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Jing M, Yang W, Rao L, Chen J, Ding X, Zhou Y, Zhang Q, Lu K, Zhu J. Mechanisms of microbial coexistence in a patchy ecosystem: Differences in ecological niche overlap and species fitness between rhythmic and non-rhythmic species. WATER RESEARCH 2024; 256:121626. [PMID: 38642534 DOI: 10.1016/j.watres.2024.121626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 03/28/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
Resource patchiness caused by external events breaks the continuity and homogeneity of resource distribution in the original ecosystem. For local organisms, this leads to drastic changes in the availability of resources, breaks down the co-existence of species, and reshuffles the local ecosystem. West Lake is a freshwater lake with resource patchiness caused by multiple exogenous disturbances that has strong environmental heterogeneity that prevents clear observation of seasonal changes in the microbial communities. Despite this, the emergence of rhythmic species in response to irregular changes in the environment has been helpful for observing microbial communities dynamics in patchy ecosystems. We investigated the ecological mechanisms of seasonal changes in microbial communities in West Lake by screening rhythmic species based on the ecological niche and modern coexistence theories. The results showed that rhythmic species were the dominant factors in microbial community changes and the effects of most environmental factors on the microbial community were indirectly realised through the rhythmic species. Random forest analyses showed that seasonal changes in the microbial community were similarly predicted by the rhythmic species. In addition, we incorporated species interactions and community phylogenetic patterns into stepwise multiple regression analyses, the results of which indicate that ecological niches and species fitness may drive the coexistence of these subcommunities. Thus, this study extends our understanding of seasonal changes in microbial communities and provides new ways for observing seasonal changes in microbial communities, especially in ecosystems with resource patches. Our study also show that combining community phylogenies with co-occurrence networks based on ecological niches and modern coexistence theory can further help us understand the ecological mechanisms of interspecies coexistence.
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Affiliation(s)
- MingFei Jing
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Wen Yang
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Lihua Rao
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Jun Chen
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Xiuying Ding
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Yinying Zhou
- Division of Hangzhou West Lake Aquatic Area Management, Hangzhou 310002, China
| | - Quanxiang Zhang
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Kaihong Lu
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China
| | - Jinyong Zhu
- School of Marine Science, Ningbo University, No.169 Qixingnan Road, Beilun District, Ningbo, Zhejiang 315800, China.
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2
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Oono R, Chou V, Irving M. How do phytophagous insects affect phyllosphere fungi? Tracking fungi from milkweed to monarch caterpillar frass reveals communities dominated by fungal yeast. ENVIRONMENTAL MICROBIOLOGY REPORTS 2024; 16:e13213. [PMID: 38738810 PMCID: PMC11089944 DOI: 10.1111/1758-2229.13213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 10/26/2023] [Indexed: 05/14/2024]
Abstract
Since a significant proportion of plant matter is consumed by herbivores, a necessary adaptation for many phyllosphere microbes could be to survive through the guts of herbivores. While many studies explore the gut microbiome of herbivores by surveying the microbiome in their frass, few studies compare the phyllosphere microbiome to the gut microbiome of herbivores. High-throughput metabarcode sequencing was used to track the fungal community from milkweed (Asclepias spp.) leaves to monarch caterpillar frass. The most commonly identified fungal taxa that dominated the caterpillar frass after the consumption of leaves were yeasts, mostly belonging to the Basidiomycota phylum. While most fungal communities underwent significant bottlenecks and some yeast taxa increased in relative abundance, a consistent directional change in community structure was not identified from leaf to caterpillar frass. These results suggest that some phyllosphere fungi, especially diverse yeasts, can survive herbivory, but whether herbivory is a key stage of their life cycle remains uncertain. For exploring phyllosphere fungi and the potential coprophilous lifestyles of endophytic and epiphytic fungi, methods that target yeast and Basidiomycota fungi are recommended.
