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Daiske Honda - One of the best experts on this subject based on the ideXlab platform.
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Nutritional Intake by Ectoplasmic Nets of Schizochytrium aggregatum (Labyrinthulomycetes, Stramenopiles).
Protist, 2018Co-Authors: Izumi Iwata, Daiske HondaAbstract:Thraustochytrid cells attach to their food via ectoplasmic nets (ENs). Here, we analyzed the cause and effect relationship between the various forms and functions of ENs of Schizochytrium aggregatum. The ENs spread out over a large area forming a fine network to efficiently search for the experimental food source. After recognizing the experimental food source, the ENs that attached to the food source became thicker, and net elements developed. The thick ENs on the surface at the attachment site were enveloped in dense materials (fibrous materials), which were visualized as fibrous layers under a transmission electron microscope. Experiments using fluorescein diacetate and the fluorescent glucose analog 2-NBDG showed that the production rate of hydrolytic enzymes and the absorption rate of glucose by ENs of S. aggregatum increased in the presence of an experimental food source. Our results reveal that ENs change their shape and function according to the presence/absence of a food source.
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Proposal of Monorhizochytrium globosum gen. nov., comb. nov. (Stramenopiles, Labyrinthulomycetes) for former Thraustochytrium globosum based on morphological features and phylogenetic relationships
Phycological Research, 2017Co-Authors: Kosaku Doi, Daiske HondaAbstract:SUMMARY Thraustochytrium is the type genus of the family Thraustochytriaceae in the class Labyrinthulomycetes. This genus is characterized by zoospore formation, namely, shape of the cell wall of sporangia and presence or absence of a proliferous body. However, there are several issues associated with the taxonomy of this genus, and these include polyphyletic taxa and overlapping of taxonomic features among species. In particular, the first and second species, T. proliferum and T. globosum, were described based on observations of the morphological features of natural samples in the absence of culture conditions. Before addressing the taxonomic issues associated with this genus, it is important to consider the taxonomic features of each species, i.e., the life history under culture conditions and the phylogenetic position. The objective of the present study was to isolate T. globosum, the second described species in the genus Thraustochytrium, from the type locality. We successfully isolated strain NBRC 112723, which exhibited characteristic features of T. globosum. Under culture conditions, strain NBRC 112723 exhibited taxonomic features observed in other thraustochytrid species. Our molecular phylogeny indicated that this strain isolated from the type locality was located in an unidentified thraustochytrid group; moreover, some strains located in this group exhibited characteristic features of strain NBRC 112723. We clearly distinguished T. globosum based on the taxonomic criteria used to classify the T. proliferum type species. Therefore, we propose the establishment of a new genus, Monorhizochytrium, for the species T. globosum in the family Thraustochytriaceae.
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Bothrosome Formation in Schizochytrium aggregatum (Labyrinthulomycetes, Stramenopiles) during Zoospore Settlement
Protist, 2017Co-Authors: Izumi Iwata, Kei Kimura, Yuji Tomaru, Taizo Motomura, Kanae Koike, Kazuhiko Koike, Daiske HondaAbstract:Labyrinthulomycetes are characterized by the presence of ectoplasmic nets originating from an organelle known as the bothrosome, whose evolutionary origin is unclear. To address this issue, we investigated the developmental process from a zoospore to a vegetative cell in Schizochytrium aggregatum. After disappearance of the flagellum during zoospore settlement, the bothrosome emerged at the anterior-ventral pole of the cells. A new Golgi body also appeared at this stage, and the bothrosome was positioned close to both the new and the old Golgi bodies. This observation suggested that the Golgi body is related to the formation of the bothrosome. Actin appeared as a spot in the same location as the newly appeared bothrosome, as determined by immunofluorescence labeling. An immunoelectron microscopic analysis revealed that actin was present in the ectoplasmic nets and in the cytoplasm around the bothrosome, indicating that the electron-dense materials of the bothrosome are not the polar center of F-actin. This suggests that actin filaments pull the endoplasmic reticulum to the bothrosome and induce the membrane to become evaginated within ectoplasmic nets.
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Ecological Dynamics of Two Distinct Viruses Infecting Marine Eukaryotic Decomposer Thraustochytrids (Labyrinthulomycetes, Stramenopiles).
