. Using stable isotopic tracers combined with secondary ion mass spectrometry (SIMS), we unravel cell-specific activities of a chain-forming diatom and interactions with attached bacteria. The uptake of 13C-bicarbonate and15N-nitrate or 15N-ammonium was studied in Chaetoceros affinis during the stationary growth phase. Low cell-to-cell variance of 13C-bicarbonate and 15N-nitrate assimilation within diatom chains prevailed during the early stationary phase. Up to 5% of freshly assimilated 13C and 15N was detected in attached bacteria within 12 h and supported bacterial C- and N-growth rates up to 0.026 h-1. During the mid-stationary phase, diatom chain-length decreased and 13C and 15N-nitrate assimilation was significantly higher in solitary cells as compared to that in chain cells. During the late stationary phase, nitrate assimilation ceased and ammonium assimilation balanced C fixation. At this stage, we observed highly active cells neighboring inactive cells within the same chain. In N-limited regimes, bacterial remineralization of N and the short diffusion distance between neighbors in chains may support surviving cells. This combination of "microbial gardening" and nutrient transfer within diatom chains represents a strategy which challenges current paradigms of nutrient fluxes in plankton communities.
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Affiliation(s)
- Rickard Stenow
- Department of Marine Sciences, University of Gothenburg, Box 461, SE, 405 30, Gothenburg, Sweden.
| | - Elizabeth K Robertson
- Department of Marine Sciences, University of Gothenburg, Box 461, SE, 405 30, Gothenburg, Sweden
| | - Martin J Whitehouse
- Swedish Museum of Natural History, Box 50 007, SE, 104 05, Stockholm, Sweden
| | - Helle Ploug
- Department of Marine Sciences, University of Gothenburg, Box 461, SE, 405 30, Gothenburg, Sweden
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3
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Houliez E, Schmitt FG, Breton E, Skouroliakou DI, Christaki U. On the conditions promoting Pseudo-nitzschia spp. blooms in the eastern English Channel and southern North Sea. HARMFUL ALGAE 2023; 125:102424. [PMID: 37220977 DOI: 10.1016/j.hal.2023.102424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/18/2023] [Accepted: 03/13/2023] [Indexed: 05/25/2023]
Abstract
This study investigated the drivers of the blooms of Pseudo-nitzschia seriata and Pseudo-nitzschia delicatissima complexes in the eastern English Channel and southern North Sea. Phytoplankton data series acquired from 1992 to 2020 were analyzed with a multivariate statistical approach based on Hutchinson's niche concept. P. seriata and P. delicatissima complexes were found to be typically present year round, but they bloomed at different periods because they occupied different realized ecological niches. P. delicatissima complex occupied a more marginal niche and was less tolerant than P. seriata complex. P. delicatissima complex typically bloomed in April-May at the same time as Phaeocystis globosa while P. seriata complex blooms were more frequently observed in June during the decline of low intensity P. globosa blooms. P. delicatissima and P. seriata complexes were both favored by low-silicate environments and relatively low turbulence but they responded differently to water temperature, light, ammonium, phosphate and nitrite + nitrate conditions. Niche shifts and biotic interactions played important roles in the control of the blooms of P. delicatissima and P. seriata complexes. The two complexes occupied different sub-niches during their respective low abundance and bloom periods. The phytoplankton community structure and the number of other taxa presenting a niche overlapping the niches of P. delicatissima and P. seriata complexes also differed between these periods. P. globosa was the taxa contributing the most to the dissimilarity in community structure. P. globosa interacted positively with P. delicatissima complex and negatively with P. seriata complex.
