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Buaya A, Thines M. Miracula polaris - A New Species of Miracula from the East Fjords of Iceland. MYCOBIOLOGY 2024; 52:117-123. [PMID: 38690034 PMCID: PMC11057556 DOI: 10.1080/12298093.2024.2333611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 03/18/2024] [Indexed: 05/02/2024]
Abstract
There is increasing evidence that holocarpic oomycetes, i.e., those converting their entire vegetative thallus into zoospores upon maturation, are a phylogenetically diverse group in both freshwater and marine ecosystems. Most of the known holocarpic oomycete species diverge before the main split of Peronosporomycetes and Saprolegniomycetes and are, thus, termed as early-diverging oomycetes. In environmental sequencing studies, it was revealed that of the early-diverging genera especially Sirolpidium, Miracula, and Diatomophthora are widespread. As in these studies especially the Arctic Ocean seemed to harbor many undiscovered species, sampling was conducted at the Blávík research station on Fáskrúðsfjörður in the East Fjords of Iceland, where there is both an influence from the Arctic Ocean and the North Atlantic. During the screening for infected diatoms, a parasitoid was found in the marine diatom genus Melosira, which is one of the most abundant genera in arctic ecosystems. Molecular phylogenetics and morphological characterization revealed that the parasitoid belonged to the genus Miracula and corresponded to one of the lineages previously found in single-cell sequencing. Thus, the current study both contributes to the knowledge of the genus Miracula and the increasing diversity of the genus suggests that the many linages found in environmental sequencing which can still not be associated with known species might represent actual species to be discovered in future studies.
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Affiliation(s)
- Anthony Buaya
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Frankfurt am Main, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
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2
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Wang FQ, Bartosik D, Sidhu C, Siebers R, Lu DC, Trautwein-Schult A, Becher D, Huettel B, Rick J, Kirstein IV, Wiltshire KH, Schweder T, Fuchs BM, Bengtsson MM, Teeling H, Amann RI. Particle-attached bacteria act as gatekeepers in the decomposition of complex phytoplankton polysaccharides. MICROBIOME 2024; 12:32. [PMID: 38374154 PMCID: PMC10877868 DOI: 10.1186/s40168-024-01757-5] [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: 11/07/2023] [Accepted: 01/04/2024] [Indexed: 02/21/2024]
Abstract
BACKGROUND Marine microalgae (phytoplankton) mediate almost half of the worldwide photosynthetic carbon dioxide fixation and therefore play a pivotal role in global carbon cycling, most prominently during massive phytoplankton blooms. Phytoplankton biomass consists of considerable proportions of polysaccharides, substantial parts of which are rapidly remineralized by heterotrophic bacteria. We analyzed the diversity, activity, and functional potential of such polysaccharide-degrading bacteria in different size fractions during a diverse spring phytoplankton bloom at Helgoland Roads (southern North Sea) at high temporal resolution using microscopic, physicochemical, biodiversity, metagenome, and metaproteome analyses. RESULTS Prominent active 0.2-3 µm free-living clades comprised Aurantivirga, "Formosa", Cd. Prosiliicoccus, NS4, NS5, Amylibacter, Planktomarina, SAR11 Ia, SAR92, and SAR86, whereas BD1-7, Stappiaceae, Nitrincolaceae, Methylophagaceae, Sulfitobacter, NS9, Polaribacter, Lentimonas, CL500-3, Algibacter, and Glaciecola dominated 3-10 µm and > 10 µm particles. Particle-attached bacteria were more diverse and exhibited more dynamic adaptive shifts over time in terms of taxonomic composition and repertoires of encoded polysaccharide-targeting enzymes. In total, 305 species-level metagenome-assembled genomes were obtained, including 152 particle-attached bacteria, 100 of which were novel for the sampling site with 76 representing new species. Compared to free-living bacteria, they featured on average larger metagenome-assembled genomes with higher proportions of polysaccharide utilization loci. The latter were predicted to target a broader spectrum of polysaccharide substrates, ranging from readily soluble, simple structured storage polysaccharides (e.g., laminarin, α-glucans) to less soluble, complex structural, or secreted polysaccharides (e.g., xylans, cellulose, pectins). In particular, the potential to target poorly soluble or complex polysaccharides was more widespread among abundant and active particle-attached bacteria. CONCLUSIONS Particle-attached bacteria represented only 1% of all bloom-associated bacteria, yet our data suggest that many abundant active clades played a pivotal gatekeeping role in the solubilization and subsequent degradation of numerous important classes of algal glycans. The high diversity of polysaccharide niches among the most active particle-attached clades therefore is a determining factor for the proportion of algal polysaccharides that can be rapidly remineralized during generally short-lived phytoplankton bloom events. Video Abstract.
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Grants
- AM 73/9-3 Deutsche Forschungsgemeinschaft,Germany
- SCHW 595/10-3 Deutsche Forschungsgemeinschaft,Germany
- TE 813/2-3 Deutsche Forschungsgemeinschaft,Germany
- RI 969/9-2 Deutsche Forschungsgemeinschaft,Germany
- BE 3869/4-3 Deutsche Forschungsgemeinschaft,Germany
- SCHW 595/11-3 Deutsche Forschungsgemeinschaft,Germany
- FU 627/2-3 Deutsche Forschungsgemeinschaft,Germany
- RI 969/9-2 Deutsche Forschungsgemeinschaft,Germany
- TE 813/2-3 Deutsche Forschungsgemeinschaft,Germany
- AM 73/9-3 Deutsche Forschungsgemeinschaft,Germany
- AWI_BAH_o 1 Biological Station Helgoland, Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research
- AWI_BAH_o 1 Biological Station Helgoland, Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research
- Max Planck Institute for Marine Microbiology (2)
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Affiliation(s)
- Feng-Qing Wang
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Daniel Bartosik
- Institute of Pharmacy, University of Greifswald, Felix-Hausdorff-Straße 3, 17489, Greifswald, Germany
- Institute of Marine Biotechnology, Walther-Rathenau-Straße 49a, 17489, Greifswald, Germany
| | - Chandni Sidhu
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Robin Siebers
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - De-Chen Lu
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
- Marine College, Shandong University, Weihai, 264209, China
| | - Anke Trautwein-Schult
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - Dörte Becher
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Carl von Linné-Weg 10, 50829, Cologne, Germany
| | - Johannes Rick
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, 27483, Germany
| | - Inga V Kirstein
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, 27483, Germany
| | - Karen H Wiltshire
- Alfred Wegener Institute for Polar and Marine Research, Biologische Anstalt Helgoland, Helgoland, 27483, Germany
| | - Thomas Schweder
- Institute of Pharmacy, University of Greifswald, Felix-Hausdorff-Straße 3, 17489, Greifswald, Germany
- Institute of Marine Biotechnology, Walther-Rathenau-Straße 49a, 17489, Greifswald, Germany
| | - Bernhard M Fuchs
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany
| | - Mia M Bengtsson
- Institute of Microbiology, University of Greifswald, Felix-Hausdorff-Straße 8, 17489, Greifswald, Germany.
| | - Hanno Teeling
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
| | - Rudolf I Amann
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359, Bremen, Germany.
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Chen X, Xu G, Xiong P, Peng J, Fang K, Wan S, Wang B, Gu F, Li J, Xiong H. Dry and wet seasonal variations of the sediment fungal community composition in the semi-arid region of the Dali River, Northwest China. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:123694-123709. [PMID: 37993647 DOI: 10.1007/s11356-023-31042-1] [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: 08/25/2023] [Accepted: 11/09/2023] [Indexed: 11/24/2023]
Abstract
Microbial communities play an important role in water quality regulation and biogeochemical cycling in freshwater ecosystems. However, there has been a lack of research on the seasonal variation of sediment microorganisms in the sediments of small river basins in typical semi-arid region. In this study, high-throughput DNA sequencing was used to investigate the fungal community and its influencing factors in the sediment of the Dali River in the dry and wet seasons. The results showed that there were obvious seasonal differences in fungal alpha diversity. The diversity and richness of fungi in the dry season were greater than that in the wet season, but the evenness of fungi in the dry season was lower than that in the wet season. In addition, Ascomycota and Basidiomycota were the most important phyla in the Dali River fungal community, but their distributions showed clear seasonal differences. In the dry season, the relative abundance of Ascomycota and Basidiomycota were 12.34-46.42% and 17.59-27.20%, respectively. In the wet season, the relative abundances of these two phyla were 24.33-36.56% and 5.75-12.26%, respectively. PICRUSt2 was used to predict the metabolic function of fungal community in the sediment, and it was found that at the first level, the proportion of biosynthesis in the dry season was higher than that in the wet season. The ecological network structure showed that the fungal community in the wet season was more complex and stable than that in the dry season. The characteristic fungi in the dry season sediment were chytrid fungi in the family Rhizophydiaceae and the order Rhizophydiales, whereas those in the wet season sediment were in the orders Eurotiales and Saccharomycetales. Canonical correspondence analysis (CCA) showed that the physicochemical properties of water and sediment together explained a greater proportion of the dry-season fungal community changes than of the wet-season changes. In the dry season, temperature and ammonia nitrogen in the water were the main factors affecting the change of fungal community, whereas in the wet season, total nitrogen concentration of the water, electrical conductivity, total organic carbon and available phosphorus of the sediment, pH, and temperature were the main factors affecting the changes in fungal community composition. The results of this study enhanced our understanding of microbial communities in semi-arid river ecosystems, and highlight the importance of the management and protection in river ecosystems.
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Affiliation(s)
- Xin Chen
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Guoce Xu
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China.
| | - Ping Xiong
- Shaanxi Forestry Survey and Planning Institute, Xi'an, 710082, Shaanxi, China
| | - Jianbo Peng
- Shaanxi Forestry Survey and Planning Institute, Xi'an, 710082, Shaanxi, China
| | - Kang Fang
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Shun Wan
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Bin Wang
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Fengyou Gu
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Jing Li
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
| | - Haijing Xiong
- Key Laboratory of National Forestry Administration on Ecological Hydrology and Disaster Prevention in Arid Regions, Xi'an University of Technology, Xi'an, 710048, Shaanxi, China
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4
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Danz A, Quandt CA. A review of the taxonomic diversity, host-parasite interactions, and experimental research on chytrids that parasitize diatoms. Front Microbiol 2023; 14:1281648. [PMID: 38029223 PMCID: PMC10643281 DOI: 10.3389/fmicb.2023.1281648] [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: 08/22/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
Diatoms (Bacillariophyta) are a major source of primary production on Earth, generating between 1/4 to 1/2 of all oxygen. They are found in almost all bodies of water, the ice of mountains, the arctic and the antarctic, and soils. Diatoms are also a major source of food in aquatic systems, a key component of the silica cycle, and are carbon capturers in oceans. Recently, diatoms have been examined as sources of biofuels, food, and other economic boons. Chytrids are members of the Kingdom fungi comprising, at a minimum, Chytridiomycota, Blastocladiomycota, and Neocallimastigales. Most chytrids are saprobes, plant pathogens, or parasites, and play an important role in aquatic ecosystems. Chytrid parasitism of diatoms has been reported to cause epidemics of over 90% fatality, though most of the information regarding these epidemics is limited to interactions between just a few hosts and parasites. Given the ubiquity of diatoms, their importance in natural and economic systems, and the massive impact epidemics can have on populations, the relative lack of knowledge regarding parasitism by chytrids is alarming. Here we present a list of the firsthand accounts of diatoms reported parasitized by chytrids. The list includes 162 named parasitic chytrid-diatom interactions, with 63 unique chytrid taxa from 11 genera, and 74 unique diatom taxa from 28 genera. Prior to this review, no list of all documented diatom-chytrid interactions existed. We also synthesize the currently known methods of infection, defense, and experiments examining diatoms and chytrids, and we document the great need for work examining both a greater breadth of taxonomic diversity of parasites and hosts, and a greater depth of experiments probing their interactions. This resource is intended to serve as a building block for future researchers studying diatom-parasite interactions and global planktonic communities in both fresh and marine systems.