PLOS ONE, 2015Co-Authors: Yoshitake Takao, Yuji Tomaru, Keizo Nagasaki, Daiske HondaAbstract:Thraustochytrids are cosmopolitan osmotrophic or heterotrophic microorganisms that are considered as important decomposers in coastal ecosystems. However, because of a lack of estimation method for each genus or systematic group of them, relatively little is known about their ecology in situ. Previously, we reported two distinct types of virus infecting thraustochytrids (AuRNAV: reported as SssRNAV, and SmDNAV) suggesting they have wide distributions in the host-virus systems of coastal environments. Here we conducted a field survey from 2004 through 2005 to show the fluctuation pattern of thraustochytrids and their viruses in Hiroshima Bay, Japan. During the field survey, we monitored the dynamics of the two types of thraustochytrid-infecting virus: small viruses causing lysis of Aurantiochytrium sp. NIBH N1-27 (identified as AuRNAV) and the large viruses of Sicyoidochytrium minutum NBRC 102975 (similar to SmDNAV in physiology and morphology). Fluctuation patterns of the two distinct types of virus were different from each other. This may reflect the difference in the preference of organic substrates; i.e., it may be likely the host of AuRNAV (Aurantiochytrium sp.) increases utilizing algal dead bodies or feeble cells as the virus shows a large increase in abundance following raphidophyte blooms; whereas, the trophic nutrient supply for S. minutum may primarily depend on other constantly-supplied organic compounds because it did not show any significant change in abundance throughout the survey. Further study concerning the population composition of thraustochytrids and their viruses may demonstrate the microbial ecology (especially concerning the detrital food web) of marine environments.
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Labyrinthulomycetes phylogeny and its implications for the evolutionary loss of chloroplasts and gain of ectoplasmic gliding
Molecular Phylogenetics and Evolution, 2009Co-Authors: Clement K. M. Tsui, Rinka Yokoyama, Daiske Honda, Wyth L Marshall, Casey J Lippmeier, Kelly D Craven, Paul D Peterson, Mary L BerbeeAbstract:Abstract The Labyrinthulomycetes, also known as the ‘Labyrinthulomycota’ are saprotrophic or less frequently parasitic stramenopilan protists, usually in marine ecosystems. Their distinguishing feature is an ‘ectoplasmic net,’ an external cytoplasmic network secreted by a specialized organelle that attaches the cell to its substrate and secretes digestive enzymes for absorptive nutrition. In this study, one of our aims was to infer the phylogenetic position of the Labyrinthulomycetes relative to the non-photosynthetic bicoeceans and oomycetes and the photosynthetic ochrophytes and thereby evaluate patterns of change from photosynthesis to saprotrophism among the stramenopiles. For the Labyrinthulomycetes, we determined sequences of the actin, beta-tubulin, and elongation factor 1-alpha gene fragments and where necessary, ribosomal small subunit (SSU) genes. Multilocus analysis using standard tree construction techniques not only strongly supported the oomycetes as the sister group to the phototrophic stramenopiles, but also, for the first time with moderate statistical support, showed that the Labyrinthulomycetes and the bicoecean as sister groups. The paraphyly of the non-photosynthetic groups was consistent with independent loss of photosynthesis in Labyrinthulomycetes and oomycetes. We also wished to develop a phylogenetically based hypothesis for the origin of the gliding cell bodies and the ectoplasmic net found in some Labyrinthulomycetes. The cells of species in Labyrinthula and Aplanochytrium share a specialized form of motility involving gliding on ectoplasmic tracks. Before our study, only ribosomal DNA genes had been determined for these genera and their phylogenetic position in the Labyrinthulomycetes was equivocal. Multilocus phylogenies applying our newly determined protein-coding sequences divided the Labyrinthulomycetes between sister clades ‘A’ and ‘B’ and showed that the monophyletic group containing all of the gliding species was nested among non-gliding species in clade B. This phylogeny suggested that species that glide via an ectoplasm evolved from species that had used the ectoplasm mainly for anchorage and assimilation rather than motility.
Mary L Berbee - One of the best experts on this subject based on the ideXlab platform.