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Affiliation(s)
- Emilie Houliez
- Univ. Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F-62930 Wimereux, France.
| | - François G Schmitt
- Univ. Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F-62930 Wimereux, France
| | - Elsa Breton
- Univ. Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F-62930 Wimereux, France
| | - Dimitra-Ioli Skouroliakou
- Univ. Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F-62930 Wimereux, France
| | - Urania Christaki
- Univ. Littoral Côte d'Opale, CNRS, Univ. Lille, UMR 8187, LOG, Laboratoire d'Océanologie et de Géosciences, F-62930 Wimereux, France
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4
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Le Moigne T, Sarti E, Nourisson A, Zaffagnini M, Carbone A, Lemaire SD, Henri J. Crystal structure of chloroplast fructose-1,6-bisphosphate aldolase from the green alga Chlamydomonas reinhardtii. J Struct Biol 2022; 214:107873. [DOI: 10.1016/j.jsb.2022.107873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 11/25/2022]
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Vicedomini R, Bouly JP, Laine E, Falciatore A, Carbone A. Multiple profile models extract features from protein sequence data and resolve functional diversity of very different protein families. Mol Biol Evol 2022; 39:6556147. [PMID: 35353898 PMCID: PMC9016551 DOI: 10.1093/molbev/msac070] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Functional classification of proteins from sequences alone has become a critical bottleneck in understanding the myriad of protein sequences that accumulate in our databases. The great diversity of homologous sequences hides, in many cases, a variety of functional activities that cannot be anticipated. Their identification appears critical for a fundamental understanding of the evolution of living organisms and for biotechnological applications. ProfileView is a sequence-based computational method, designed to functionally classify sets of homologous sequences. It relies on two main ideas: the use of multiple profile models whose construction explores evolutionary information in available databases, and a novel definition of a representation space in which to analyse sequences with multiple profile models combined together. ProfileView classifies protein families by enriching known functional groups with new sequences and discovering new groups and subgroups. We validate ProfileView on seven classes of widespread proteins involved in the interaction with nucleic acids, amino acids and small molecules, and in a large variety of functions and enzymatic reactions. Profile-View agrees with the large set of functional data collected for these proteins from the literature regarding the organisation into functional subgroups and residues that characterise the functions. In addition, ProfileView resolves undefined functional classifications and extracts the molecular determinants underlying protein functional diversity, showing its potential to select sequences towards accurate experimental design and discovery of novel biological functions. On protein families with complex domain architecture, ProfileView functional classification reconciles domain combinations, unlike phylogenetic reconstruction. ProfileView proves to outperform the functional classification approach PANTHER, the two k-mer based methods CUPP and eCAMI and a neural network approach based on Restricted Boltzmann Machines. It overcomes time complexity limitations of the latter.
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Affiliation(s)
- R Vicedomini
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 place Jussieu, 75005 Paris, France.,Sorbonne Université, Institut des Sciences du Calcul et des Données
| | - J P Bouly
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 place Jussieu, 75005 Paris, France.,CNRS, Sorbonne Université Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae - UMR7141, Paris, France
| | - E Laine
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 place Jussieu, 75005 Paris, France
| | - A Falciatore
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 place Jussieu, 75005 Paris, France.,CNRS, Sorbonne Université Institut de Biologie Physico-Chimique, Laboratory of Chloroplast Biology and Light Sensing in Microalgae - UMR7141, Paris, France
| | - A Carbone
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative - UMR 7238, 4 place Jussieu, 75005 Paris, France.,Institut Universitaire de France, Paris 75005, France
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6
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Vicedomini R, Blachon C, Oteri F, Carbone A. MyCLADE: a multi-source domain annotation server for sequence functional exploration. Nucleic Acids Res 2021; 49:W452-W458. [PMID: 34023906 PMCID: PMC8262732 DOI: 10.1093/nar/gkab395] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 04/27/2021] [Accepted: 04/29/2021] [Indexed: 11/13/2022] Open
Abstract
The ever-increasing number of genomic and metagenomic sequences accumulating in our databases requires accurate approaches to explore their content against specific domain targets. MyCLADE is a user-friendly webserver designed for targeted functional profiling of genomic and metagenomic sequences based on a database of a few million probabilistic models of Pfam domains. It uses the MetaCLADE multi-source domain annotation strategy, modelling domains based on multiple probabilistic profiles. MyCLADE takes a list of protein sequences and possibly a target set of domains/clans as input and, for each sequence, it provides a domain architecture built from the targeted domains or from all Pfam domains. It is linked to the Pfam and QuickGO databases in multiple ways for easy retrieval of domain and clan information. E-value, bit-score, domain-dependent probability scores and logos representing the match of the model with the sequence are provided to help the user to assess the quality of each annotation. Availability and implementation: MyCLADE is freely available at http://www.lcqb.upmc.fr/myclade.