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Affiliation(s)
- Ryoko Oono
- Department of Ecology, Evolution, and Marine BiologyUniversity of CaliforniaSanta BarbaraCaliforniaUSA
| | - Vanessa Chou
- Department of Ecology, Evolution, and Marine BiologyUniversity of CaliforniaSanta BarbaraCaliforniaUSA
| | - Mari Irving
- Department of Ecology, Evolution, and Marine BiologyUniversity of CaliforniaSanta BarbaraCaliforniaUSA
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3
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Thomé PC, Wolinska J, Van Den Wyngaert S, Reñé A, Ilicic D, Agha R, Grossart HP, Garcés E, Monaghan MT, Strassert JFH. Phylogenomics including new sequence data of phytoplankton-infecting chytrids reveals multiple independent lifestyle transitions across the phylum. Mol Phylogenet Evol 2024; 197:108103. [PMID: 38754710 DOI: 10.1016/j.ympev.2024.108103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 12/01/2023] [Accepted: 05/11/2024] [Indexed: 05/18/2024]
Abstract
Parasitism is the most common lifestyle on Earth and has emerged many times independently across the eukaryotic tree of life. It is frequently found among chytrids (Chytridiomycota), which are early-branching unicellular fungi that feed osmotrophically via rhizoids as saprotrophs or parasites. Chytrids are abundant in most aquatic and terrestrial environments and fulfil important ecosystem functions. As parasites, they can have significant impacts on host populations. They cause global amphibian declines and influence the Earth's carbon cycle by terminating algal blooms. To date, the evolution of parasitism within the chytrid phylum remains unclear due to the low phylogenetic resolution of rRNA genes for the early diversification of fungi, and because few parasitic lineages have been cultured and genomic data for parasites is scarce. Here, we combine transcriptomics, culture-independent single-cell genomics and a phylogenomic approach to overcome these limitations. We newly sequenced 29 parasitic taxa and combined these with existing data to provide a robust backbone topology for the diversification of Chytridiomycota. Our analyses reveal multiple independent lifestyle transitions between parasitism and saprotrophy among chytrids and multiple host shifts by parasites. Based on these results and the parasitic lifestyle of other early-branching holomycotan lineages, we hypothesise that the chytrid last common ancestor was a parasite of phytoplankton.
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Affiliation(s)
- Pauline C Thomé
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Justyna Wolinska
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Silke Van Den Wyngaert
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany; Department of Biology, University of Turku, Turku, Finland
| | - Albert Reñé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Barcelona, Spain
| | - Doris Ilicic
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany
| | - Ramsy Agha
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Stechlin, Germany; Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, Barcelona, Spain
| | - Michael T Monaghan
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany; Institut für Biologie, Freie Universität Berlin, Berlin, Germany
| | - Jürgen F H Strassert
- Department of Evolutionary and Integrative Ecology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany.
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4
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Fernández-Valero AD, Karpov SA, Sampedro N, Gordi J, Timoneda N, Garcés E, Reñé A. Newly identified diversity of Dinomycetaceae (Rhizophydiales, Chytridiomycota), a family of fungal parasites of marine dinoflagellates. Eur J Protistol 2024; 93:126053. [PMID: 38350179 DOI: 10.1016/j.ejop.2024.126053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/15/2024]
Abstract
We identified two new parasite species of Chytridiomycota isolated during blooms of the dinoflagellate Alexandrium minutum in the coastal Mediterranean Sea. Light and electron microscopy together with molecular characterization of the nuclear 18S, ITS, and 28S rDNA regions led to their identification as two new species, Dinomyces gilberthii and Paradinomyces evelyniae, both belonging to the family Dinomycetaceae, order Rhizophydiales. Dinomyces gilberthii differs from the previously described D. arenysensis by the presence of discharge papillae and the development of a drop-shaped sporangium. Paradinomyces evelyniae differs from the previously described P. triforaminorum by the prominent lipid globule present in early sporangia and by the pointed end producing a rhizoid. The two chytrids differed in their geographical distribution. Dinomyces gilberthii was detected in several Mediterranean habitats, including harbours and beaches, and was particularly prevalent during summer dinoflagellate blooms. Its widespread occurrence in coastal ecosystems suggested a high level of adaptability to this environment. Paradinomyces evelyniae had a more restricted distribution in the coastal-marine environment, occurring in harbour sediments and only occasionally in the water column during winter and early spring. Paradinomyces evelyniae has previously been detected in the Baltic Sea, suggesting that its distribution encompasses contrasting coastal environments, although its presence is rare.