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Affiliation(s)
- August Danz
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
- University of Colorado Museum of Natural History, Boulder, CO, United States
| | - C. Alisha Quandt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, United States
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5
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Yang Y, Rivera Pérez CA, Richter-Heitmann T, Nimzyk R, Friedrich MW, Reich M. Effects of oxygen availability on mycobenthic communities of marine coastal sediments. Sci Rep 2023; 13:15218. [PMID: 37709848 PMCID: PMC10502103 DOI: 10.1038/s41598-023-42329-1] [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: 04/17/2023] [Accepted: 09/08/2023] [Indexed: 09/16/2023] Open
Abstract
In coastal marine sediments, oxygen availability varies greatly, and anoxic conditions can develop quickly over low spatial resolution. Although benthic fungi are important players in the marine carbon cycle, little is known about their adaptation to fluctuating availability of oxygen as terminal electron acceptor. Here, we study which part of a mycobenthic community from oxic coastal sediments can thrive under temporarily anoxic conditions. We test whether phylogeny or certain fungal traits promote plasticity in respect to changes in oxygen availability. Therefore, we incubated mycobenthos under oxic and anoxic conditions, performed ITS2 Illumina tag-sequencing and an additional meta-analysis on a literature survey. Half of all OTUs showed a plasticity towards changing oxygen availability and exhibited different strategies towards anoxic conditions, with rapid response within hours or a delayed one after several days. The strategy of dimorphism and facultative yeasts were significantly linked to OTU occurrence in anoxic conditions, while phylogeny and other traits had less effect. Our results suggest that different fungal niches are formed over the duration of prolonged anoxic conditions. The taxon-specific proliferation seems to be regulated by the fine-tuning of various traits and factors. It is essential to take these results into account when conducting conceptual work on the functionality of the marine benthos.
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Affiliation(s)
- Yanyan Yang
- Molecular Ecology Group, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Carmen Alicia Rivera Pérez
- Molecular Ecology Group, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
- Biodiversity and Evolution of Plants, Institute of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Oldenburg, Germany
| | - Tim Richter-Heitmann
- Microbial Ecophysiology Group, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Rolf Nimzyk
- Microbial Ecophysiology Group, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
| | - Michael W Friedrich
- Microbial Ecophysiology Group, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany
| | - Marlis Reich
- Molecular Ecology Group, Faculty of Biology and Chemistry, University of Bremen, Bremen, Germany.
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6
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Catlett D, Peacock EE, Crockford ET, Futrelle J, Batchelder S, Stevens BLF, Gast RJ, Zhang WG, Sosik HM. Temperature dependence of parasitoid infection and abundance of a diatom revealed by automated imaging and classification. Proc Natl Acad Sci U S A 2023; 120:e2303356120. [PMID: 37399413 PMCID: PMC10334780 DOI: 10.1073/pnas.2303356120] [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: 02/27/2023] [Accepted: 05/19/2023] [Indexed: 07/05/2023] Open
Abstract
Diatoms are a group of phytoplankton that contribute disproportionately to global primary production. Traditional paradigms that suggest diatoms are consumed primarily by larger zooplankton are challenged by sporadic parasitic "epidemics" within diatom populations. However, our understanding of diatom parasitism is limited by difficulties in quantifying these interactions. Here, we observe the dynamics of Cryothecomonas aestivalis (a protist) infection of an important diatom on the Northeast U.S. Shelf (NES), Guinardia delicatula, with a combination of automated imaging-in-flow cytometry and a convolutional neural network image classifier. Application of the classifier to >1 billion images from a nearshore time series and >20 survey cruises across the broader NES reveals the spatiotemporal gradients and temperature dependence of G. delicatula abundance and infection dynamics. Suppression of parasitoid infection at temperatures <4 °C drives annual cycles in both G. delicatula infection and abundance, with an annual maximum in infection observed in the fall-winter preceding an annual maximum in host abundance in the winter-spring. This annual cycle likely varies spatially across the NES in response to variable annual cycles in water temperature. We show that infection remains suppressed for ~2 mo following cold periods, possibly due to temperature-induced local extinctions of the C. aestivalis strain(s) that infect G. delicatula. These findings have implications for predicting impacts of a warming NES surface ocean on G. delicatula abundance and infection dynamics and demonstrate the potential of automated plankton imaging and classification to quantify phytoplankton parasitism in nature across unprecedented spatiotemporal scales.
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Affiliation(s)
- Dylan Catlett
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA02543
| | - Emily E. Peacock
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA02543
| | - E. Taylor Crockford
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA02543
| | - Joe Futrelle
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA02543
| | - Sidney Batchelder
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA02543
| | | | - Rebecca J. Gast
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA02543
| | - Weifeng G. Zhang
- Department of Applied Ocean Physics and Engineering, Woods Hole Oceanographic Institution, Woods Hole, MA02543
| | - Heidi M. Sosik
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA02543
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7
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O'Neill EA, Rowan NJ. Potential disruptive effects of zoosporic parasites on peatland-based organic freshwater aquaculture: Case study from the Republic of Ireland. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 868:161495. [PMID: 36634789 DOI: 10.1016/j.scitotenv.2023.161495] [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: 10/21/2022] [Revised: 01/05/2023] [Accepted: 01/05/2023] [Indexed: 06/17/2023]
Abstract
Irish freshwater aquaculture holds great potential for aiding food security. However, its necessary expansion has been hampered by the adoption of important environmental EU directives. A novel peatland-based recirculating aquaculture multi-trophic pond system (RAMPS) was developed to assess its potential to assist in the sustainable development of industry whilst remaining aligned with environmental protection by adhering to organic aquaculture practices. Microalgae play a pivotal role in the farms' wastewater bioremediation. However, a collapse of the algal population within the system towards the end of the pilot study was observed. No relationship between physicochemical fluctuations and the collapse were indicated. Further investigations into the potential presence of biological agents were then conducted and fourteen species of zoosporic parasites from five different genera (Labyrinthula, Vampyrella, Amoeboaphelidium, Paraphelidium and Aphelidium) were identified after conducting next-generation sequencing (MinION). The presence of these species indicated the potential cause of algal collapse. Additionally, changes in weather conditions may have also contributed to the issue. Given the lack of data available on zoosporic parasites and their potential impact on organic aquaculture practices, additional research needs to be conducted. Developing a means to monitor and mitigate against these complex zoosporic parasites will inform food security, it will particularly help safeguard "organic" freshwater aquaculture where there is a reliance on using natural-based approaches to address disease mitigation. This information will in turn inform the replication of this RAMPs system in peatlands internationally creating local employment in green technologies, as communities' transition away from burning peat as fossil fuel. Also, zoosporic parasites may reduce important microalgae in peatland-based culture ponds that serve as exceptional sequesters of carbon. Findings of this study will inform related research that focus on the emergence of microbial pathogens in local aquatic ecosystems brought on by variances in climate.
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Affiliation(s)
- Emer A O'Neill
- Centre for Sustainable Disinfection and Sustainability, Bioscience Research Institute, Technological University of the Shannon: Midlands Midwest, Athlone Campus, University Road, Athlone, Co. Westmeath, Ireland; Faculty of Science & Health, Technological University of the Shannon: Midlands Midwest, Athlone Campus, University Road, Athlone, Co. Westmeath, Ireland.
| | - Neil J Rowan
- Centre for Sustainable Disinfection and Sustainability, Bioscience Research Institute, Technological University of the Shannon: Midlands Midwest, Athlone Campus, University Road, Athlone, Co. Westmeath, Ireland; Faculty of Science & Health, Technological University of the Shannon: Midlands Midwest, Athlone Campus, University Road, Athlone, Co. Westmeath, Ireland
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8
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Klawonn I, Dunker S, Kagami M, Grossart HP, Van den Wyngaert S. Intercomparison of Two Fluorescent Dyes to Visualize Parasitic Fungi (Chytridiomycota) on Phytoplankton. MICROBIAL ECOLOGY 2023; 85:9-23. [PMID: 34854932 PMCID: PMC9849195 DOI: 10.1007/s00248-021-01893-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/04/2021] [Indexed: 06/13/2023]
Abstract
Fungal microparasites (here chytrids) are widely distributed and yet, they are often overlooked in aquatic environments. To facilitate the detection of microparasites, we revisited the applicability of two fungal cell wall markers, Calcofluor White (CFW) and wheat germ agglutinin (WGA), for the direct visualization of chytrid infections on phytoplankton in laboratory-maintained isolates and field-sampled communities. Using a comprehensive set of chytrid-phytoplankton model pathosystems, we verified the staining pattern on diverse morphological structures of chytrids via fluorescence microscopy. Empty sporangia were stained most effectively, followed by encysted zoospores and im-/mature sporangia, while the staining success was more variable for rhizoids, stalks, and resting spores. In a few instances, the staining was unsuccessful (mostly with WGA), presumably due to insufficient cell fixation, gelatinous cell coatings, and multilayered cell walls. CFW and WGA staining could be done in Utermöhl chambers or on polycarbonate filters, but CFW staining on filters seemed less advisable due to high background fluorescence. To visualize chytrids, 1 µg dye mL-1 was sufficient (but 5 µg mL-1 are recommended). Using a dual CFW-WGA staining protocol, we detected multiple, mostly undescribed chytrids in two natural systems (freshwater and coastal), while falsely positive or negative stained cells were well detectable. As a proof-of-concept, we moreover conducted imaging flow cytometry, as a potential high-throughput technology for quantifying chytrid infections. Our guidelines and recommendations are expected to facilitate the detection of chytrid epidemics and to unveil their ecological and economical imprint in natural and engineered aquatic systems.
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Affiliation(s)
- Isabell Klawonn
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Berlin, Germany.
- Leibniz Institute for Baltic Sea Research (IOW), Seestrasse 15, 18119, Rostock, Germany.
| | - Susanne Dunker
- Department for Physiological Diversity, Helmholtz Centre for Environmental Research (UFZ), 04318, Leipzig, Germany
- German Centre for Integrative Biodiversity Research (iDiv), 04103, Leipzig, 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 Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Berlin, Germany
- Institute of Biochemistry and Biology, Potsdam University, 14476, Potsdam, Germany
| | - Silke Van den Wyngaert
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), 12587, Berlin, Germany.
- WasserCluster Lunz, Biologische Station, Dr. Carl Kupelwieser Promenade 5, 3293, Lunz am See, Austria.
- Department of Biology, University of Turku, Vesilinnantie 5, 20014, Turku, Finland.
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Buaya A, Thines M. Miracula blauvikensis: a new species of Miracula from Iceland, and report of a co-cultivation system for studying oomycete-diatom interactions. Fungal Syst Evol 2022; 10:169-175. [PMID: 36741555 PMCID: PMC9875693 DOI: 10.3114/fuse.2022.10.07] [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: 09/30/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022] Open
Abstract
The genus Miracula represents an early-diverging lineage of diatom-parasitic Oomycota, straminipilous eukaryotes that have evolved fungal features independent from the opisthokont Fungi. Recent studies have revealed that diatom parasitoids are much more species-rich than previously thought and may play an important role in limnic and marine ecosystems. Of the different diatom-parasitic lineages, the genus Miracula is one of the most abundant in marine ecosystems. Here a species of Miracula parasitising Fragilaria capucina s.l. from Iceland is described as Miracula blauvikensis. In addition, its phylogenetic position is clarified and its life-cycle documented. The species has been brought into co-cultivation with its host, and due to the ease of cultivation and the convenient microscopy of the diatom threads, this co-culture might be a useful tool to study oomycete-diatom interactions in the future. Citation: Buaya A, Thines M (2022). Miracula blauvikensis: a new species of Miracula from Iceland, and report of a co-cultivation system for studying oomycete-diatom interactions. Fungal Systematics and Evolution 10: 169-175. doi: 10.3114/fuse.2022.10.07.