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Affiliation(s)
- Riccardo Vicedomini
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris 75005, France
- Sorbonne Université, CNRS, Institut des Sciences du Calcul et des Données (ISCD), France
| | - Clémence Blachon
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris 75005, France
| | - Francesco Oteri
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris 75005, France
| | - Alessandra Carbone
- Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), UMR 7238, Paris 75005, France
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7
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Santin A, Caputi L, Longo A, Chiurazzi M, Ribera d'Alcalà M, Russo MT, Ferrante MI, Rogato A. Integrative omics identification, evolutionary and structural analysis of low affinity nitrate transporters in diatoms, diNPFs. Open Biol 2021; 11:200395. [PMID: 33823659 PMCID: PMC8025304 DOI: 10.1098/rsob.200395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Diatoms are one of the major and most diverse groups of phytoplankton, with chimeric genomes harbouring a combination of genes of bacterial, animal and plant origin. They have developed sophisticated mechanisms to face environmental variations. In marine environments, nutrients concentration shows significant temporal and spatial variability, influencing phytoplankton growth. Among nutrients, nitrogen, present at micromolar levels, is often a limiting resource. Here, we report a comprehensive characterization of the Nitrate Transporter 1/Peptide Transporter Family (NPF) in diatoms, diNPFs. NPFs are well characterized in many organisms where they recognize a broad range of substrates, ranging from short-chained di- and tri-peptides in bacteria, fungi and mammals to a wide variety of molecules including nitrate in higher plants. Scarce information is available for diNPFs. We integrated-omics, phylogenetic, structural and expression analyses, to infer information on their role in diatoms. diNPF genes diverged to produce two distinct clades with strong sequence and structural homology with either bacterial or plant NPFs, with different predicted sub-cellular localization, suggesting that the divergence resulted in functional diversification. Moreover, transcription analysis of diNPF genes under different laboratory and environmental growth conditions suggests that diNPF diversification led to genetic adaptations that might contribute to diatoms ability to flourish in diverse environmental conditions.
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Affiliation(s)
- Anna Santin
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Luigi Caputi
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy
| | - Antonella Longo
- BioDiscovery Institute, Denton, TX, USA.,Department of Biological Sciences, University of North Texas, Denton, TX, USA
| | - Maurizio Chiurazzi
- Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, 80131 Naples, Italy
| | | | | | | | - Alessandra Rogato
- Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.,Institute of Biosciences and BioResources, CNR, Via P. Castellino 111, 80131 Naples, Italy
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8
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Bistability in oxidative stress response determines the migration behavior of phytoplankton in turbulence. Proc Natl Acad Sci U S A 2021; 118:2005944118. [PMID: 33495340 PMCID: PMC7865155 DOI: 10.1073/pnas.2005944118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Turbulence has long been known to drive phytoplankton fitness and species succession: motile species dominate in calmer environments and non-motile species in turbulent conditions. Yet a mechanistic understanding of the effect of turbulence on phytoplankton migratory behavior and physiology is lacking. By combining a method to generate turbulent cues, quantification of stress accumulation and physiology, and a mathematical model of stress dynamics, we show that motile phytoplankton use their mechanical stability to sense the intensity of turbulent cues and integrate these cues in time via stress signaling to trigger switches in migratory behavior. The stress-mediated warning strategy we discovered provides a paradigm for how phytoplankton cope with turbulence, thereby potentially governing which species will be