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Affiliation(s)
- Alan Denis Fernández-Valero
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain.
| | - Sergey A Karpov
- Department of Invertebrate Zoology, Biological Faculty, St Petersburg State University, Universitetskaya nab. 7/9, St Petersburg 199034, Russia; Zoological Institute of Russian Academy of Sciences, Universitetskaya nab. 1, St Petersburg 199034, Russia; North-Western State Medical University named after I.I. Mechnikov, Kirochnaya st. 41, St Petersburg 191015, Russia
| | - Nagore Sampedro
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain
| | - Jordina Gordi
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain
| | - Natàlia Timoneda
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain
| | - Albert Reñé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003 Barcelona, Catalonia, Spain
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5
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Bonito G. Ecology and evolution of algal-fungal symbioses. Curr Opin Microbiol 2024; 79:102452. [PMID: 38461593 DOI: 10.1016/j.mib.2024.102452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 02/06/2024] [Accepted: 02/15/2024] [Indexed: 03/12/2024]
Abstract
Ecological interactions and symbiosis between algae and fungi are ancient, widespread, and diverse with many independent origins. The heterotrophic constraint on fungal nutrition drives fungal interactions with autotrophic organisms, including algae. While ancestors of modern fungi may have evolved as parasites of algae, there remains a latent ability in algae to detect and respond to fungi through a range of symbioses that are witnessed today in the astounding diversity of lichens, associations with corticoid and polypore fungi, and endophytic associations with macroalgae. Research into algal-fungal interactions and biotechnological innovation have the potential to improve our understanding of their diversity and functions in natural systems, and to harness this knowledge to develop sustainable and novel approaches for producing food, energy, and bioproducts.
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Affiliation(s)
- Gregory Bonito
- Plant Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, USA; Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI 48824, USA; Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824, USA.
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6
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Rungjindamai N, Jones EBG. Why Are There So Few Basidiomycota and Basal Fungi as Endophytes? A Review. J Fungi (Basel) 2024; 10:67. [PMID: 38248976 PMCID: PMC10820240 DOI: 10.3390/jof10010067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/06/2024] [Accepted: 01/11/2024] [Indexed: 01/23/2024] Open
Abstract
A review of selected studies on fungal endophytes confirms the paucity of Basidiomycota and basal fungi, with almost 90% attributed to Ascomycota. Reasons for the low number of Basidiomycota and basal fungi, including the Chytridiomycota, Mucoromycota, and Mortierellomycota, are advanced, including isolation procedure and media, incubation period and the slow growth of basidiomycetes, the identification of non-sporulating isolates, endophyte competition, and fungus-host interactions. We compare the detection of endophytes through culture-dependent methods and culture-independent methods, the role of fungi on senescence of the host plant, and next-generation studies.
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Affiliation(s)
- Nattawut Rungjindamai
- Department of Biology, School of Science, King Mongkut’s Institute of Technology Ladkrabang (KMITL), Chalongkrung Road, Ladkrabang, Bangkok 10520, Thailand
| | - E. B. Gareth Jones
- Department of Botany and Microbiology, College of Science, King Saud University, P.O. Box 2455, Riyadh 11451, Saudi Arabia;
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7
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Monjot A, Bronner G, Courtine D, Cruaud C, Da Silva C, Aury JM, Gavory F, Moné A, Vellet A, Wawrzyniak I, Colombet J, Billard H, Debroas D, Lepère C. Functional diversity of microbial eukaryotes in a meromictic lake: Coupling between metatranscriptomic and a trait-based approach. Environ Microbiol 2023; 25:3406-3422. [PMID: 37916456 DOI: 10.1111/1462-2920.16531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/19/2023] [Indexed: 11/03/2023]
Abstract
The advent of high-throughput sequencing has led to the discovery of a considerable diversity of microbial eukaryotes in aquatic ecosystems, nevertheless, their function and contribution to the trophic food web functioning remain poorly characterized especially in freshwater ecosystems. Based on metabarcoding data obtained from a meromictic lake ecosystem (Pavin, France), we performed a morpho-physio-phenological traits-based approach to infer functional groups of microbial eukaryotes. Metatranscriptomic data were also analysed to assess the metabolic potential of these groups across the diel cycle, size fraction, sampling depth, and periods. Our analysis highlights a huge microbial eukaryotic diversity in the monimolimnion characterized by numerous saprotrophs expressing transcripts related to sulfur and nitrate metabolism as well as dissolved and particulate organic matter degradation. We also describe strong seasonal variations of microbial eukaryotes in the mixolimnion, especially for parasites and mixoplankton. It appears that the water mixing (occurring during spring and autumn) which benefits photosynthetic host communities also promotes parasitic fungi dissemination and over-expression of genes involved in the zoospore phototaxis and stage transition in the parasitic cycle. Mixoplanktonic haptophytes over-expressing photosynthesis-, endocytosis- and phagosome-linked genes under nutrient limitation also suggest that phagotrophy may provide them an advantage over non-phagotrophic phytoplankton.