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Labyrinthulomycetes phylogeny and its implications for the evolutionary loss of chloroplasts and gain of ectoplasmic gliding
Molecular Phylogenetics and Evolution, 2009Co-Authors: Clement K. M. Tsui, Rinka Yokoyama, Daiske Honda, Wyth L Marshall, Casey J Lippmeier, Kelly D Craven, Paul D Peterson, Mary L BerbeeAbstract:Abstract The Labyrinthulomycetes, also known as the ‘Labyrinthulomycota’ are saprotrophic or less frequently parasitic stramenopilan protists, usually in marine ecosystems. Their distinguishing feature is an ‘ectoplasmic net,’ an external cytoplasmic network secreted by a specialized organelle that attaches the cell to its substrate and secretes digestive enzymes for absorptive nutrition. In this study, one of our aims was to infer the phylogenetic position of the Labyrinthulomycetes relative to the non-photosynthetic bicoeceans and oomycetes and the photosynthetic ochrophytes and thereby evaluate patterns of change from photosynthesis to saprotrophism among the stramenopiles. For the Labyrinthulomycetes, we determined sequences of the actin, beta-tubulin, and elongation factor 1-alpha gene fragments and where necessary, ribosomal small subunit (SSU) genes. Multilocus analysis using standard tree construction techniques not only strongly supported the oomycetes as the sister group to the phototrophic stramenopiles, but also, for the first time with moderate statistical support, showed that the Labyrinthulomycetes and the bicoecean as sister groups. The paraphyly of the non-photosynthetic groups was consistent with independent loss of photosynthesis in Labyrinthulomycetes and oomycetes. We also wished to develop a phylogenetically based hypothesis for the origin of the gliding cell bodies and the ectoplasmic net found in some Labyrinthulomycetes. The cells of species in Labyrinthula and Aplanochytrium share a specialized form of motility involving gliding on ectoplasmic tracks. Before our study, only ribosomal DNA genes had been determined for these genera and their phylogenetic position in the Labyrinthulomycetes was equivocal. Multilocus phylogenies applying our newly determined protein-coding sequences divided the Labyrinthulomycetes between sister clades ‘A’ and ‘B’ and showed that the monophyletic group containing all of the gliding species was nested among non-gliding species in clade B. This phylogeny suggested that species that glide via an ectoplasm evolved from species that had used the ectoplasm mainly for anchorage and assimilation rather than motility.
Seshagiri Raghukumar - One of the best experts on this subject based on the ideXlab platform.
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Animals in Coastal Benthic Ecosystem and Aquaculture Systems
Fungi in Coastal and Oceanic Marine Ecosystems, 2017Co-Authors: Seshagiri RaghukumarAbstract:Fungi occur as symbionts and saprotrophs in marine animals. Thraustochytrids, yeasts, and trichomycetes grow as commensals in invertebrate guts. Many fungi are found in sponges. Oomycetes are the most prevalent among a variety of fungal parasites in marine animals. They attack eggs and larvae and often cause serious commercial losses in aquaculture facilities. Lagenidium species, Haliphthoros milfordensis, Salilagenidium myophilum, Sirolpidium zoophthorum, Atkinsiella dubia, and Halocrusticida spp. are well-known pathogens. “Black gill” and other diseases of prawns as well as diseases of crabs, lobsters, and molluscs are common. Several yeasts as well as Fusarium sp., a terrestrial mycetaen species, are frequent parasites. The Labyrinthulomycetes Aplanochytrium haliotidis and the QPX parasite are devastating parasites of molluscs. Few effective strategies are available to combat fungal diseases in aquaculture industries. Saprobic fungi are frequent in exoskeletons and calcareous shells of marine invertebrates. Endolithic fungi cause bioerosion of calcareous shells.
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Fungi: Characteristics and Classification
Fungi in Coastal and Oceanic Marine Ecosystems, 2017Co-Authors: Seshagiri RaghukumarAbstract:Fungi are osmoheterotrophic eukaryotes that play a key role in sustaining life on earth. Fungi are found in the Kingdom Mycetae (also called Kingdom Fungi) and the Kingdom Straminipila. Their vegetative structure may be filamentous or unicellular. Fungal cell walls are made of chitin, chitosan or polysaccharides. They reproduce by spores produced asexually or sexually. Spores of marine fungi are adapted to aquatic conditions. The Kingdom Mycetae consists of the phyla Chytridiomycota, Neocallimastigomycota, Blastocladiomycota, Kickxellomycota, Entomophthoromycota, Mucoromycota, Glomeromycota, Ascomycota, and Basidiomycota, all of which are osmoheterotrophic and thus are fungi. Fungi in the Kingdom Straminipila are found only in the Classes Hyphochytriomycetes, Oomycetes, and Labyrinthulomycetes, the others being photosynthetic or phagotrophic.