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Affiliation(s)
- A. Buaya
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany,*Corresponding authors: ,
| | - M. Thines
- Senckenberg Biodiversity and Climate Research Centre (SBiK-F), Senckenberganlage 25, 60325 Frankfurt am Main, Germany,Goethe University Frankfurt am Main, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60438 Frankfurt am Main, Germany,*Corresponding authors: ,
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10
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Ollison GA, Hu SK, Hopper JV, Stewart BP, Smith J, Beatty JL, Rink LK, Caron DA. Daily dynamics of contrasting spring algal blooms in Santa Monica Bay (central Southern California Bight). Environ Microbiol 2022; 24:6033-6051. [PMID: 35880671 PMCID: PMC10087728 DOI: 10.1111/1462-2920.16137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 07/11/2022] [Accepted: 07/13/2022] [Indexed: 01/12/2023]
Abstract
Protistan algae (phytoplankton) dominate coastal upwelling ecosystems where they form massive blooms that support the world's most important fisheries and constitute an important sink for atmospheric CO2 . Bloom initiation is well understood, but the biotic and abiotic forces that shape short-term dynamics in community composition are still poorly characterized. Here, high-frequency (daily) changes in relative abundance dynamics of the metabolically active protistan community were followed via expressed 18S V4 rRNA genes (RNA) throughout two algal blooms during the spring of 2018 and 2019 in Santa Monica Bay (central Southern California Bight). A diatom bloom formed after wind-driven, nutrient upwelling events in both years, but different taxa dominated each year. Whereas diatoms bloomed following elevated nutrients and declined after depletion each year, a massive dinoflagellate bloom manifested under relatively low inorganic nitrogen conditions following diatom bloom senescence in 2019 but not 2018. Network analysis revealed associations between diatoms and cercozoan putative parasitic taxa and syndinean parasites during 2019 that may have influenced the demise of the diatoms, and the transition to a dinoflagellate-dominated bloom.
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Affiliation(s)
- Gerid A Ollison
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Sarah K Hu
- Woods Hole Oceanographic Institution, Marine Chemistry and Geochemistry, Woods Hole, Massachusetts, USA
| | - Julie V Hopper
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Brittany P Stewart
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Jayme Smith
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Jennifer L Beatty
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
| | - Laura K Rink
- Heal the Bay Aquarium, Santa Monica, California, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, California, USA
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11
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Glycoside hydrolase from the GH76 family indicates that marine Salegentibacter sp. Hel_I_6 consumes alpha-mannan from fungi. THE ISME JOURNAL 2022; 16:1818-1830. [PMID: 35414716 PMCID: PMC9213526 DOI: 10.1038/s41396-022-01223-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 02/10/2022] [Accepted: 03/11/2022] [Indexed: 11/08/2022]
Abstract
AbstractMicrobial glycan degradation is essential to global carbon cycling. The marine bacterium Salegentibacter sp. Hel_I_6 (Bacteroidota) isolated from seawater off Helgoland island (North Sea) contains an α-mannan inducible gene cluster with a GH76 family endo-α-1,6-mannanase (ShGH76). This cluster is related to genetic loci employed by human gut bacteria to digest fungal α-mannan. Metagenomes from the Hel_I_6 isolation site revealed increasing GH76 gene frequencies in free-living bacteria during microalgae blooms, suggesting degradation of α-1,6-mannans from fungi. Recombinant ShGH76 protein activity assays with yeast α-mannan and synthetic oligomannans showed endo-α-1,6-mannanase activity. Resolved structures of apo-ShGH76 (2.0 Å) and of mutants co-crystalized with fungal mannan-mimicking α-1,6-mannotetrose (1.90 Å) and α-1,6-mannotriose (1.47 Å) retained the canonical (α/α)6 fold, despite low identities with sequences of known GH76 structures (GH76s from gut bacteria: <27%). The apo-form active site differed from those known from gut bacteria, and co-crystallizations revealed a kinked oligomannan conformation. Co-crystallizations also revealed precise molecular-scale interactions of ShGH76 with fungal mannan-mimicking oligomannans, indicating adaptation to this particular type of substrate. Our data hence suggest presence of yet unknown fungal α-1,6-mannans in marine ecosystems, in particular during microalgal blooms.
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12
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Roik A, Reverter M, Pogoreutz C. A roadmap to understanding diversity and function of coral reef-associated fungi. FEMS Microbiol Rev 2022; 46:6615459. [PMID: 35746877 PMCID: PMC9629503 DOI: 10.1093/femsre/fuac028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 06/01/2022] [Accepted: 06/14/2022] [Indexed: 01/09/2023] Open
Abstract
Tropical coral reefs are hotspots of marine productivity, owing to the association of reef-building corals with endosymbiotic algae and metabolically diverse bacterial communities. However, the functional importance of fungi, well-known for their contribution to shaping terrestrial ecosystems and global nutrient cycles, remains underexplored on coral reefs. We here conceptualize how fungal functional traits may have facilitated the spread, diversification, and ecological adaptation of marine fungi on coral reefs. We propose that functions of reef-associated fungi may be diverse and go beyond their hitherto described roles of pathogens and bioeroders, including but not limited to reef-scale biogeochemical cycles and the structuring of coral-associated and environmental microbiomes via chemical mediation. Recent technological and conceptual advances will allow the elucidation of the physiological, ecological, and chemical contributions of understudied marine fungi to coral holobiont and reef ecosystem functioning and health and may help provide an outlook for reef management actions.
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Affiliation(s)
- Anna Roik
- Corresponding author: Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Ammerländer Heerstrasse 231, D-26129 Oldenburg, Germany. E-mail:
| | - Miriam Reverter
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University of Oldenburg, Wilhelmshaven, 26046, Germany,School of Biological and Marine Sciences, University of Plymouth, Plymouth PL4 8AA, United Kingdom
| | - Claudia Pogoreutz
- Corresponding author: Laboratory for Biological Geochemistry, School of Architecture, Civil and Environmental Engineering, Ecole Polytechnique Federale de Lausanne (EPFL), 1015 Lausanne, Switzerland.,
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Sehein TR, Gast RJ, Pachiadaki M, Guillou L, Edgcomb VP. Parasitic infections by Group II Syndiniales target selected dinoflagellate host populations within diverse protist assemblages in a model coastal pond. Environ Microbiol 2022; 24:1818-1834. [PMID: 35315564 DOI: 10.1111/1462-2920.15977] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 03/13/2022] [Indexed: 11/29/2022]
Abstract
Protists are integral to marine food webs and biogeochemical cycles; however, there is a paucity of data describing specific ecological niches for some of the most abundant taxa in marker gene libraries. Syndiniales are one such group, often representing the majority of sequence reads recovered from picoplankton samples across the global ocean. However, the prevalence and impacts of syndinian parasitism in marine environments remains unclear. We began to address these critical knowledge gaps by generating a high-resolution time series (March-October 2018) in a productive coastal pond. Seasonal shifts in protist populations, including parasitic Syndiniales, were documented during periods of higher primary productivity and increased summer temperature-driven stratification. Elevated concentrations of infected hosts and free-living parasite spores occurred at nearly monthly intervals in July, August, and September. We suggest intensifying stratification during this period correlated with the increased prevalence of dinoflagellates that were parasitized by Group II Syndiniales. Infections in some protist populations were comparable to previously reported large single-taxon dinoflagellate blooms. Infection dynamics in Salt Pond demonstrated the propagation of syndinian parasites through mixed protist assemblages and highlighted patterns of host/parasite interactions that better reflect many other marine environments where single taxon blooms are uncommon.
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Affiliation(s)
- Taylor R Sehein
- MIT-WHOI Joint Program in Biological Oceanography, Cambridge and Woods Hole, MA, United States
| | - Rebecca J Gast
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Maria Pachiadaki
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
| | - Laure Guillou
- Sorbonne Université & Centre National pour la Recherche Scientifique, Station Biologique de Roscoff, UMR7144, Roscoff, France
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA, United States
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14
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Ilicic D, Woodhouse J, Karsten U, Zimmermann J, Wichard T, Quartino ML, Campana GL, Livenets A, Van den Wyngaert S, Grossart HP. Antarctic Glacial Meltwater Impacts the Diversity of Fungal Parasites Associated With Benthic Diatoms in Shallow Coastal Zones. Front Microbiol 2022; 13:805694. [PMID: 35308360 PMCID: PMC8931407 DOI: 10.3389/fmicb.2022.805694] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 01/12/2022] [Indexed: 01/04/2023] Open
Abstract
Aquatic ecosystems are frequently overlooked as fungal habitats, although there is increasing evidence that their diversity and ecological importance are greater than previously considered. Aquatic fungi are critical and abundant components of nutrient cycling and food web dynamics, e.g., exerting top-down control on phytoplankton communities and forming symbioses with many marine microorganisms. However, their relevance for microphytobenthic communities is almost unexplored. In the light of global warming, polar regions face extreme changes in abiotic factors with a severe impact on biodiversity and ecosystem functioning. Therefore, this study aimed to describe, for the first time, fungal diversity in Antarctic benthic habitats along the salinity gradient and to determine the co-occurrence of fungal parasites with their algal hosts, which were dominated by benthic diatoms. Our results reveal that Ascomycota and Chytridiomycota are the most abundant fungal taxa in these habitats. We show that also in Antarctic waters, salinity has a major impact on shaping not just fungal but rather the whole eukaryotic community composition, with a diversity of aquatic fungi increasing as salinity decreases. Moreover, we determined correlations between putative fungal parasites and potential benthic diatom hosts, highlighting the need for further systematic analysis of fungal diversity along with studies on taxonomy and ecological roles of Chytridiomycota.
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Affiliation(s)
- Doris Ilicic
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | - Jason Woodhouse
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | - Ulf Karsten
- Institute of Biological Sciences, Applied Ecology and Phycology, University of Rostock, Rostock, Germany
| | - Jonas Zimmermann
- Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, Berlin, Germany
| | - Thomas Wichard
- Institute for Inorganic and Analytical Chemistry, Friedrich-Schiller-University Jena, Jena, Germany
| | | | - Gabriela Laura Campana
- Department of Coastal Biology, Argentinean Antarctic Institute, Buenos Aires, Argentina
- Department of Basic Sciences, National University of Luján, Luján, Buenos Aires, Argentina
| | - Alexandra Livenets
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
| | | | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Neuglobsow, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- *Correspondence: Hans-Peter Grossart,
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15
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Pham TT, Dinh KV, Nguyen VD. Biodiversity and Enzyme Activity of Marine Fungi with 28 New Records from the Tropical Coastal Ecosystems in Vietnam. MYCOBIOLOGY 2021; 49:559-581. [PMID: 35035248 PMCID: PMC8725946 DOI: 10.1080/12298093.2021.2008103] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 11/09/2021] [Accepted: 11/15/2021] [Indexed: 06/14/2023]
Abstract
The coastal marine ecosystems of Vietnam are one of the global biodiversity hotspots, but the biodiversity of marine fungi is not well known. To fill this major gap of knowledge, we assessed the genetic diversity (ITS sequence) of 75 fungal strains isolated from 11 surface coastal marine and deeper waters in Nha Trang Bay and Van Phong Bay using a culture-dependent approach and 5 OTUs (Operational Taxonomic Units) of fungi in three representative sampling sites using next-generation sequencing. The results from both approaches shared similar fungal taxonomy to the most abundant phylum (Ascomycota), genera (Candida and Aspergillus) and species (Candida blankii) but were different at less common taxa. Culturable fungal strains in this study belong to 3 phyla, 5 subdivisions, 7 classes, 12 orders, 17 families, 22 genera and at least 40 species, of which 29 species have been identified and several species are likely novel. Among identified species, 12 and 28 are new records in global and Vietnamese marine areas, respectively. The analysis of enzyme activity and the checklist of trophic mode and guild assignment provided valuable additional biological information and suggested the ecological function of planktonic fungi in the marine food web. This is the largest dataset of marine fungal biodiversity on morphology, phylogeny and enzyme activity in the tropical coastal ecosystems of Vietnam and Southeast Asia. Biogeographic aspects, ecological factors and human impact may structure mycoplankton communities in such aquatic habitats.