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Affiliation(s)
- Arthur Monjot
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Gisèle Bronner
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Damien Courtine
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Corinne Cruaud
- Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Frederick Gavory
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Anne Moné
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Agnès Vellet
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ivan Wawrzyniak
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jonathan Colombet
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Hermine Billard
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Didier Debroas
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Cécile Lepère
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
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8
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Buaya A, Thines M. Ducellierialesord. nov. and evidence for a novel clade of endobiotic pollen-infecting "lagenidiaceous" Peronosporomycetes. Fungal Syst Evol 2023; 12:247-254. [PMID: 38455952 PMCID: PMC10918624 DOI: 10.3114/fuse.2023.12.12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 08/31/2023] [Indexed: 03/09/2024] Open
Abstract
The genus Ducellieria (Ducellieriaceae) contains three species (D. chodatii, D. tricuspidata, D. corcontica), and a single variety (D. chodatii var. armata) of obligate endobiotic pollen parasites. These organisms have been first assigned to the green alga genus Coelastrum, as they form very similar spherical structures, but the observation of heterokont zoospores has led to their reclassification to the phylum Oomycota. However, despite their widespread nature, these organisms are only known from their descriptive morphology, and life cycle traits of some species still remain incompletely known. Only the type species, D. chodatii, has been rediscovered several times, but the phylogeny of the genus remains unresolved, since none of its species has been studied for their molecular phylogeny. At present the genus is still included in some algal databases. To clarify the evolutionary affiliation of Ducellieria, efforts were undertaken to isolate D. chodatii from pollen grains, to infer its phylogenetic placement based on nrSSU sequences. By targeted isolation, the pollen endoparasitoid was rediscovered from three lakes in Germany (Mummelsee, Okertalsperre, Knappensee). Apart from the typical coelastrum-like spheroids, oomycetes sporulating directly from pollen grains in a lagenidium-like fashion were observed, and molecular sequences of both types of oomycetes were obtained. Phylogenetic reconstruction revealed that coelastrum-like and lagenidium-like forms are unrelated, with the former embedded within the deep branching early-diverging lineages, and the later stage forming a distinct clade in Peronosporales. Consequently, the life cycle of D. chodatii needs careful revision using single-spore isolates of the species, to infer if previous lifecycle reconstructions that involve various different thallus types are stages of a single species or potentially of several ones. Citation: Buaya AT, Thines M (2023). Ducellieriales ord. nov. and evidence for a novel clade of endobiotic pollen-infecting "lagenidiaceous" Peronosporomycetes. Fungal Systematics and Evolution 12: 247-254. doi: 10.3114/fuse.2023.12.12.
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Affiliation(s)
- A.T. Buaya
- Goethe-Universität Frankfurt am Main, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue Str. 13, D-60438 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - M. Thines
- Goethe-Universität Frankfurt am Main, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue Str. 13, D-60438 Frankfurt am Main, Germany
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
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9
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Fernández-Valero AD, Reñé A, Timoneda N, Pou-Solà N, Gordi J, Sampedro N, Garcés E. The succession of epiphytic microalgae conditions fungal community composition: how chytrids respond to blooms of dinoflagellates. ISME COMMUNICATIONS 2023; 3:103. [PMID: 37752353 PMCID: PMC10522651 DOI: 10.1038/s43705-023-00304-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 08/31/2023] [Accepted: 09/05/2023] [Indexed: 09/28/2023]
Abstract
This study aims to investigate the temporal dynamics of the epiphytic protist community on macroalgae, during the summer months, with a specific focus on fungi, and the interactions between zoosporic chytrid parasites and the proliferation of the dinoflagellates. We employed a combination of environmental sequencing techniques, incubation of natural samples, isolation of target organisms and laboratory experiments. Metabarcoding sequencing revealed changes in the dominant members of the epiphytic fungal community. Initially, fungi comprised < 1% of the protist community, mostly accounted for by Basidiomycota and Ascomycota, but with the emergence of Chytridiomycota during the mature phase of the biofilm, the fungal contribution increased to almost 30%. Chytridiomycota became dominant in parallel with an increase in the relative abundance of dinoflagellates in the community. Microscopy observations showed a general presence of chytrids following the peak proliferation of the dinoflagellate Ostreopsis sp., with the parasite, D. arenysensis as the dominant chytrid. The maximum infection prevalence was 2% indicating host-parasite coexistence. To further understand the in-situ prevalence of chytrids, we characterised the dynamics of the host abundance and prevalence of chytrids through co-culture. These laboratory experiments revealed intraspecific variability of D. arenysensis in its interaction with Ostreopsis, exhibiting a range from stable coexistence to the near-extinction of the host population. Moreover, while chytrids preferentially parasitized dinoflagellate cells, one of the strains examined displayed the ability to utilize pollen as a resource to maintain its viability, thus illustrating a facultative parasitic lifestyle. Our findings not only enrich our understanding of the diversity, ecology, and progression of epiphytic microalgal and fungal communities on Mediterranean coastal macroalgae, but they also shed light on the presence of zoosporic parasites in less-explored benthic habitats.