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The Seagrass Ecosystem
Fungi in Coastal and Oceanic Marine Ecosystems, 2017Co-Authors: Seshagiri RaghukumarAbstract:Sublittoral seagrass vegetations are important primary producers in coastal waters. Several facultatively marine fungi as well as Labyrinthulomycetes might live as endophytes within living seagrass. Some fungi, termed as DSEs, form intimate associations within rhizomes of the seagrass Posidonia oceanica. Fungi may also form rhizosphere associations with seagrasses. The straminipilan fungus Labyrinthula zosterae is a pathogen of the seagrass Zostera marina and caused massive devastations in many parts of the world. Endophytic fungi that were present in living plants as well as obligate and facultative marine fungi from the environment colonize and decompose dead seagrass tissues and contribute to the living organic matter of the detritus. Thraustochytrids are common in seagrass sediments. The role of fungi in decomposition of seagrass detritus and their role in detrital dynamics are poorly known.
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Methods to Study Marine Fungi
Fungi in Coastal and Oceanic Marine Ecosystems, 2017Co-Authors: Seshagiri RaghukumarAbstract:Appropriate methods are necessary to study diversity, ecology, and physiology of marine fungi. Obligate marine fungi are cultured directly from their sporulating structures in decomposing wood and other substrates. Surface sterilization and plating as well as particle plating are useful methods to culture obligate and facultative marine fungi. Zoosporic fungi can be cultured using baiting methods. Fungi are generally identified based on their morphology, development, and life cycles. Molecular methods are helpful in authenticating identifications as well as in metagenomic studies of diversity. Mycelial fungi and Labyrinthulomycetes can be detected in natural substrates and their biomass estimated using epifluorescence microscopy methods. Biochemical indicators such as ergosterol are useful for mycetaen fungi. Culturing of deep-sea fungi requires special methods and equipments. A variety of culture media is used to cultivate marine fungi.
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The Mangrove Ecosystem
Fungi in Coastal and Oceanic Marine Ecosystems, 2017Co-Authors: Seshagiri RaghukumarAbstract:Mangroves are tropical and subtropical coastal vegetations and contribute an enormous amount of organic matter to the surrounding waters. Fungi densely colonize lignocellulosic mangrove detritus. Manglicolous fungi, of which about 200 species are known, are lignicolous fungi exclusive to decaying mangrove wood. Most of these belong to Ascomycota. A succession of species colonizes dead mangrove wood. Their diversity is regulated by the wood species, geographical location, salinity, and position in the intertidal region. Most mangrove lignicolous fungi produce a variety of lignocellulase enzymes and cause wood degradation. Mangrove leaves that fall into waters are immediately colonized by the oomycete belonging to species of Halophytophthora, as well as a number of thraustochytrids. This is followed by a mycosere. Decaying mangrove leaves undergo the typical leaching phase, a fungal degradation and biomass buildup phase, and a final fragmentation phase. Fungi alter the biochemical properties of mangrove leaf detritus, lower the C/N ratio, and make them more palatable to detritivores. Chytrids and Labyrinthulomycetes are found in mangrove waters and sediments. Mycetaen fungi may occur in the anoxic mangrove sediments. Fungi are an important component of outwelled mangrove detritus.
Yoshitake Takao - One of the best experts on this subject based on the ideXlab platform.
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Ecological Dynamics of Two Distinct Viruses Infecting Marine Eukaryotic Decomposer Thraustochytrids (Labyrinthulomycetes, Stramenopiles).