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Affiliation(s)
- Thu Thuy Pham
- Institute of Biotechnology and Environment, Nha Trang University, Nha Trang, Vietnam
| | - Khuong V. Dinh
- Institute of Aquaculture, Nha Trang University, Nha Trang, Vietnam
| | - Van Duy Nguyen
- Institute of Biotechnology and Environment, Nha Trang University, Nha Trang, Vietnam
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16
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Wietz M, Bienhold C, Metfies K, Torres-Valdés S, von Appen WJ, Salter I, Boetius A. The polar night shift: seasonal dynamics and drivers of Arctic Ocean microbiomes revealed by autonomous sampling. ISME COMMUNICATIONS 2021; 1:76. [PMID: 37938651 PMCID: PMC9723606 DOI: 10.1038/s43705-021-00074-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 11/03/2021] [Accepted: 11/15/2021] [Indexed: 06/15/2023]
Abstract
The Arctic Ocean features extreme seasonal differences in daylight, temperature, ice cover, and mixed layer depth. However, the diversity and ecology of microbes across these contrasting environmental conditions remain enigmatic. Here, using autonomous samplers and sensors deployed at two mooring sites, we portray an annual cycle of microbial diversity, nutrient concentrations and physical oceanography in the major hydrographic regimes of the Fram Strait. The ice-free West Spitsbergen Current displayed a marked separation into a productive summer (dominated by diatoms and carbohydrate-degrading bacteria) and regenerative winter state (dominated by heterotrophic Syndiniales, radiolarians, chemoautotrophic bacteria, and archaea). The autumn post-bloom with maximal nutrient depletion featured Coscinodiscophyceae, Rhodobacteraceae (e.g. Amylibacter) and the SAR116 clade. Winter replenishment of nitrate, silicate and phosphate, linked to vertical mixing and a unique microbiome that included Magnetospiraceae and Dadabacteriales, fueled the following phytoplankton bloom. The spring-summer succession of Phaeocystis, Grammonema and Thalassiosira coincided with ephemeral peaks of Aurantivirga, Formosa, Polaribacter and NS lineages, indicating metabolic relationships. In the East Greenland Current, deeper sampling depth, ice cover and polar water masses concurred with weaker seasonality and a stronger heterotrophic signature. The ice-related winter microbiome comprised Bacillaria, Naviculales, Polarella, Chrysophyceae and Flavobacterium ASVs. Low ice cover and advection of Atlantic Water coincided with diminished abundances of chemoautotrophic bacteria while others such as Phaeocystis increased, suggesting that Atlantification alters microbiome structure and eventually the biological carbon pump. These insights promote the understanding of microbial seasonality and polar night ecology in the Arctic Ocean, a region severely affected by climate change.
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Affiliation(s)
- Matthias Wietz
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Christina Bienhold
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katja Metfies
- Polar Biological Oceanography, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Sinhué Torres-Valdés
- Marine BioGeoScience, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Wilken-Jon von Appen
- Physical Oceanography of the Polar Seas, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Ian Salter
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Faroe Marine Research Institute, Tórshavn, Faroe Islands
| | - Antje Boetius
- Deep-Sea Ecology and Technology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
- MARUM Center for Marine Environmental Sciences, University of Bremen, Bremen, Germany.
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17
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Reñé A, Alacid E, Gallisai R, Chambouvet A, Fernández-Valero AD, Garcés E. New Perkinsea Parasitoids of Dinoflagellates Distantly Related to Parviluciferaceae Members. Front Microbiol 2021; 12:701196. [PMID: 34421856 PMCID: PMC8375308 DOI: 10.3389/fmicb.2021.701196] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/12/2021] [Indexed: 11/16/2022] Open
Abstract
Perkinsea is a phylogenetic group of protists that includes parasites of distantly related hosts. However, its diversity is still mainly composed of environmental sequences, mostly obtained from freshwater environments. Efforts to isolate and culture parasitoids of dinoflagellates have led to the description of several phylogenetically closely related species constituting the Parviluciferaceae family. In this study, two new parasitoid species infecting dinoflagellates during recurrent coastal blooms are reported. Using the ribosomal RNA (rRNA) gene phylogenies, we show that both cluster within Perkinsea, one of them at the base of Parviluciferaceae and the other in a distinct branch unrelated to other described species. The establishment of host-parasite lab cultures of the latter allowed its morphological characterization, resulting in the formal description of Maranthos nigrum gen. nov., sp. nov. The life-cycle development of the two parasitoids is generally the same as that of other members of the Parviluciferaceae family but they differ in the features of the trophont and sporont stages, including the arrangement of zoospores during the mature sporangium stage and the lack of specialized structures that release the zoospores into the environment. Laboratory cross-infection experiments showed that the parasitoid host range is restricted to dinoflagellates, although it extends across several different genera. The maximum prevalence reached in the tested host populations was lower than in other Parviluciferaceae members. The findings from this study suggest that Perkinsea representatives infecting dinoflagellates are more widespread than previously thought.
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Affiliation(s)
- Albert Reñé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Elisabet Alacid
- Living Systems Institute, School of Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom.,Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Rachele Gallisai
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | | | - Alan D Fernández-Valero
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Barcelona, Spain
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC), Barcelona, Spain
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Buaya AT, Scholz B, Thines M. A New Marine Species of Miracula ( Oomycota) Parasitic to Minidiscus sp. in Iceland †. MYCOBIOLOGY 2021; 49:355-362. [PMID: 34512079 PMCID: PMC8409938 DOI: 10.1080/12298093.2021.1952813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 06/29/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
Obligate endoparasitic oomycetes are known to ubiquitously occur in marine and freshwater diatoms, but their diversity is still largely unexplored. Many of these parasitoids are members of the early-diverging oomycete lineages (Miracula, Diatomophthora), others are within the Leptomitales of the Saprolegniomycetes (Ectrogella, Lagenisma) and some have been described in the Peronosporomycetes (Aphanomycopsis, Lagenidium). Even though some species have been recently described and two new genera were introduced (Miracula and Diatomophthora), the phylogeny and taxonomy of most of these organisms remain unresolved. This is contrasted by the high number of sequences from unclassified species, as recently revealed from environmental sequencing, suggesting the presence of several undiscovered species. In this study, a new species of Miracula is reported from a marine centric diatom (Minidiscus sp.) isolated from Skagaströnd harbor in Northwest Iceland. The morphology and life cycle traits of this novel oomycete parasite are described herein, and its taxonomic placement within the genus Miracula is confirmed by molecular phylogeny. As it cannot be assigned to any previously described species, it is introduced as Miracula islandica in this study. The genus Miracula thus contains three described holocarpic species (M. helgolandica, M. islandica, M. moenusica) to which likely additional species will need to be added in the future, considering the presence of several lineages known only from environmental sequencing that clustered within the Miracula clade.
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Affiliation(s)
- Anthony T. Buaya
- Senckenberg Biodiversity and Climate Research Center, Frankfurt am Main, Germany
| | | | - Marco Thines
- Senckenberg Biodiversity and Climate Research Center, Frankfurt am Main, Germany
- Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Goethe-Universität Frankfurt am Main, Frankfurt am Main, Germany
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19
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Tomaru Y, Yamaguchi H, Miki T. Growth Rate-dependent Cell Death of Diatoms due to Viral Infection and Their Subsequent Coexistence in a Semi-continuous Culture System. Microbes Environ 2021; 36. [PMID: 33390375 PMCID: PMC7966941 DOI: 10.1264/jsme2.me20116] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Viral infections are a major factor in diatom cell death. However, the effects of viruses on diatom dynamics remain unclear. Based on laboratory studies, it is hypothesized that virus-induced diatom mortality is dependent on the diatom growth rate. The present study aimed to elucidate the relationship between the diatom growth rate and virus-induced mortality using model systems of the marine planktonic diatom, Chaetoceros tenuissimus and its infectious viruses. We also examined the fate of diatom populations in a semi-continuous dilution culture system, in which host growth rates were controlled at 0.69, 2.08, and 3.47 day–1. Diatom populations gradually decreased following the viral inoculation of each culture system, and virus-induced mortality inversely correlated with the diatom growth rate. Furthermore, the viral burst size was slightly higher in lower growth rate cultures. These results suggested that the host physiological status related to the growth rate affected viral infection and proliferation. Diatom populations were not completely lysed or washed out in any of the dilution systems; they showed steady growth in the presence of infectious viruses. This may be partially explained by defective interference particles from viruses and cell debris. The present results indicate that diatoms in dilution environments maintain their populations, even under viral pressure. Moreover, diatom populations with a low growth rate may partially sustain higher growth populations through nutrient recycling following virus-induced cell death. The results of the present study provide insights into diatom dynamics in natural environments in the presence of infectious viruses.
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Affiliation(s)
- Yuji Tomaru
- Hatsukaichi Field Station, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, National Research and Development Agency
| | | | - Takeshi Miki
- Ecology and Environmental Engineering, Faculty of Advanced Science and Technology, Ryukoku University
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21
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Lin J, Yan H, Zhao L, Li Y, Nahidian B, Zhu M, Hu Q, Han D. Interaction between the cell walls of microalgal host and fungal carbohydrate-activate enzymes is essential for the pathogenic parasitism process. Environ Microbiol 2021; 23:5114-5130. [PMID: 33723900 DOI: 10.1111/1462-2920.15465] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 02/07/2021] [Accepted: 03/13/2021] [Indexed: 12/22/2022]
Abstract
Fungi can parasitize microalgae, exerting profound impacts on both the aquatic ecosystems and microalgal mass cultures. In this study, the unicellular green alga Haematococcus pluvialis and the blastocladialean fungus Paraphysoderma sedebokerense were used as a model system to address the mechanisms underlying the fungal parasitism on the algal host. High-throughput metabolic assay indicated that P. sedebokerense can utilize several carbon sources with a preference for mannose, glucose and their oligosaccharides, which was compatible with the profile of the host algal cell walls enriched with glucan and mannan. The results of dual transcriptomics analysis suggested that P. sedebokerense can upregulate a large number of putative carbohydrate-activate enzymes (CAZymes) encoding genes, including those coding for the endo-1,4-β-glucanase and endo-1,4-β-mannanase during the infection process. The cell walls of H. pluvialis can be decomposed by both P. sedebokerense and commercial CAZymes (e.g. cellulase and endo-1,4-β-mannanase) to produce mannooligomers, while several putative parasitism-related genes of P. sedebokerense can be in turn upregulated by mannooligomers. In addition, the parasitism can be blocked by interfering the selected CAZymes including glucanase, mannanase and lysozyme with the specific inhibitors, which provided a framework for screening suitable compounds for pathogen mitigation in algal mass culture.