successful in a changing ocean. Turbulence is an important determinant of phytoplankton physiology, often leading to cell stress and damage. Turbulence affects phytoplankton migration both by transporting cells and by triggering switches in migratory behavior, whereby vertically migrating cells can actively invert their direction of migration upon exposure to turbulent cues. However, a mechanistic link between single-cell physiology and vertical migration of phytoplankton in turbulence is currently missing. Here, by combining physiological and behavioral experiments with a mathematical model of stress accumulation and dissipation, we show that the mechanism responsible for the switch in the direction of migration in the marine raphidophyte Heterosigma akashiwo is the integration of reactive oxygen species (ROS) signaling generated by turbulent cues. Within timescales as short as tens of seconds, the emergent downward-migrating subpopulation exhibited a twofold increase in ROS, an indicator of stress, 15% lower photosynthetic efficiency, and 35% lower growth rate over multiple generations compared to the upward-migrating subpopulation. The origin of the behavioral split as a result of a bistable oxidative stress response is corroborated by the observation that exposure of cells to exogenous stressors (H2O2, UV-A radiation, or high irradiance), in lieu of turbulence, caused comparable ROS accumulation and an equivalent split into the two subpopulations. By providing a mechanistic link between the single-cell mechanics of swimming and physiology on the one side and the emergent population-scale migratory response and impact on fitness on the other, the ROS-mediated early warning response we discovered contributes to our understanding of phytoplankton community composition in future ocean conditions.
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Arrieta J, Jeanneret R, Roig P, Tuval I. On the fate of sinking diatoms: the transport of active buoyancy-regulating cells in the ocean. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2020; 378:20190529. [PMID: 32762433 PMCID: PMC7422867 DOI: 10.1098/rsta.2019.0529] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 04/02/2020] [Indexed: 06/11/2023]
Abstract
Diatoms are one of the most abundant, diverse and ecologically relevant phytoplanktonic group, contributing enormously to global biogeochemical processes like the carbon and silica cycles. This large success has been partly attributed to the mechanical and optical properties of the silica shell (the frustule) that envelops their body. But since they lack motility it is difficult to conceive how they cope with the fast-fluctuating environment they live in and where distributions of resources are very heterogeneous and dynamical. This pinpoints an important but yet poorly understood feature of diatoms physiology: buoyancy regulation that helps them controlling their sinking speed and position in the water column. While buoyancy regulation by light and nutrients availability has been well studied, the effect of hydromechanical stress via fluid shear has been rather overlooked when considering diatoms dynamics. Here, we aim to start filling this gap by first presenting direct experimental evidences for buoyancy control in response to hydro-mechanical stress and then review recent theoretical models where simple couplings between local shear and buoyancy control always result in heterogeneous cell distributions, specific accumulation regions within complex flows and increased sedimentation times to the depths, features of direct ecological relevance. We conclude by suggesting future experiments aiming to unveil such coupling and therefore gain better understanding on the fate of these fascinating microorganisms in their natural habitat. This article is part of the theme issue 'Stokes at 200 (part 2)'.
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Affiliation(s)
- J. Arrieta
- Instituto Mediterráneo de Estudios Avanzados, IMEDEA, UIB-CSIC, 07190 Esporles, Spain
| | - R. Jeanneret
- Laboratoire de Physique de l’Ecole normale supérieure, ENS, Université PSL, CNRS, Sorbonne Université, Université de Paris, F-75005 Paris, France
| | - P. Roig
- Instituto Mediterráneo de Estudios Avanzados, IMEDEA, UIB-CSIC, 07190 Esporles, Spain
| | - I. Tuval
- Instituto Mediterráneo de Estudios Avanzados, IMEDEA, UIB-CSIC, 07190 Esporles, Spain