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Affiliation(s)
- Alan Denis Fernández-Valero
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain.
| | - Albert Reñé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain
| | - Natàlia Timoneda
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain
| | - Núria Pou-Solà
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain
| | - Jordina Gordi
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain
| | - Nagore Sampedro
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Pg. Marítim de la Barceloneta, 37-49, 08003, Barcelona, Catalonia, Spain
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10
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Seto K, Simmons DR, Quandt CA, Frenken T, Dirks AC, Clemons RA, McKindles KM, McKay RML, James TY. A combined microscopy and single-cell sequencing approach reveals the ecology, morphology, and phylogeny of uncultured lineages of zoosporic fungi. mBio 2023; 14:e0131323. [PMID: 37486265 PMCID: PMC10470594 DOI: 10.1128/mbio.01313-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 06/06/2023] [Indexed: 07/25/2023] Open
Abstract
Environmental DNA analyses of fungal communities typically reveal a much larger diversity than can be ascribed to known species. Much of this hidden diversity lies within undescribed fungal lineages, especially the early diverging fungi (EDF). Although these EDF often represent new lineages even at the phylum level, they have never been cultured, making their morphology and ecology uncertain. One of the methods to characterize these uncultured fungi is a single-cell DNA sequencing approach. In this study, we established a large data set of single-cell sequences of EDF by manually isolating and photographing parasitic fungi on various hosts such as algae, protists, and micro-invertebrates, combined with subsequent long-read sequencing of the ribosomal DNA locus (rDNA). We successfully obtained rDNA sequences of 127 parasitic fungal cells, which clustered into 71 phylogenetic lineages belonging to seven phylum-level clades of EDF: Blastocladiomycota, Chytridiomycota, Aphelidiomycota, Rozellomycota, and three unknown phylum-level clades. Most of our single cells yielded novel sequences distinguished from both described taxa and existing metabarcoding data, indicating an expansive and hidden diversity of parasitic taxa of EDF. We also revealed an unexpected diversity of endobiotic Olpidium-like chytrids and hyper-parasitic lineages. Overall, by combining photographs of parasitic fungi with phylogenetic analyses, we were able to better understand the ecological function and morphology of many of the branches on the fungal tree of life known only from DNA sequences. IMPORTANCE Much of the diversity of microbes from natural habitats, such as soil and freshwater, comprise species and lineages that have never been isolated into pure culture. In part, this stems from a bias of culturing in favor of saprotrophic microbes over the myriad symbiotic ones that include parasitic and mutualistic relationships with other taxa. In the present study, we aimed to shed light on the ecological function and morphology of the many undescribed lineages of aquatic fungi by individually isolating and sequencing molecular barcodes from 127 cells of host-associated fungi using single-cell sequencing. By adding these sequences and their photographs into the fungal tree, we were able to understand the morphology of reproductive and vegetative structures of these novel fungi and to provide a hypothesized ecological function for them. These individual host-fungal cells revealed themselves to be complex environments despite their small size; numerous samples were hyper-parasitized with other zoosporic fungal lineages such as Rozellomycota.