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Affiliation(s)
- Juan Lin
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,Poyang Lake Eco-economy Research Center, Jiujiang University, Jiujiang, 332005, China
| | - Hailong Yan
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang Zhao
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yanhua Li
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Bahareh Nahidian
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Mianmian Zhu
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qiang Hu
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,Institute for Advanced Study, Shenzhen University, Shenzhen, 51806, China.,Key Laboratory for Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Danxiang Han
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China.,Key Laboratory for Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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22
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Parasitoid chytridiomycete Ericiomyces syringoforeus gen. et sp. nov. has unique cellular structures to infect the host. Mycol Prog 2021. [DOI: 10.1007/s11557-020-01652-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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23
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Käse L, Metfies K, Neuhaus S, Boersma M, Wiltshire KH, Kraberg AC. Host-parasitoid associations in marine planktonic time series: Can metabarcoding help reveal them? PLoS One 2021; 16:e0244817. [PMID: 33411833 PMCID: PMC7790432 DOI: 10.1371/journal.pone.0244817] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 12/16/2020] [Indexed: 11/26/2022] Open
Abstract
In this study, we created a dataset of a continuous three-year 18S metabarcoding survey to identify eukaryotic parasitoids, and potential connections to hosts at the Long-Term Ecological Research station Helgoland Roads. The importance of parasites and parasitoids for food web dynamics has previously been recognized mostly in terrestrial and freshwater systems, while marine planktonic parasitoids have been understudied in comparison to those. Therefore, the occurrence and role of parasites and parasitoids remains mostly unconsidered in the marine environment. We observed high abundances and diversity of parasitoid operational taxonomic units in our dataset all year round. While some parasitoid groups were present throughout the year and merely fluctuated in abundances, we also detected a succession of parasitoid groups with peaks of individual species only during certain seasons. Using co-occurrence and patterns of seasonal occurrence, we were able to identify known host-parasitoid dynamics, however identification of new potential host-parasitoid interactions was not possible due to their high dynamics and variability in the dataset.
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Affiliation(s)
- Laura Käse
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Schleswig-Holstein, Germany
| | - Katja Metfies
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Bremen, Germany
- Helmholtz-Institut für Funktionelle Marine Biodiversität, Oldenburg, Germany
| | - Stefan Neuhaus
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Bremen, Germany
| | - Maarten Boersma
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Schleswig-Holstein, Germany
- University of Bremen, Bremen, Bremen, Germany
| | - Karen Helen Wiltshire
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Biologische Anstalt Helgoland, Helgoland, Schleswig-Holstein, Germany
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Wadden Sea Station, List auf Sylt, Schleswig-Holstein, Germany
| | - Alexandra Claudia Kraberg
- Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar- und Meeresforschung, Bremerhaven, Bremen, Germany
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24
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Priest T, Fuchs B, Amann R, Reich M. Diversity and biomass dynamics of unicellular marine fungi during a spring phytoplankton bloom. Environ Microbiol 2020; 23:448-463. [PMID: 33201558 DOI: 10.1111/1462-2920.15331] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/01/2022]
Abstract
Microbial communities have important functions during spring phytoplankton blooms, regulating bloom dynamics and processing organic matter. Despite extensive research into such processes, an in-depth assessment of the fungal component is missing, especially for the smaller size fractions. We investigated the dynamics of unicellular mycoplankton during a spring phytoplankton bloom in the North Sea by 18S rRNA gene tag sequencing and a modified CARD-FISH protocol. Visualization and enumeration of dominant taxa revealed unique cell count patterns that varied considerably over short time scales. The Rozellomycota sensu lato (s.l.) reached a maximum of 105 cells L-1 , being comparable to freshwater counts. The abundance of Dikarya surpassed previous values by two orders of magnitude (105 cells L-1 ) and the corresponding biomass (maximum of 8.9 mg C m-3 ) was comparable to one reported for filamentous fungi with assigned ecological importance. Our results show that unicellular fungi are an abundant and, based on high cellular ribosome content and fast dynamics, active part of coastal microbial communities. The known ecology of the visualized taxa and the observed dynamics suggest the existence of different ecological niches that link primary and secondary food chains, highlighting the importance of unicellular fungi in food web structures and carbon transfer.
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Affiliation(s)
- Taylor Priest
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Bernhard Fuchs
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Marlis Reich
- Molecular Ecology Group, FB2, University of Bremen, Bremen, Germany
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25
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Hittorf M, Letsch-Praxmarer S, Windegger A, Bass D, Kirchmair M, Neuhauser S. Revised Taxonomy and Expanded Biodiversity of the Phytomyxea (Rhizaria, Endomyxa). J Eukaryot Microbiol 2020; 67:648-659. [PMID: 32654223 PMCID: PMC7756720 DOI: 10.1111/jeu.12817] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 05/21/2020] [Accepted: 06/25/2020] [Indexed: 12/27/2022]
Abstract
Phytomyxea (phytomyxids) is a group of obligate biotrophic pathogens belonging to the Rhizaria. Some phytomyxids are well studied and include known plant pathogens such as Plasmodiophora brassicae, the causal agent of clubroot disease. Despite this economic importance, the taxonomy and biodiversity of this group are largely cryptic, with many species described in the premolecular area. Some of these species were key for establishing the morphotaxonomic concepts that define most genera to this day, but systematic efforts to include and integrate those species into molecular studies are still lacking. The aim of this study was to expand our understanding of phytomyxid biodiversity in terrestrial environments. Thirty-eight environmental samples from habitats in which novel and known diversity of Phytomyxea was expected were analysed. We were able to generate 18S rRNA sequences from Ligniera verrucosa, a species which is well defined based on ultrastructure. Phylogenetic analyses of the collected sequences rendered the genera Lignera, Plasmodiophora and Spongospora polyphyletic, and identified two novel and apparently diverse lineages (clade 17, clade 18). Based on these findings and on data from previous studies, we formally establish the new genera Pseudoligniera n. gen. for L. verrucosa,Hillenburgia n. gen. for Spongospora nasturtii and revert Plasmodiophora diplantherae to its original name Ostenfeldiella diplantherae.
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Affiliation(s)
- Michaela Hittorf
- Institute of Microbiology, University of Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria
| | | | - Alexandra Windegger
- Institute of Microbiology, University of Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria
| | - David Bass
- Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, United Kingdom.,Centre for Environment, Fisheries and Aquaculture Science (Cefas), Barrack Road, The Nothe, Weymouth, DT4 8UB, United Kingdom
| | - Martin Kirchmair
- Institute of Microbiology, University of Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria
| | - Sigrid Neuhauser
- Institute of Microbiology, University of Innsbruck, Technikerstr. 25, 6020, Innsbruck, Austria
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26
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Luo Y, Wei X, Yang S, Gao YH, Luo ZH. Fungal diversity in deep-sea sediments from the Magellan seamounts as revealed by a metabarcoding approach targeting the ITS2 regions. Mycology 2020; 11:214-229. [PMID: 33062383 PMCID: PMC7534268 DOI: 10.1080/21501203.2020.1799878] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 07/03/2020] [Indexed: 12/11/2022] Open
Abstract
Recent reports have revealed diverse and abundant fungal communities in the deep-sea biosphere, while their composition, distribution, and variations in seamount zones are poorly understood. Using a metabarcoding approach targeting the ITS2 regions, we present the structure of the fungal community in 18 sediment samples from the Magellan seamount area of the northwest Pacific. A total of 1,979 fungal OTUs was obtained, which were taxonomically assigned to seven phyla, 17 classes, 43 orders, 7 families, and 98 genera. The majority of these OTUs were affiliated to Basidiomycota (873 OTUs, 44.11% of total OTUs) and Ascomycota (486 OTUs, 24.56% of total OTUs), followed by other five minor phyla (Mortierellomycota, Chytridiomycota, Mucoromycota, Glomeromycota, and Monoblepharidomycota). Sordriomycetes is the most abundant class, followed by Eurotiomycetes, and Dothideomycetes. Five genera were common in most of the samples, including worldwide reported genera Aspergillus, Cladosporium, Fusarium, Chaetomium, and Penicillium. The environmental data we collected (sampling depth, sampling location latitude and longitude, organic carbon content, and organic nitrogen content in the sediment) had no significant influence on the composition and distribution of fungal communities. Our findings provide valuable information for understanding the distribution and potential ecological functions of fungi in the deep-sea sediments of the Magellan seamounts.
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Affiliation(s)
- Ye Luo
- Key Laboratory of Marine Biogenetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, PR China
| | - Xu Wei
- Key Laboratory of Marine Biogenetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, PR China
| | - Shuai Yang
- Key Laboratory of Marine Biogenetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, PR China
| | - Yuan-Hao Gao
- Key Laboratory of Marine Biogenetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, PR China
| | - Zhu-Hua Luo
- Key Laboratory of Marine Biogenetic Resources, Ministry of Natural Resources, Third Institute of Oceanography, Xiamen, PR China
- School of Marine Sciences, Nanjing University of Information Science & Technology, Nanjing, PR China
- Co-Innovation Center of Jiangsu Marine Bioindustry Technology, Jiangsu Ocean University, Lianyungang, PR China
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27
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Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome. Nat Microbiol 2020; 5:1262-1270. [PMID: 32690954 PMCID: PMC7508674 DOI: 10.1038/s41564-020-0755-4] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 06/16/2020] [Indexed: 12/26/2022]
Abstract
RNA viruses in aquatic environments remain poorly studied. Here, we analysed the RNA virome from approximately 10 l water from Yangshan Deep-Water Harbour near the Yangtze River estuary in China and identified more than 4,500 distinct RNA viruses, doubling the previously known set of viruses. Phylogenomic analysis identified several major lineages, roughly, at the taxonomic ranks of class, order and family. The 719-member-strong Yangshan virus assemblage is the sister clade to the expansive class Alsuviricetes and consists of viruses with simple genomes that typically encode only RNA-dependent RNA polymerase (RdRP), capping enzyme and capsid protein. Several clades within the Yangshan assemblage independently evolved domain permutation in the RdRP. Another previously unknown clade shares ancestry with Potyviridae, the largest known plant virus family. The ‘Aquatic picorna-like viruses/Marnaviridae’ clade was greatly expanded, with more than 800 added viruses. Several RdRP-linked protein domains not previously detected in any RNA viruses were identified, such as the small ubiquitin-like modifier (SUMO) domain, phospholipase A2 and PrsW-family protease domain. Multiple viruses utilize alternative genetic codes implying protist (especially ciliate) hosts. The results reveal a vast RNA virome that includes many previously unknown groups. However, phylogenetic analysis of the RdRPs supports the previously established five-branch structure of the RNA virus evolutionary tree, with no additional phyla. Metagenomic analysis of a single RNA virome from the Yangshan Deep-Water Harbour in China enabled the recovery of more than 4,500 distinct RNA viruses, doubling the known set of RNA viruses to date, and provided insights into their biology.