- Departamento de Física, Universitat de les Illes Balears, 07122 Palma de Mallorca, Spain
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10
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Dellero Y, Maës C, Morabito C, Schuler M, Bournaud C, Aiese Cigliano R, Maréchal E, Amato A, Rébeillé F. The zoospores of the thraustochytridAurantiochytrium limacinum: Transcriptional reprogramming and lipid metabolism associated to their specific functions. Environ Microbiol 2020; 22:1901-1916. [DOI: 10.1111/1462-2920.14978] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/04/2020] [Accepted: 03/05/2020] [Indexed: 12/26/2022]
Affiliation(s)
- Younès Dellero
- Laboratoire de Physiologie Cellulaire VégétaleUniversité Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV 38054 Grenoble Cedex 9 France
| | - Cécile Maës
- Laboratoire de Physiologie Cellulaire VégétaleUniversité Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV 38054 Grenoble Cedex 9 France
| | - Christian Morabito
- INRAE Metagenopolis Unit, Domaine de Vilvert Bât. 325. 78 352 Jouy‐en‐Josas France
| | - Martin Schuler
- Laboratoire de Physiologie Cellulaire VégétaleUniversité Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV 38054 Grenoble Cedex 9 France
| | - Caroline Bournaud
- Laboratoire de Physiologie Cellulaire VégétaleUniversité Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV 38054 Grenoble Cedex 9 France
| | - Riccardo Aiese Cigliano
- Sequentia Biotech Campus UAB, Edifici Eureka Av. de Can Domènech s/n 08193 Bellaterra (Cerdanyola del Vallès) Spain
| | - Eric Maréchal
- Laboratoire de Physiologie Cellulaire VégétaleUniversité Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV 38054 Grenoble Cedex 9 France
| | - Alberto Amato
- Laboratoire de Physiologie Cellulaire VégétaleUniversité Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV 38054 Grenoble Cedex 9 France
| | - Fabrice Rébeillé
- Laboratoire de Physiologie Cellulaire VégétaleUniversité Grenoble Alpes, CEA, CNRS, INRA, IRIG‐LPCV 38054 Grenoble Cedex 9 France
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11
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Zhao G, Gao X, Zhang C, Sang G. The effects of turbulence on phytoplankton and implications for energy transfer with an integrated water quality-ecosystem model in a shallow lake. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2020; 256:109954. [PMID: 31822459 DOI: 10.1016/j.jenvman.2019.109954] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 11/30/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
Turbulence has significant influences on the growth rate and community structure of phytoplankton in large shallow lakes. Phytoplankton in moving water may be influenced by turbulence and nutrient concentration gradients on a short time scale. To assess this issue, our research used an ensemble water quality and ecological model by internally coupling the three-dimensional hydrodynamic model, the Environmental Fluid Dynamics Code (EFDC), and the one-dimensional ecosystem model, PCLake. The results showed that turbulence dramatically inhibited phytoplankton growth, while nutrients had the opposite effect. In addition, turbulence was the key factor contributing to phytoplankton growth. However, the effects of turbulence on phytoplankton correlated with nutrient concentrations. For lower nutrient concentrations, phytoplankton growth was controlled by nutrients. Logistic regression models were established with the modeled chlorophyll a, total nitrogen (TN), total phosphorus (TP) and turbulent kinetic energy (Ke). The results also showed that turbulence could improve nutrient uptake by phytoplankton, especially at low nutrient levels. The effects of turbulence on phytoplankton may imply that energy transfer occurs between water turbulence and phytoplankton. Our study will provide insight into management and remediation strategies of ecosystems based on energy processes in the future.
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Affiliation(s)
- Guixia Zhao
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, 300072, China.
| | - Xueping Gao
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, 300072, China.
| | - Chen Zhang
- State Key Laboratory of Hydraulic Engineering Simulation and Safety, Tianjin University, Tianjin, 300072, China.