PLOS ONE, 2015Co-Authors: Yoshitake Takao, Yuji Tomaru, Keizo Nagasaki, Daiske HondaAbstract:Thraustochytrids are cosmopolitan osmotrophic or heterotrophic microorganisms that are considered as important decomposers in coastal ecosystems. However, because of a lack of estimation method for each genus or systematic group of them, relatively little is known about their ecology in situ. Previously, we reported two distinct types of virus infecting thraustochytrids (AuRNAV: reported as SssRNAV, and SmDNAV) suggesting they have wide distributions in the host-virus systems of coastal environments. Here we conducted a field survey from 2004 through 2005 to show the fluctuation pattern of thraustochytrids and their viruses in Hiroshima Bay, Japan. During the field survey, we monitored the dynamics of the two types of thraustochytrid-infecting virus: small viruses causing lysis of Aurantiochytrium sp. NIBH N1-27 (identified as AuRNAV) and the large viruses of Sicyoidochytrium minutum NBRC 102975 (similar to SmDNAV in physiology and morphology). Fluctuation patterns of the two distinct types of virus were different from each other. This may reflect the difference in the preference of organic substrates; i.e., it may be likely the host of AuRNAV (Aurantiochytrium sp.) increases utilizing algal dead bodies or feeble cells as the virus shows a large increase in abundance following raphidophyte blooms; whereas, the trophic nutrient supply for S. minutum may primarily depend on other constantly-supplied organic compounds because it did not show any significant change in abundance throughout the survey. Further study concerning the population composition of thraustochytrids and their viruses may demonstrate the microbial ecology (especially concerning the detrital food web) of marine environments.
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Squashed ball-like dsDNA virus infecting a marine fungoid protist Sicyoidochytrium minutum (Thraustochytriaceae, Labyrinthulomycetes)
Aquatic Microbial Ecology, 2007Co-Authors: Yoshitake Takao, Keizo Nagasaki, Daiske HondaAbstract:Thraustochytrids are cosmopolitan osmoterotrophic microorganisms that play imtrophic or heterotrophic microorganisms that play important roles as decomposers, producers of polyunsaturated fatty acids, and pathogens of mollusks, especially in coastal ecosystems. Sicyoidochytrium minutum DNA virus (SmDNAV), a novel double-stranded DNA (dsDNA) virus infecting a marine eukaryotic decomposer, S. minutum (formerly Ulkenia minuta), was isolated from the estuary of the Shukugawa River, Hyogo Prefecture, Japan in July 2003, and its basic characteristics were examined. The morphology of the virus particles is 'squashed ball-like' (ca. 146 and 112 nm in length and width, respectively) and lacking a tail, distinctive from any other previously known viruses. Virions are formed in the cytoplasm of host cells, frequently accompanied by the disappearance of the nucleus. The lytic cycle and the burst size were estimated at
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squashed ball like dsdna virus infecting a marine fungoid protist sicyoidochytrium minutum thraustochytriaceae Labyrinthulomycetes
Aquatic Microbial Ecology, 2007Co-Authors: Yoshitake Takao, Keizo Nagasaki, Daiske HondaAbstract:Thraustochytrids are cosmopolitan osmoterotrophic microorganisms that play imtrophic or heterotrophic microorganisms that play important roles as decomposers, producers of polyunsaturated fatty acids, and pathogens of mollusks, especially in coastal ecosystems. Sicyoidochytrium minutum DNA virus (SmDNAV), a novel double-stranded DNA (dsDNA) virus infecting a marine eukaryotic decomposer, S. minutum (formerly Ulkenia minuta), was isolated from the estuary of the Shukugawa River, Hyogo Prefecture, Japan in July 2003, and its basic characteristics were examined. The morphology of the virus particles is 'squashed ball-like' (ca. 146 and 112 nm in length and width, respectively) and lacking a tail, distinctive from any other previously known viruses. Virions are formed in the cytoplasm of host cells, frequently accompanied by the disappearance of the nucleus. The lytic cycle and the burst size were estimated at <8 h and 3.6 x 10 2 to 1.1 x 10 3 infectious units per host cell, respectively. SmDNAV harbored a single molecule of dsDNA approximately 200 kbp in length. This is the first report of a marine fungoid protist-infecting DNA virus that has been isolated and characterized.