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28
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Possible control of acute outbreaks of a marine fungal pathogen by nominally herbivorous tropical reef fish. Oecologia 2020; 193:603-617. [PMID: 32656606 PMCID: PMC7406524 DOI: 10.1007/s00442-020-04697-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 06/11/2020] [Indexed: 11/07/2022]
Abstract
Primary producers in terrestrial and marine systems can be affected by fungal pathogens threatening the provision of critical ecosystem services. Crustose coralline algae (CCA) are ecologically important members of tropical reef systems and are impacted by coralline fungal disease (CFD) which manifests as overgrowth of the CCA crust by fungal lesions causing partial to complete mortality of the CCA host. No natural controls for CFD have been identified, but nominally herbivorous fish could play a role by consuming pathogenic fungi. We documented preferential grazing on fungal lesions by adults of six common reef-dwelling species of herbivorous Acanthuridae and Labridae, (surgeonfish and parrotfish) which collectively demonstrated an ~ 80-fold higher grazing rate on fungal lesions relative to their proportionate benthic coverage, and a preference for lesions over other palatable substrata (e.g. live scleractinian coral, CCA, or algae). Furthermore, we recorded a ~ 600% increase in live CFD lesion size over an approximately 2-week period when grazing by herbivorous fish was experimentally excluded suggesting that herbivorous reef fish could control CFD progression by directly reducing biomass of the fungal pathogen. Removal rates may be sufficient to allow CCA to recover from infection and explain historically observed natural waning behaviour after an outbreak. Thus, in addition to their well-known role as determinants of macroalgal overgrowth of reefs, herbivorous fish could thus also be important in control of diseases affecting crustose coralline algae that stabilize the foundation of coral reef substrata.
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29
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Metfies K, Hessel J, Klenk R, Petersen W, Wiltshire KH, Kraberg A. Uncovering the intricacies of microbial community dynamics at Helgoland Roads at the end of a spring bloom using automated sampling and 18S meta-barcoding. PLoS One 2020; 15:e0233921. [PMID: 32569285 PMCID: PMC7307782 DOI: 10.1371/journal.pone.0233921] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 05/14/2020] [Indexed: 11/19/2022] Open
Abstract
In May 2016, the remote-controlled Automated Filtration System for Marine Microbes (AUTOFIM) was implemented in parallel to the Long Term Ecological Research (LTER) observatory Helgoland Roads in the German Bight. We collected samples for characterization of dynamics within the eukaryotic microbial communities at the end of a phytoplankton bloom via 18S meta-barcoding. Understanding consequences of environmental change for key marine ecosystem processes, such as phytoplankton bloom dynamics requires information on biodiversity and species occurrences with adequate temporal and taxonomic resolution via time series observations. Sampling automation and molecular high throughput methods can serve these needs by improving the resolution of current conventional marine time series observations. A technical evaluation based on an investigation of eukaryotic microbes using the partial 18S rRNA gene suggests that automated filtration with the AUTOFIM device and preservation of the plankton samples leads to highly similar 18S community profiles, compared to manual filtration and snap freezing. The molecular data were correlated with conventional microscopic counts. Overall, we observed substantial change in the eukaryotic microbial community structure during the observation period. A simultaneous decline of diatom and ciliate sequences succeeded a peak of Miracula helgolandica, suggesting a potential impact of these oomycete parasites on diatom bloom dynamics and phenology in the North Sea. As oomycetes are not routinely counted at Helgoland Roads LTER, our findings illustrate the benefits of combining automated filtration with metabarcodingto augment classical time series observations, particularly for taxa currently neglected due to methodological constraints.
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Affiliation(s)
- Katja Metfies
- Helmholtz Young Investigators Group PLANKTOSENS, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
| | - Johanna Hessel
- Helmholtz Young Investigators Group PLANKTOSENS, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Robin Klenk
- Biologische Anstalt Helgoland, Shelf Sea System Ecology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Helgoland, Germany
| | - Wilhelm Petersen
- Institute of Coastal Research, Helmholtz Zentrum Geesthacht Centre for Materials and Coastal Research, Geesthacht, Germany
| | - Karen Helen Wiltshire
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
- Biologische Anstalt Helgoland Coastal Ecology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, List, Germany
| | - Alexandra Kraberg
- Biologische Anstalt Helgoland, Shelf Sea System Ecology, Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Helgoland, Germany
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30
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Buaya A, Thines M. Diatomophthoraceae - a new family of olpidiopsis-like diatom parasitoids largely unrelated to Ectrogella. Fungal Syst Evol 2020; 5:113-118. [PMID: 32467917 PMCID: PMC7250014 DOI: 10.3114/fuse.2020.05.06] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The oomycete genus Ectrogella currently comprises a rather heterogeneous group of obligate endoparasitoids, mostly of diatoms and algae. Despite their widespread occurrence, little is known regarding the phylogenetic affinities of these bizarre organisms. Traditionally, the genus was included within the Saprolegniales, based on zoospore diplanetism and a saprolegnia/achlya-like zoospore discharge. The genus has undergone multiple re-definitions in the past, and has often been used largely indiscriminately for oomycetes forming sausage-like thalli in diatoms. While the phylogenetic affinity of the polyphyletic genus Olpidiopsis has recently been partially resolved, taxonomic placement of the genus Ectrogella remained unresolved, as no sequence data were available for species of this genus. In this study, we report the phylogenetic placement of Ectrogella bacillariacearum infecting the freshwater diatom Nitzschia sigmoidea. The phylogenetic reconstruction shows that Ectrogella bacillariacearum is grouped among the early diverging lineages of the Saprolegniomycetes with high support, and is unrelated to the monophyletic diatom-infecting olpidiopsis-like species. As these species are neither related to Ectrogella, nor to the early diverging lineages of Olpidiopsis s. str. and Miracula, they are placed in a new genus, Diatomophthora, in the present study.
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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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31
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Hassett BT. A Widely Distributed Thraustochytrid Parasite of Diatoms Isolated from the Arctic Represents a gen. and sp. nov. J Eukaryot Microbiol 2020; 67:480-490. [DOI: 10.1111/jeu.12796] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 03/23/2020] [Accepted: 03/25/2020] [Indexed: 01/06/2023]
Affiliation(s)
- Brandon T. Hassett
- UiT Norges arktiske universtiet, BFE, NFH bygget Framstredet 6 9019 Tromsø Norway
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32
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Kilias ES, Junges L, Šupraha L, Leonard G, Metfies K, Richards TA. Chytrid fungi distribution and co-occurrence with diatoms correlate with sea ice melt in the Arctic Ocean. Commun Biol 2020; 3:183. [PMID: 32317738 PMCID: PMC7174370 DOI: 10.1038/s42003-020-0891-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 03/09/2020] [Indexed: 11/09/2022] Open
Abstract
Global warming is rapidly altering physicochemical attributes of Arctic waters. These changes are predicted to alter microbial networks, potentially perturbing wider community functions including parasite infections and saprotrophic recycling of biogeochemical compounds. Specifically, the interaction between autotrophic phytoplankton and heterotrophic fungi e.g. chytrids (fungi with swimming tails) requires further analysis. Here, we investigate the diversity and distribution patterns of fungi in relation to abiotic variables during one record sea ice minimum in 2012 and explore co-occurrence of chytrids with diatoms, key primary producers in these changing environments. We show that chytrid fungi are primarily encountered at sites influenced by sea ice melt. Furthermore, chytrid representation positively correlates with sea ice-associated diatoms such as Fragilariopsis or Nitzschia. Our findings identify a potential future scenario where chytrid representation within these communities increases as a consequence of ice retreat, further altering community structure through perturbation of parasitic or saprotrophic interaction networks. Estelle. S. Kilias et al. show that chytrid fungi exhibiting swimming tales are primarily encountered at sites influenced by sea ice melt and that its representation positively correlates with sea ice-associated diatoms. This study predicts that chytrid representation within its Arctic communities may increase as ice retreats further.
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Affiliation(s)
- Estelle S Kilias
- University of Exeter, Bioscience, Living System Institute, Exeter, UK. .,University of Oxford, Department of Zoology, Oxford, UK.
| | - Leandro Junges
- Centre for Systems Modelling and Quantitative Biomedicine, University of Birmingham, Birmingham, UK.,Institute of Metabolism and Systems Research, University of Birmingham, Birmingham, UK
| | - Luka Šupraha
- University of Oslo, Department of Biosciences, Oslo, Norway
| | - Guy Leonard
- University of Oxford, Department of Zoology, Oxford, UK
| | - Katja Metfies
- Alfred Wegener Institute for Polar and Marine Research, Bremerhaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
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33
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Buaya AT, Thines M. Bolbea parasitica gen. et sp. nov., a cultivable holocarpic parasitoid of the early-diverging Saprolegniomycetes. Fungal Syst Evol 2020; 6:129-137. [PMID: 32904153 PMCID: PMC7451777 DOI: 10.3114/fuse.2020.06.07] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Holocarpic oomycetes convert their entire cytoplasm into zoospores and thus do not form dedicated sporangia or hyphal compartments for asexual reproduction. The majority of holocarpic oomycetes are obligate parasites and parasitoids of a diverse suite of organisms, among them green and red algae, brown seaweeds, diatoms, fungi, oomycetes and invertebrates. Most of them are found among the early diverging oomycetes or the Peronosporomycetes, and some in the early-diverging Saprolegniomycetes (Leptomitales). The obligate parasitism renders it difficult to study some of these organisms. Only a few members of the genus Haliphthoross. l. have been cultured without their hosts, and of the parasitoid Leptomitales, some transient cultures have been established, which are difficult to maintain. Here, the cultivation of a new holocarpic oomycete genus of the Leptomitales, Bolbea, is presented. Bolbea is parasitic to ostracods, is readily cultivable on malt extract agar, and upon contact with water converts its cytoplasm into zoospores. Its morphology and phylogenetic relationships are reported. Due to the ease of cultivation and the ready triggering of zoospore development, similar to some lagenidiaceous oomycetes, the species could be a promising model to study sporulation processes in detail.
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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, Senckenberg Gesellschaft für Naturforschung, 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, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany.,LOEWE Centre for Translational Biodiversity Genomics, Georg-Voigt-Str. 14-16, D-60325 Frankfurt am Main, Germany
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34
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Hervé V, Lopez PJ. Analysis of interdomain taxonomic patterns in urban street mats. Environ Microbiol 2020; 22:1280-1293. [PMID: 31997567 DOI: 10.1111/1462-2920.14933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 01/15/2020] [Accepted: 01/27/2020] [Indexed: 11/28/2022]
Abstract
Streets are constantly crossed by billions of vehicles and pedestrians. Their gutters, which convey stormwater and contribute to waste management, and are important for human health and well-being, probably play a number of ecological roles. Street surfaces may also represent an important part of city surface areas. To better characterize the ecology of this yet poorly explored compartment, we used filtration and DNA metabarcoding to address microbial community composition and assembly across the city of Paris, France. Diverse bacterial and eukaryotic taxonomic groups were identified, including members involved in key biogeochemical processes, along with a number of parasites and putative pathogens of human, animals and plants. We showed that the beta diversity patterns between bacterial and eukaryotic communities were correlated, suggesting interdomain associations. Beta diversity analyses revealed the significance of biotic factors (cohesion metrics) in shaping gutter microbial community assembly and, to a lesser extent, the contribution of abiotic factors (pH and conductivity). Co-occurrences analysis confirmed contrasting non-random patterns both within and between domains of life, specifically when comparing diatoms and fungi. Our results highlight microbial coexistence patterns in streets and reinforce the need to further explore biodiversity in urban ground transportation infrastructures.