| | - Guoqing Sang
- School of Water Conservancy and Environment, University of Jinan, Jina, China
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12
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García-Portela M, Reguera B, Ribera d'Alcalà M, Rodríguez F, Montresor M. Effects of small-scale turbulence on two species of Dinophysis. HARMFUL ALGAE 2019; 89:101654. [PMID: 31672223 DOI: 10.1016/j.hal.2019.101654] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/21/2019] [Accepted: 07/31/2019] [Indexed: 06/10/2023]
Abstract
Dinoflagellate species of Dinophysis, in particular D. acuminata and D. acuta, produce lipophilic toxins that pose a threat to human health when concentrated in shellfish and jeopardize shellfish exploitations in western Europe. In northwestern Iberia, D. acuminata has a long growing season, from spring to early autumn, and populations develop as soon as shallow stratification forms when the upwelling season begins. In contrast, D. acuta blooms in late summer, when the depth of the pycnocline is maximal and upwelling pulses are moderate. In situ observations on the hydrodynamic regimes during the two windows of opportunity for Dinophysis species led us to hypothesize that D. acuta should be more sensitive to turbulence than D. acuminata. To test this hypothesis, we studied the response of D. acuminata and D. acuta to three realistic turbulence levels low (LT), ε ≈ 10-6 m2 s-3; medium (MT), ε ≈ 10-5 m2 s-3 and high (HT), ε ≈ 10-4 m2 s-3generated by Turbogen, a highly reproducible, computer-controlled system. Cells of both species exposed to LT and MT grew at rates similar to the controls. Marked differences were found in the response to HT: D. acuminata grew slowly after an initial lag phase, whereas D. acuta cell numbers declined. Results from this study support the hypothesis that turbulence may play a role in shaping the spatio-temporal distribution of individual species of Dinophysis. We also hypothesize that, in addition to cell disturbance affecting division, sustained high shear generated by microturbulence may cause a decline in Dinophysis numbers due to decreased densities of ciliate prey.
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Affiliation(s)
- María García-Portela
- Harmful Microalgae Group (VGOHAB), Centro Oceanográfico de Vigo, IEO, Vigo, Spain.
| | - Beatriz Reguera
- Harmful Microalgae Group (VGOHAB), Centro Oceanográfico de Vigo, IEO, Vigo, Spain.
| | | | - Francisco Rodríguez
- Harmful Microalgae Group (VGOHAB), Centro Oceanográfico de Vigo, IEO, Vigo, Spain.
| | - Marina Montresor
- Department of Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Naples, Italy.
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13
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Borgnino M, Arrieta J, Boffetta G, De Lillo F, Tuval I. Turbulence induces clustering and segregation of non-motile, buoyancy-regulating phytoplankton. J R Soc Interface 2019; 16:20190324. [PMID: 31640498 PMCID: PMC6833313 DOI: 10.1098/rsif.2019.0324] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/01/2019] [Indexed: 11/12/2022] Open
Abstract
Turbulence plays a major role in shaping marine community structure as it affects organism dispersal and guides fundamental ecological interactions. Below oceanographic mesoscale dynamics, turbulence also impinges on subtle physical-biological coupling at the single cell level, setting a sea of chemical gradients and determining microbial interactions with profound effects on scales much larger than the organisms themselves. It has been only recently that we have started to disentangle details of this coupling for swimming microorganisms. However, for non-motile species, which comprise some of the most abundant phytoplankton groups on Earth, a similar level of mechanistic understanding is still missing. Here, we explore by means of extensive numerical simulations the interplay between buoyancy regulation in non-motile phytoplankton and cellular responses to turbulent mechanical cues. Using a minimal mechano-response model, we show how such a mechanism would contribute to spatial heterogeneity and affect vertical fluxes and trigger community segregation.