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Fluorescence in situ hybridization using 18S rRNA- targeted probe for specific detection of thraustochytrids (Labyrinthulomycetes)
Plankton and Benthos Research, 2007Co-Authors: Yoshitake Takao, Rinka Yokoyama, Yuji Tomaru, Keizo Nagasaki, Yukari Sasakura, Daiske HondaAbstract:Thraustochytrids are cosmopolitan osmotrophic or heterotrophic microorganisms that play, especially in coastal ecosystems, important roles as decomposers and producers of polyunsaturated fatty acids (PUFA), and are also known to be pathogens of mollusks and seaweeds. However, because of shortcomings in the current methods for detec- tion and enumeration of thraustochytrids, very little information is available concerning their natural dynamics and eco- logical roles. In this study, we propose a new method for detecting thraustochytrids using a fluorescent 18S ribosomal RNA (rRNA)-targeted oligonucleotide probe (Probe ThrFL1). Detection of thraustochytrids by means of the fluores- cence in situ hybridization (FISH) technique with ThrFL1 was specific; the probe did not react with the other stra- menopile organisms or with the dinoflagellate that was tested. Because of the high specificity and intense reactivity, the FISH protocol is expected to be a strong tool for examining ecological features of thraustochytrids.
Fabrice Rebeille - One of the best experts on this subject based on the ideXlab platform.
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The zoospores of the thraustochytrid Aurantiochytrium limacinum: Transcriptional reprogramming and lipid metabolism associated to their specific functions.
Environmental Microbiology, 2020Co-Authors: Younes Dellero, Christian Morabito, Eric Marechal, Alberto Amato, Cécile Maës, Martin Schuler, Caroline Bournaud, Riccardo Aiese Cigliano, Fabrice RebeilleAbstract:Aurantiochytrium limacinum (Thraustochytriaceae, class Labyrinthulomycetes) is a marine Stramenopile and a pioneering mangrove decomposer. Its life cycle involves a non-motile stage and zoospore production. We observed that the composition of the medium, the presence of amino acids in particular, affects the release of zoospores. Two opposite conditions were defined, one with a cell population mainly composed of zoospores and another one with almost only non-motile cells. In silico allelic frequency analysis and flow cytometry suggest that zoospores and non-motile cells share the same ploidy level and are diploid. Through an RNA-seq approach, the transcriptional reprogramming accompanying the formation of zoospores was investigated, with a particular focus on their lipid metabolism. Based on a differential expression analysis, zoospores are characterized by high motility, very active signal transduction, an arrest of the cell division, a low amino acid metabolism and low glycolysis. Focusing on lipid metabolism, genes involved in lipase activities and peroxisomal β-oxidation are upregulated. qRT-PCR of selected lipid genes and lipid analyses during the life span of zoospores confirmed these observations. These results highlight the importance of the lipid dynamics in zoospores and show the metabolic processes required to use these energy-dense molecules as fuel for zoospore survival during their quest of new territories.
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ecophysiology and lipid dynamics of a eukaryotic mangrove decomposer
Environmental Microbiology, 2018Co-Authors: Younes Dellero, Suzanne Rose, Coralie Metton, Christian Morabito, Josselin Lupette, Juliette Jouhet, Eric Marechal, Fabrice Rebeille, Alberto AmatoAbstract:: Aurantiochytrium limacinum is an osmo-heterotrophic Stramenopile and a pioneering mangrove decomposer which is taxonomically assigned to the family of Thraustochytriaceae (class: Labyrinthulomycetes). The life cycle of A. limacinum involves different cell types including mono- and multi-nucleated cells as well as flagellated zoospores which colonize new fallen leaves. The ecological relevance of thraustochytrids is underestimated and eclipsed by their biotechnological importance, due to their ability to accumulate large amount of lipids, mainly triacylglycerols (TAGs). In this study, we aimed to understand the ecophysiological parameters that trigger zoospore production and the interplay between the life cycle of A. limacinum and its lipid metabolism. When grown in a rich medium, cells accumulated large amounts of TAGs at the end of their growth period, but no zoospores were produced. In poor media such as artificial sea water, zoospores were produced in massive quantities. In the absence of organic carbon, the zoospores remained swimming for at least 6 days, consuming their TAGs in the process. Addition of glucose rapidly triggered the maturation of the zoospores. On the basis of these data, we propose a life cycle for A. limacinum integrating the potential perturbations/changes in the environment surrounding a mangrove leaf that could lead to the production of zoospores and colonization of new areas.