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Affiliation(s)
- Vincent Hervé
- Max Planck Institute for Terrestrial Microbiology, Karl-von-Frisch-Strasse 10, 35043, Marburg, Germany
| | - Pascal Jean Lopez
- Laboratoire Biologie des ORganismes et Ecosystèmes Aquatiques (BOREA), Muséum national d'Histoire naturelle, Centre National de la Recherche Scientifique, Sorbonne Université, Institut de Recherche pour le Développement, Université de Caen Normandie, Université des Antilles, 43 rue Cuvier, 75005, Paris, France
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35
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Chambouvet A, Monier A, Maguire F, Itoïz S, del Campo J, Elies P, Edvardsen B, Eikreim W, Richards TA. Intracellular Infection of Diverse Diatoms by an Evolutionary Distinct Relative of the Fungi. Curr Biol 2019; 29:4093-4101.e4. [DOI: 10.1016/j.cub.2019.09.074] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 07/12/2019] [Accepted: 09/30/2019] [Indexed: 11/29/2022]
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36
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Bjorbækmo MFM, Evenstad A, Røsæg LL, Krabberød AK, Logares R. The planktonic protist interactome: where do we stand after a century of research? ISME JOURNAL 2019; 14:544-559. [PMID: 31685936 PMCID: PMC6976576 DOI: 10.1038/s41396-019-0542-5] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 09/17/2019] [Accepted: 09/24/2019] [Indexed: 12/16/2022]
Abstract
Microbial interactions are crucial for Earth ecosystem function, but our knowledge about them is limited and has so far mainly existed as scattered records. Here, we have surveyed the literature involving planktonic protist interactions and gathered the information in a manually curated Protist Interaction DAtabase (PIDA). In total, we have registered ~2500 ecological interactions from ~500 publications, spanning the last 150 years. All major protistan lineages were involved in interactions as hosts, symbionts (mutualists and commensalists), parasites, predators, and/or prey. Predation was the most common interaction (39% of all records), followed by symbiosis (29%), parasitism (18%), and ‘unresolved interactions’ (14%, where it is uncertain whether the interaction is beneficial or antagonistic). Using bipartite networks, we found that protist predators seem to be ‘multivorous’ while parasite–host and symbiont–host interactions appear to have moderate degrees of specialization. The SAR supergroup (i.e., Stramenopiles, Alveolata, and Rhizaria) heavily dominated PIDA, and comparisons against a global-ocean molecular survey (TARA Oceans) indicated that several SAR lineages, which are abundant and diverse in the marine realm, were underrepresented among the recorded interactions. Despite historical biases, our work not only unveils large-scale eco-evolutionary trends in the protist interactome, but it also constitutes an expandable resource to investigate protist interactions and to test hypotheses deriving from omics tools.
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Affiliation(s)
- Marit F Markussen Bjorbækmo
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, N-0316, Oslo, Norway
| | - Andreas Evenstad
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, N-0316, Oslo, Norway
| | - Line Lieblein Røsæg
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, N-0316, Oslo, Norway
| | - Anders K Krabberød
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, N-0316, Oslo, Norway.
| | - Ramiro Logares
- Department of Biosciences, Section for Genetics and Evolutionary Biology (Evogene), University of Oslo, Blindernv. 31, N-0316, Oslo, Norway. .,Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain.
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37
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Vallet M, Baumeister TUH, Kaftan F, Grabe V, Buaya A, Thines M, Svatoš A, Pohnert G. The oomycete Lagenisma coscinodisci hijacks host alkaloid synthesis during infection of a marine diatom. Nat Commun 2019; 10:4938. [PMID: 31666506 PMCID: PMC6821873 DOI: 10.1038/s41467-019-12908-w] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 10/03/2019] [Indexed: 01/01/2023] Open
Abstract
Flagellated oomycetes frequently infect unicellular algae, thus limiting their proliferation. Here we show that the marine oomycete Lagenisma coscinodisci rewires the metabolome of the bloom-forming diatom Coscinodiscus granii, thereby promoting infection success. The algal alkaloids β-carboline and 4-carboxy-2,3,4,9-tetrahydro-1H-β-carboline are induced during infection. Single-cell profiling with AP-MALDI-MS and confocal laser scanning microscopy reveals that algal carbolines accumulate in the reproductive form of the parasite. The compounds arrest the algal cell division, increase the infection rate and induce plasmolysis in the host. Our results indicate that the oomycete manipulates the host metabolome to support its own multiplication. Flagellated oomycetes frequently infect unicellular algae, thus limiting their proliferation. Here, the authors show that an oomycete rewires the metabolome of a marine bloom-forming diatom, thereby promoting infection success.
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Affiliation(s)
- Marine Vallet
- Research Group Plankton Community Interaction, Max Planck Institute for Chemical Ecology, Jena, Germany.
| | - Tim U H Baumeister
- Research Group Plankton Community Interaction, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Filip Kaftan
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Veit Grabe
- Research Group Olfactory Coding, Department of Evolutionary Neuroethology, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Anthony Buaya
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre, Frankfurt am Main, Germany.,Department of Biological Sciences, Institute for Ecology, Evolution and Diversity, Goethe University, Frankfurt am Main, Germany
| | - Aleš Svatoš
- Research Group Mass Spectrometry/Proteomics, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Georg Pohnert
- Research Group Plankton Community Interaction, Max Planck Institute for Chemical Ecology, Jena, Germany. .,Bioorganic Analytics, Institute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany. .,Microverse Cluster, Friedrich Schiller University Jena, Neugasse 23, 07743, Jena, Germany.
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38
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Ding Y, Wen X, Peng X, Zhang A, Wang Z, Geng Y, Li Y. Surfactants as fungal parasite control agents in oleaginous microalga, Graesiella sp. WBG-1, mass culture. ALGAL RES 2019. [DOI: 10.1016/j.algal.2019.101539] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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39
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Hassett BT, Thines M, Buaya A, Ploch S, Gradinger R. A glimpse into the biogeography, seasonality, and ecological functions of arctic marine Oomycota. IMA Fungus 2019; 10:6. [PMID: 32647615 PMCID: PMC7325649 DOI: 10.1186/s43008-019-0006-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/03/2019] [Indexed: 02/05/2023] Open
Abstract
High-latitude environments are warming, leading to changes in biological diversity patterns of taxa. Oomycota are a group of fungal-like organisms that comprise a major clade of eukaryotic life and are parasites of fish, agricultural crops, and algae. The diversity, functionality, and distribution of these organisms are essentially unknown in the Arctic marine environment. Thus, it was our aim to conduct a first screening, using a functional gene assay and high-throughput sequencing of two gene regions within the 18S rRNA locus to examine the diversity, richness, and phylogeny of marine Oomycota within Arctic sediment, seawater, and sea ice. We detected Oomycota at every site sampled and identified regionally localized taxa, as well as taxa that existed in both Alaska and Svalbard. While the recently described diatom parasite Miracula helgolandica made up about 50% of the oomycete reads found, many lineages were observed that could not be assigned to known species, including several that clustered with another recently described diatom parasite, Olpidiopsis drebesii. Across the Arctic, Oomycota comprised a maximum of 6% of the entire eukaryotic microbial community in Barrow, Alaska May sediment and 10% in sea ice near the Svalbard archipelago. We found Arctic marine Oomycota encode numerous genes involved in parasitism and carbon cycling processes. Ultimately, these data suggest that Arctic marine Oomycota are a reservoir of uncharacterized biodiversity, the majority of which are probably parasites of diatoms, while others might cryptically cycle carbon or interface other unknown ecological processes. As the Arctic continues to warm, lower-latitude Oomycota might migrate into the Arctic Ocean and parasitize non-coevolved hosts, leading to incalculable shifts in the primary producer community.
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Affiliation(s)
- Brandon T Hassett
- UiT-Norges arktiske universitet, BFE, NFH bygget, Framstredet 6, 9019 Tromsø, Norway
| | - Marco Thines
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.,Department of Biological Sciences, Goethe University, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60435 Frankfurt am Main, Germany.,Translational Biodiversity Genomics Centre, Georg-Voigt-Str. 14-16, 60325 Frankfurt am Main, Germany
| | - Anthony Buaya
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany.,Department of Biological Sciences, Goethe University, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, 60435 Frankfurt am Main, Germany
| | - Sebastian Ploch
- Senckenberg Biodiversity and Climate Research Centre, Senckenberganlage 25, 60325 Frankfurt am Main, Germany
| | - R Gradinger
- UiT-Norges arktiske universitet, BFE, NFH bygget, Framstredet 6, 9019 Tromsø, Norway
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40
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Jones EBG, Pang KL, Abdel-Wahab MA, Scholz B, Hyde KD, Boekhout T, Ebel R, Rateb ME, Henderson L, Sakayaroj J, Suetrong S, Dayarathne MC, Kumar V, Raghukumar S, Sridhar KR, Bahkali AHA, Gleason FH, Norphanphoun C. An online resource for marine fungi. FUNGAL DIVERS 2019. [DOI: 10.1007/s13225-019-00426-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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41
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Rediscovery and phylogenetic placement of Olpidiopsis gillii (de Wildeman) Friedmann, a holocarpic oomycete parasitoid of freshwater diatoms. MYCOSCIENCE 2019. [DOI: 10.1016/j.myc.2019.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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42
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Amend A, Burgaud G, Cunliffe M, Edgcomb VP, Ettinger CL, Gutiérrez MH, Heitman J, Hom EFY, Ianiri G, Jones AC, Kagami M, Picard KT, Quandt CA, Raghukumar S, Riquelme M, Stajich J, Vargas-Muñiz J, Walker AK, Yarden O, Gladfelter AS. Fungi in the Marine Environment: Open Questions and Unsolved Problems. mBio 2019; 10:e01189-18. [PMID: 30837337 PMCID: PMC6401481 DOI: 10.1128/mbio.01189-18] [Citation(s) in RCA: 128] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Terrestrial fungi play critical roles in nutrient cycling and food webs and can shape macroorganism communities as parasites and mutualists. Although estimates for the number of fungal species on the planet range from 1.5 to over 5 million, likely fewer than 10% of fungi have been identified so far. To date, a relatively small percentage of described species are associated with marine environments, with ∼1,100 species retrieved exclusively from the marine environment. Nevertheless, fungi have been found in nearly every marine habitat explored, from the surface of the ocean to kilometers below ocean sediments. Fungi are hypothesized to contribute to phytoplankton population cycles and the biological carbon pump and are active in the chemistry of marine sediments. Many fungi have been identified as commensals or pathogens of marine animals (e.g., corals and sponges), plants, and algae. Despite their varied roles, remarkably little is known about the diversity of this major branch of eukaryotic life in marine ecosystems or their ecological functions. This perspective emerges from a Marine Fungi Workshop held in May 2018 at the Marine Biological Laboratory in Woods Hole, MA. We present the state of knowledge as well as the multitude of open questions regarding the diversity and function of fungi in the marine biosphere and geochemical cycles.