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Affiliation(s)
- Matteo Borgnino
- Department of Physics and INFN, Università di Torino, via P. Giuria 1, Torino 10125, Italy
| | - Jorge Arrieta
- Instituto Mediterráneo de Estudios Avanzados, IMEDEA, UIB-CSIC, Esporles 07190, Spain
| | - Guido Boffetta
- Department of Physics and INFN, Università di Torino, via P. Giuria 1, Torino 10125, Italy
| | - Filippo De Lillo
- Department of Physics and INFN, Università di Torino, via P. Giuria 1, Torino 10125, Italy
| | - Idan Tuval
- Instituto Mediterráneo de Estudios Avanzados, IMEDEA, UIB-CSIC, Esporles 07190, Spain
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14
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Wheeler JD, Secchi E, Rusconi R, Stocker R. Not Just Going with the Flow: The Effects of Fluid Flow on Bacteria and Plankton. Annu Rev Cell Dev Biol 2019; 35:213-237. [PMID: 31412210 DOI: 10.1146/annurev-cellbio-100818-125119] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Microorganisms often live in habitats characterized by fluid flow, from lakes and oceans to soil and the human body. Bacteria and plankton experience a broad range of flows, from the chaotic motion characteristic of turbulence to smooth flows at boundaries and in confined environments. Flow creates forces and torques that affect the movement, behavior, and spatial distribution of microorganisms and shapes the chemical landscape on which they rely for nutrient acquisition and communication. Methodological advances and closer interactions between physicists and biologists have begun to reveal the importance of flow-microorganism interactions and the adaptations of microorganisms to flow. Here we review selected examples of such interactions from bacteria, phytoplankton, larvae, and zooplankton. We hope that this article will serve as a blueprint for a more in-depth consideration of the effects of flow in the biology of microorganisms and that this discussion will stimulate further multidisciplinary effort in understanding this important component of microorganism habitats.
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Affiliation(s)
- Jeanette D Wheeler
- Institute of Environmental Engineering, Department of Civil, Environmental, and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland;
| | - Eleonora Secchi
- Institute of Environmental Engineering, Department of Civil, Environmental, and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland;
| | - Roberto Rusconi
- Department of Biomedical Sciences, Humanitas University, 20090 Pieve Emanuele (MI), Italy.,Humanitas Clinical and Research Center-IRCCS, 20089 Rozzano (MI), Italy
| | - Roman Stocker
- Institute of Environmental Engineering, Department of Civil, Environmental, and Geomatic Engineering, ETH Zürich, 8093 Zürich, Switzerland;
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15
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Athanasakoglou A, Kampranis SC. Diatom isoprenoids: Advances and biotechnological potential. Biotechnol Adv 2019; 37:107417. [PMID: 31326522 DOI: 10.1016/j.biotechadv.2019.107417] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 06/09/2019] [Accepted: 07/15/2019] [Indexed: 12/31/2022]
Abstract
Diatoms are among the most productive and ecologically important groups of microalgae in contemporary oceans. Due to their distinctive metabolic and physiological features, they offer exciting opportunities for a broad range of commercial and industrial applications. One such feature is their ability to synthesize a wide diversity of isoprenoid compounds. However, limited understanding of how these molecules are synthesized have until recently hindered their exploitation. Following comprehensive genomic and transcriptomic analysis of various diatom species, the biosynthetic mechanisms and regulation of the different branches of the pathway are now beginning to be elucidated. In this review, we provide a summary of the recent advances in understanding diatom isoprenoid synthesis and discuss the exploitation potential of diatoms as chassis for high-value isoprenoid synthesis.
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Affiliation(s)
- Anastasia Athanasakoglou
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark
| | - Sotirios C Kampranis
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, 1871 Frederiksberg C, Denmark.
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16
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Orefice I, Musella M, Smerilli A, Sansone C, Chandrasekaran R, Corato F, Brunet C. Role of nutrient concentrations and water movement on diatom's productivity in culture. Sci Rep 2019; 9:1479. [PMID: 30728371 PMCID: PMC6365584 DOI: 10.1038/s41598-018-37611-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 12/10/2018] [Indexed: 02/06/2023] Open
Abstract
Microalgal growth maximization is becoming a duty for enhancing the biotechnological fate of these photosynthetic microorganisms. This study, based on an extensive set of data, aims to revisit diatom’s cultivation in laboratory with the objective to increase growth rate and biomass production. We investigated the growth ability and resource requirements of the coastal diatom Skeletonema marinoi Sarno & Zingone grown in laboratory in the conventional f/2 medium with aeration and in two modified conditions: (i) the same medium with water movement inside and (ii) an enriched medium with the same water movement. Results revealed that, by doubling the concentration of phosphate, silicate, microelements and vitamins, growth rate was successfully enhanced, preventing phosphate or silicate limitation in the f/2 culture medium. Yet, irrespective of the media (f/2 or enriched one), water movement induced an increase of growth efficiency compared to aeration, affecting nutrients’ requirement and consumption by diatoms. This study is an important step for enhancing diatom biomass production, reducing its cost, as required in the blue biotechnology context.