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Affiliation(s)
- Kensuke Seto
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, Japan
| | - D. Rabern Simmons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, Indiana, USA
| | - C. Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, Colorado, USA
| | - Thijs Frenken
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- Cluster Nature and Society, HAS University of Applied Sciences, 's-Hertogenbosch, the Netherlands
| | - Alden C. Dirks
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Rebecca A. Clemons
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Integrative Biology, The University of Texas at Austin, Austin, Texas, USA
| | - Katelyn M. McKindles
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
| | - R. Michael L. McKay
- Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
- Great Lakes Center for Fresh Waters and Human Health, Bowling Green State University, Bowling Green, Ohio, USA
| | - Timothy Y. James
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
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11
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Nakanishi H, Seto K, Takeuchi N, Kagami M. Novel parasitic chytrids infecting snow algae in an alpine snow ecosystem in Japan. Front Microbiol 2023; 14:1201230. [PMID: 37408638 PMCID: PMC10318532 DOI: 10.3389/fmicb.2023.1201230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 05/30/2023] [Indexed: 07/07/2023] Open
Abstract
Introduction Microbial communities are important components of glacier and snowpack ecosystems that influence biogeochemical cycles and snow/ice melt. Recent environmental DNA surveys have revealed that chytrids dominate the fungal communities in polar and alpine snowpacks. These could be parasitic chytrids that infect snow algae as observed microscopically. However, the diversity and phylogenetic position of parasitic chytrids has not been identified due to difficulties in establishing their culture and subsequent DNA sequencing. In this study, we aimed to identify the phylogenetic positions of chytrids infecting the snow algae, Chloromonas spp., bloomed on snowpacks in Japan. Methods By linking a microscopically picked single fungal sporangium on a snow algal cell to a subsequent sequence of ribosomal marker genes, we identified three novel lineages with distinct morphologies. Results All the three lineages belonged to Mesochytriales, located within "Snow Clade 1", a novel clade consisting of uncultured chytrids from snow-covered environments worldwide. Additionally, putative resting spores of chytrids attached to snow algal cells were observed. Discussion This suggests that chytrids may survive as resting stage in soil after snowmelt. Our study highlights the potential importance of parasitic chytrids that infect snow algal communities.
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Affiliation(s)
- Hiroaki Nakanishi
- Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, Japan
| | - Kensuke Seto
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, Japan
| | - Nozomu Takeuchi
- Department of Earth Sciences, Graduate School of Science, Chiba University, Chiba, Japan
| | - Maiko Kagami
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, Japan
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12
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Klawonn I, Van den Wyngaert S, Iversen MH, Walles TJW, Flintrop CM, Cisternas-Novoa C, Nejstgaard JC, Kagami M, Grossart HP. Fungal parasitism on diatoms alters formation and bio-physical properties of sinking aggregates. Commun Biol 2023; 6:206. [PMID: 36810576 PMCID: PMC9944279 DOI: 10.1038/s42003-023-04453-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/10/2023] [Indexed: 02/24/2023] Open
Abstract
Phytoplankton forms the base of aquatic food webs and element cycling in diverse aquatic systems. The fate of phytoplankton-derived organic matter, however, often remains unresolved as it is controlled by complex, interlinked remineralization and sedimentation processes. We here investigate a rarely considered control mechanism on sinking organic matter fluxes: fungal parasites infecting phytoplankton. We demonstrate that bacterial colonization is promoted 3.5-fold on fungal-infected phytoplankton cells in comparison to non-infected cells in a cultured model pathosystem (diatom Synedra, fungal microparasite Zygophlyctis, and co-growing bacteria), and even ≥17-fold in field-sampled populations (Planktothrix, Synedra, and Fragilaria). Additional data obtained using the Synedra-Zygophlyctis model system reveals that fungal infections reduce the formation of aggregates. Moreover, carbon respiration is 2-fold higher and settling velocities are 11-48% lower for similar-sized fungal-infected vs. non-infected aggregates. Our data imply that parasites can effectively control the fate of phytoplankton-derived organic matter on a single-cell to single-aggregate scale, potentially enhancing remineralization and reducing sedimentation in freshwater and coastal systems.
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Affiliation(s)
- Isabell Klawonn
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany.