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Affiliation(s)
- Ida Orefice
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa comunale, 80121, Napoli, Italy
| | - Margherita Musella
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa comunale, 80121, Napoli, Italy
| | - Arianna Smerilli
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa comunale, 80121, Napoli, Italy
| | - Clementina Sansone
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa comunale, 80121, Napoli, Italy
| | - Raghu Chandrasekaran
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa comunale, 80121, Napoli, Italy.,CAS in Marine Biology, Faculty of Marine Sciences, Annamalai University, Parangipettai, 608502, Tamil Nadu, India
| | - Federico Corato
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa comunale, 80121, Napoli, Italy
| | - Christophe Brunet
- Stazione Zoologica Anton Dohrn, Istituto Nazionale di Biologia, Ecologia e Biotecnologie Marine, Villa comunale, 80121, Napoli, Italy.
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17
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Dell'Aquila G, Ferrante MI, Gherardi M, Cosentino Lagomarsino M, Ribera d'Alcalà M, Iudicone D, Amato A. Nutrient consumption and chain tuning in diatoms exposed to storm-like turbulence. Sci Rep 2017; 7:1828. [PMID: 28500335 PMCID: PMC5431809 DOI: 10.1038/s41598-017-02084-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 04/07/2017] [Indexed: 11/09/2022] Open
Abstract
Current information on the response of phytoplankton to turbulence is linked to cell size and nutrient availability. Diatoms are considered to be favored by mixing as dissolved nutrients are more easily accessible for non-motile cells. We investigated how diatoms exploit microscale turbulence under nutrient repletion and depletion conditions. Here, we show that the chain-forming diatom Chaetoceros decipiens, continues to take up phosphorus and carbon even when silicon is depleted during turbulence. Our findings indicate that upon silica depletion, during turbulence, chain spectra of C. decipiens remained unchanged. We show here that longer chains are maintained during turbulence upon silica depletion whereas under still conditions, shorter chains are enriched. We interpret this as a sign of good physiological state leading to a delay of culture senescence. Our results show that C. decipiens senses and responds to turbulence both in nutrient repletion and depletion. This response is noteworthy due to the small size of the species. The coupling between turbulence and biological response that we depict here may have significant ecological implications. Considering the predicted increase of storms in Northern latitudes this response might modify community structure and succession. Our results partly corroborate Margalef's mandala and provide additional explanations for that conceptualization.
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Affiliation(s)
- Gianluca Dell'Aquila
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale, 80121, Naples, Italy.,Zellbiologie Philipps-Universität Marburg, Karl-von-Frisch Str., 8 35043, Marburg, Germany
| | - Maria I Ferrante
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale, 80121, Naples, Italy
| | - Marco Gherardi
- Dipartimento di Fisica, Università di Milano, Via Celoria 16, 20133, Milan, Italy.,UMR 7238 CNRS Computational and Quantitative Biology, University Pierre et Marie Curie, 15, rue de l'Ecole de Médecine, 75006, Paris, France
| | - Marco Cosentino Lagomarsino
- UMR 7238 CNRS Computational and Quantitative Biology, University Pierre et Marie Curie, 15, rue de l'Ecole de Médecine, 75006, Paris, France
| | - Maurizio Ribera d'Alcalà
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale, 80121, Naples, Italy
| | - Daniele Iudicone
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale, 80121, Naples, Italy.
| | - Alberto Amato
- Stazione Zoologica Anton Dohrn, Department of Integrative Marine Ecology, Villa Comunale, 80121, Naples, Italy. .,Laboratoire de Physiologie Cellulaire et Végétale, UMR5168 CNRS-CEA-INRA-Université de Grenoble Alpes, Institut de Recherche en Science et Technologies pour le Vivant, CEA Grenoble, 17 rue des Martyrs, 38054, Grenoble Cédex 9, France.
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