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde (IOW), 18119, Rostock, Germany.
| | - Silke Van den Wyngaert
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Morten H Iversen
- Alfred Wegener Institute (AWI), Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
- Centre for Marine Environmental Sciences (MARUM) and University of Bremen, 28359, Bremen, Germany
| | - Tim J W Walles
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany
| | - Clara M Flintrop
- Alfred Wegener Institute (AWI), Helmholtz Centre for Polar and Marine Research, 27570, Bremerhaven, Germany
- Centre for Marine Environmental Sciences (MARUM) and University of Bremen, 28359, Bremen, Germany
- The Inter-University Institute for Marine Sciences in Eilat, Eilat, 8810302, Israel
| | - Carolina Cisternas-Novoa
- Helmholtz Centre for Ocean Research (GEOMAR), 24148, Kiel, Germany
- Ocean Sciences Centre, Memorial University of Newfoundland, St. John's, NL, A1C 5S7, Canada
| | - Jens C Nejstgaard
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany
| | - Maiko Kagami
- Faculty of Science, Toho University, Funabashi, Chiba, 274‑8510, Japan
- Faculty of Environment and Information Sciences, Yokohama National University, Yokohama, Kanagawa, 240‑8502, Japan
| | - Hans-Peter Grossart
- Department of Plankton and Microbial Ecology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 16775, Stechlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, 14469, Potsdam, Germany
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13
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Li B, Liu X, Zhu D, Su H, Guo K, Sun G, Li X, Sun L. Crop diversity promotes the recovery of fungal communities in saline-alkali areas of the Western Songnen Plain. Front Microbiol 2023; 14:1091117. [PMID: 36819047 PMCID: PMC9930164 DOI: 10.3389/fmicb.2023.1091117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 01/05/2023] [Indexed: 02/04/2023] Open
Abstract
Introduction Phytoremediation is an effective strategy for saline land restoration. In the Western Songnen Plain, northeast China, soil fungal community recovery for saline phytoremediation has not been well documented among different cropping patterns. In this study, we tested how rotation, mixture, and monoculture cropping patterns impact fungal communities in saline-alkali soils to assess the variability between cropping patterns. Methods The fungal communities of the soils of the different cropping types were determined using Illumina Miseq sequencing. Results Mixture and rotation promoted an increase in operational taxonomic unit (OTU) richness, and OTU richness in the mixture system decreased with increasing soil depth. A principal coordinate analysis (PCoA) showed that cropping patterns and soil depths influenced the structure of fungal communities, which may be due to the impact of soil chemistry. This was reflected by soil total nitrogen (TN) and electrical conductivity (EC) being the key factors driving OTU richness, while soil available potassium (AK) and total phosphorus (TP) were significantly correlated with the relative abundance of fungal dominant genus. The relative abundance of Leptosphaerulina, Alternaria, Myrothecium, Gibberella, and Tetracladium varied significantly between cropping patterns, and Leptosphaerulina was significantly associated with soil chemistry. Soil depth caused significant differences in the relative abundance of Fusarium in rotation and mixture soils, with Fusarium more commonly active at 0-15 cm deep soil. Null-model analysis revealed that the fungal community assembly of the mixture soils in 0-15 cm deep soil was dominated by deterministic processes, unlike the other two cropping patterns. Furthermore, fungal symbiotic networks were more complex in rotation and mixture than in monoculture soils, reflected in more nodes, more module hubs, and connectors. The fungal networks in rotation and mixture soils were more stable than in monoculture soils, and mixture networks were obviously more connected than rotations. FUNGuild showed that the relative proportion of saprotroph in rotation and mixture was significantly higher than that in monocultures. The highest proportion of pathotroph and symbiotroph was exhibited in rotation and mixture soils, respectively. Discussion Overall, mixture is superior to crop rotation and monocultures in restoring fungal communities of the saline-alkali soils of the Western Songnen Plain, northeast China.
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Affiliation(s)
- Bin Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Xiaoqian Liu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Dan Zhu
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Heng Su
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Kaiwen Guo
- College of Resources and Environment, Northeast Agricultural University, Harbin, China
| | - Guangyu Sun
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Xin Li
- College of Resources and Environment, Northeast Agricultural University, Harbin, China,School of Forestry, Northeast Forestry University, Harbin, China,*Correspondence: Xin Li, ✉
| | - Lei Sun
- College of Resources and Environment, Northeast Agricultural University, Harbin, China,Lei Sun, ✉
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14
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Van Den Wyngaert S, Kainz MJ, Ptacnik R. Mucilage protects the planktonic desmid Staurodesmus sp. against parasite attack by a chytrid fungus. JOURNAL OF PLANKTON RESEARCH 2023; 45:3-14. [PMID: 36751484 PMCID: PMC9896892 DOI: 10.1093/plankt/fbac071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/23/2022] [Indexed: 06/18/2023]
Abstract
Zoosporic fungi of the phylum Chytridiomycota are ubiquitous parasites of phytoplankton in aquatic ecosystems, but little is known about phytoplankton defense strategies against parasitic chytrid attacks. Using a model chytrid-phytoplankton pathosystem, we experimentally tested the hypothesis that the mucilage envelope of a mucilage-forming desmid species provides protection against the parasitic chytrid Staurastromyces oculus. Mucilage-forming Staurodesmus cells were not accessible to the chytrid, whereas physical removal of the mucilage envelope rendered the same Staurodesmus sp. strain equally susceptible to chytrid infections as the original non-mucilage-forming host Staurastrum sp. Epidemic spread of the parasite only occurred in Staurastrum sp., whereas non-mucilage-bearing Staurodesmus sp. allowed for co-existence of host and parasite, and mucilage-bearing Staurodesmus sp. caused parasite extinction. In addition to the mucilage defense barrier, we also demonstrate the ability of both Staurastrum sp. and Staurodesmus sp. to resist infection by preventing chytrid development while still remaining viable and being able to reproduce and thus recover from an infection. This study extends our knowledge on phytoplankton defense traits and the functional role of mucilage in phytoplankton as a physical barrier against fungal parasites.
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Affiliation(s)
| | - Martin J Kainz
- Wassercluster – Biologische Station Lunz, Dr Carl Kupelwieser Promenade 5, 3293 Lunz Am See, Austria
- Department of Biomedical Research, Danube University, Dr Karl Dorrek Strasse 20, 3500 Krems, Austria
| | - Robert Ptacnik
- Wassercluster – Biologische Station Lunz, Dr Carl Kupelwieser Promenade 5, 3293 Lunz Am See, Austria
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15
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Thongthaisong P, Kasada M, Grossart H, Wollrab S. Critical role of parasite‐mediated energy pathway on community response to nutrient enrichment. Ecol Evol 2022; 12:e9622. [PMCID: PMC9748242 DOI: 10.1002/ece3.9622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 09/30/2022] [Accepted: 11/20/2022] [Indexed: 12/15/2022] Open
Affiliation(s)
- Patch Thongthaisong
- Department of Plankton and Microbial Ecology Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Institute for Biochemistry and Biology Potsdam University Potsdam Germany
| | - Minoru Kasada
- Department of Plankton and Microbial Ecology Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Graduate School of Life Sciences Tohoku University Sendai Japan
| | - Hans‐Peter Grossart
- Department of Plankton and Microbial Ecology Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Institute for Biochemistry and Biology Potsdam University Potsdam Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
| | - Sabine Wollrab
- Department of Plankton and Microbial Ecology Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB) Berlin Germany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB) Berlin Germany
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16
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Fernández-Valero AD, Reñé A, Timoneda N, Sampedro N, Garcés E. Dinoflagellate hosts determine the community structure of marine Chytridiomycota: Demonstration of their prominent interactions. Environ Microbiol 2022; 24:5951-5965. [PMID: 36057937 PMCID: PMC10087856 DOI: 10.1111/1462-2920.16182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/26/2022] [Indexed: 01/12/2023]
Abstract
The interactions of parasitic fungi with their phytoplankton hosts in the marine environment are mostly unknown. In this study, we evaluated the diversity of Chytridiomycota in phytoplankton communities dominated by dinoflagellates at several coastal locations in the NW Mediterranean Sea and demonstrated the most prominent interactions of these parasites with their hosts. The protist community in seawater differed from that in sediment, with the latter characterized by a greater heterogeneity of putative hosts, such as dinoflagellates and diatoms, as well as a chytrid community more diverse in its composition and with a higher relative abundance. Chytrids accounted for 77 amplicon sequence variants, of which 70 were found exclusively among different blooming host species. The relative abundance of chytrids was highest in samples dominated by the dinoflagellate genera Ostreopsis and Alexandrium, clearly indicating the presence of specific chytrid communities. The establishment of parasitoid-host co-cultures of chytrids and dinoflagellates allowed the morphological identification and molecular characterization of three species of Chytridiomycota, including Dinomyces arenysensis, as one of the most abundant environmental sequences, and the discovery of two other species not yet described.
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Affiliation(s)
- Alan Denis Fernández-Valero
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Albert Reñé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Natàlia Timoneda
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Nagore Sampedro
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Barcelona, Catalonia, Spain
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