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Affiliation(s)
- Anthony Amend
- Department of Botany, University of Hawai'i at Manoa, Honolulu, Hawaii, USA
| | - Gaetan Burgaud
- Université de Brest, EA 3882, Laboratoire Universitaire de Biodiversité et Ecologie Microbienne, ESIAB, Technopôle Brest-Iroise, Plouzané, France
| | - Michael Cunliffe
- Marine Biological Association of the United Kingdom, The Laboratory, Citadel Hill, Plymouth, United Kingdom
| | - Virginia P Edgcomb
- Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
| | | | - M H Gutiérrez
- Departamento de Oceanografía, Centro de Investigación Oceanográfica COPAS Sur-Austral, Universidad de Concepción, Concepción, Chile
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Erik F Y Hom
- Department of Biology, University of Mississippi, Oxford, Mississippi, USA
| | - Giuseppe Ianiri
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA
| | - Adam C Jones
- Gordon and Betty Moore Foundation, Palo Alto, California, USA
| | - Maiko Kagami
- Graduate School of Environment and Information Sciences, Yokohama National University, Yokohama, Japan
| | - Kathryn T Picard
- Department of Botany, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - C Alisha Quandt
- Ecology and Evolutionary Biology Department, University of Colorado, Boulder, Colorado, USA
| | | | - Mertixell Riquelme
- Department of Microbiology, Centro de Investigación Científica y Educación Superior de Ensenada (CICESE), Ensenada, Baja California, Mexico
| | - Jason Stajich
- Department of Microbiology & Plant Pathology and Institute for Integrative Genome Biology, University of California-Riverside, Riverside, California, USA
| | - José Vargas-Muñiz
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Allison K Walker
- Department of Biology, Acadia University, Wolfville, Nova Scotia, Canada
| | - Oded Yarden
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Amy S Gladfelter
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Marine Biological Laboratory, Woods Hole, Massachusetts, USA
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43
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Ramond P, Sourisseau M, Simon N, Romac S, Schmitt S, Rigaut-Jalabert F, Henry N, de Vargas C, Siano R. Coupling between taxonomic and functional diversity in protistan coastal communities. Environ Microbiol 2019; 21:730-749. [PMID: 30672084 DOI: 10.1111/1462-2920.14537] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/19/2019] [Indexed: 01/11/2023]
Abstract
The study of protistan functional diversity is crucial to understand the dynamics of oceanic ecological processes. We combined the metabarcoding data of various coastal ecosystems and a newly developed trait-based approach to study the link between taxonomic and functional diversity across marine protistan communities of different size-classes. Environmental DNA was extracted and the V4 18S rDNA genomic region was amplified and sequenced. In parallel, we tried to annotate the operational taxonomic units (OTUs) from our metabarcoding dataset to 30 biological traits using published and accessible information on protists. We then developed a method to study trait correlations across protists (i.e. trade-offs) in order to build the best functional groups. Based on the annotated OTUs and our functional groups, we demonstrated that the functional diversity of marine protist communities varied in parallel with their taxonomic diversity. The coupling between functional and taxonomic diversity was conserved across different protist size classes. However, the smallest size-fraction was characterized by wider taxonomic and functional groups diversity, corroborating the idea that nanoplankton and picoplankton are part of a more stable ecological background on which larger protists and metazoans might develop.
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Affiliation(s)
- Pierre Ramond
- IFREMER, Dyneco Pelagos, BP 70, 29280 Plouzané, France.,Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France
| | | | - Nathalie Simon
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France
| | - Sarah Romac
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | | | - Fabienne Rigaut-Jalabert
- Sorbonne Université, CNRS - FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29688 Roscoff, France
| | - Nicolas Henry
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Colomban de Vargas
- Sorbonne University, CNRS, Station Biologique de Roscoff, UMR7144, ECOMAP, 29688 Roscoff, France.,Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 rue Michel-Ange, 75016 Paris, France
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44
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Buaya AT, Thines M. Miracula moenusica, a new member of the holocarpic parasitoid genus from the invasive freshwater diatom Pleurosira laevis. Fungal Syst Evol 2019; 3:35-40. [PMID: 32478313 PMCID: PMC7252423 DOI: 10.3114/fuse.2019.03.04] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Holocarpic oomycetes are poorly known but widespread parasites in freshwater and marine ecosystems. Most of the holocarpic species seem to belong to clades that diverge before the two crown lineages of the oomycetes, the Saprolegniomycetes and the Peronosporomycetes. Recently, the genus Miracula was described to accommodate Miracula helgolandica, a holocarpic parasitoid of Pseudo-nitzschia diatoms, which received varying support for its placement as the earliest-diverging oomycete lineage. In the same phylogenetic reconstruction, Miracula helgolandica was grouped with some somewhat divergent sequences derived from environmental sequencing, indicating that Miracula would not remain monotypic. Here, a second species of Miracula is reported, which was found as a parasitoid in the limnic centric diatom Pleurosira leavis. Its life-cycle stages are described and depicted in this study and its phylogenetic placement in the genus Miracula revealed. As a consequence, the newly discovered species is introduced as Miracula moenusica.
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Affiliation(s)
- A T Buaya
- Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, D-60486 Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
| | - M Thines
- Goethe University, Department of Biological Sciences, Institute of Ecology, Evolution and Diversity, Max-von-Laue-Str. 13, D-60486 Frankfurt am Main, Germany.,Senckenberg Biodiversity and Climate Research Centre, Senckenberg Gesellschaft für Naturforschung, Senckenberganlage 25, D-60325 Frankfurt am Main, Germany
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45
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Arsenieff L, Simon N, Rigaut-Jalabert F, Le Gall F, Chaffron S, Corre E, Com E, Bigeard E, Baudoux AC. First Viruses Infecting the Marine Diatom Guinardia delicatula. Front Microbiol 2019; 9:3235. [PMID: 30687251 PMCID: PMC6334475 DOI: 10.3389/fmicb.2018.03235] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/12/2018] [Indexed: 11/17/2022] Open
Abstract
The marine diatom Guinardia delicatula is a cosmopolitan species that dominates seasonal blooms in the English Channel and the North Sea. Several eukaryotic parasites are known to induce the mortality of this species. Here, we report the isolation and characterization of the first viruses that infect G. delicatula. Viruses were isolated from the Western English Channel (SOMLIT-Astan station) during the late summer bloom decline of G. delicatula. A combination of laboratory approaches revealed that these lytic viruses (GdelRNAV) are small tailless particles of 35–38 nm in diameter that replicate in the host cytoplasm where both unordered particles and crystalline arrays are formed. GdelRNAV display a linear single-stranded RNA genome of ~9 kb, including two open reading frames encoding for replication and structural polyproteins. Phylogenetic relationships based on the RNA-dependent-RNA-polymerase gene marker showed that GdelRNAV are new members of the Bacillarnavirus, a monophyletic genus belonging to the order Picornavirales. GdelRNAV are specific to several strains of G. delicatula. They were rapidly and largely produced (<12 h, 9.34 × 104 virions per host cell). Our analysis points out the host's variable viral susceptibilities during the early exponential growth phase. Interestingly, we consistently failed to isolate viruses during spring and early summer while G. delicatula developed important blooms. While our study suggests that viruses do contribute to the decline of G. delicatula's late summer bloom, they may not be the primary mortality agents during the remaining blooms at SOMLIT-Astan. Future studies should focus on the relative contribution of the viral and eukaryotic pathogens to the control of Guinardia's blooms to understand the fate of these prominent organisms in marine systems.
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Affiliation(s)
- Laure Arsenieff
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
| | - Nathalie Simon
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
| | - Fabienne Rigaut-Jalabert
- Sorbonne Université, CNRS Fédération de Recherche FR2424 - Station Biologique de Roscoff, Roscoff, France
| | - Florence Le Gall
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
| | - Samuel Chaffron
- Laboratoire des Sciences du Numérique de Nantes (LS2N), CNRS UMR 6004 - Université de Nantes, Nantes, France
| | - Erwan Corre
- Sorbonne Université, CNRS Fédération de Recherche FR2424 - Station Biologique de Roscoff, Roscoff, France
| | - Emmanuelle Com
- Univ Rennes, Inserm, EHESP, Irset (Institut de recherche en santé, environnement et travail) - UMR_S 1085, Rennes, France.,Protim, Univ Rennes, Rennes, France
| | - Estelle Bigeard
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
| | - Anne-Claire Baudoux
- Sorbonne Université, CNRS UMR 7144, Diversity and Interactions in Oceanic Plankton - Station Biologique de Roscoff, Roscoff, France
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46
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Garvetto A, Nézan E, Badis Y, Bilien G, Arce P, Bresnan E, Gachon CMM, Siano R. Novel Widespread Marine Oomycetes Parasitising Diatoms, Including the Toxic Genus Pseudo-nitzschia: Genetic, Morphological, and Ecological Characterisation. Front Microbiol 2018; 9:2918. [PMID: 30559730 PMCID: PMC6286980 DOI: 10.3389/fmicb.2018.02918] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 11/13/2018] [Indexed: 01/16/2023] Open
Abstract
Parasites are key drivers of phytoplankton bloom dynamics and related aquatic ecosystem processes. Yet, the dearth of morphological and molecular information hinders the assessment of their diversity and ecological role. Using single-cell techniques, we characterise morphologically and molecularly, intracellular parasitoids infecting four potentially toxin-producing Pseudo-nitzschia and one Melosira species on the North Atlantic coast. These sequences define two, morphologically indistinguishable clades within the phylum Oomycota, related to the genera of algal parasites Anisolpidium and Olpidiopsis and the diatom parasitoid species Miracula helgolandica. Our morphological data are insufficient to attribute either clade to the still unsequenced genus Ectrogella; hence it is proposed to name the clades OOM_1 and OOM_2. A screening of global databases of the barcode regions V4 and V9 of the 18S rDNA demonstrate the presence of these parasitoids beyond the North Atlantic coastal region. During a biweekly metabarcoding survey (Concarneau Bay, France), reads associated with one sequenced parasitoid coincided with the decline of Cerataulina pelagica bloom, whilst the other parasitoids co-occurred at low abundance with Pseudo-nitzschia. Our data highlight a complex and unexplored diversity of the oomycete parasitoids of diatoms and calls for the investigation of their phenology, evolution, and potential contribution in controlling their host spatial-temporal dynamics.
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Affiliation(s)
- Andrea Garvetto
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
| | - Elisabeth Nézan
- IFREMER, ODE/UL/LER BO, Station de Biologie Marine de Concarneau, Concarneau, France
| | - Yacine Badis
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
| | - Gwenael Bilien
- IFREMER, ODE/UL/LER BO, Station de Biologie Marine de Concarneau, Concarneau, France
| | - Paola Arce
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
| | - Eileen Bresnan
- Marine Scotland Science, Marine Laboratory, Aberdeen, United Kingdom
| | - Claire M. M. Gachon
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
| | - Raffaele Siano
- IFREMER – Centre de Brest, DYNECO PELAGOS, Plouzané, France
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A High-Resolution Time Series Reveals Distinct Seasonal Patterns of Planktonic Fungi at a Temperate Coastal Ocean Site (Beaufort, North Carolina, USA). Appl Environ Microbiol 2018; 84:AEM.00967-18. [PMID: 30143506 DOI: 10.1128/aem.00967-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 08/17/2018] [Indexed: 11/20/2022] Open
Abstract
There is a growing awareness of the ecological and biogeochemical importance of fungi in coastal marine systems. While highly diverse fungi have been discovered in these marine systems, still, little is known about their seasonality and associated drivers in coastal waters. Here, we examined fungal communities over 3 years of weekly sampling at a dynamic, temperate coastal site (Pivers Island Coastal Observatory [PICO], Beaufort, NC, USA). Fungal 18S rRNA gene abundance, operational taxonomic unit (OTU) richness, and Shannon's diversity index values exhibited prominent seasonality. Fungal 18S rRNA gene copies peaked in abundance during the summer and fall, with positive correlations with chlorophyll a, SiO4, and oxygen saturation. Diversity (measured using internal transcribed spacer [ITS] libraries) was highest during winter and lowest during summer; it was linked to temperature, pH, chlorophyll a, insolation, salinity, and dissolved inorganic carbon (DIC). Fungal communities derived from ITS libraries were dominated throughout the year by Ascomycota, with contributions from Basidiomycota, Chytridiomycota, and Mucoromycotina, and their seasonal patterns linked to water temperature, light, and the carbonate system. Network analysis revealed that while cooccurrence and exclusion existed within fungus networks, exclusion dominated the fungus-and-phytoplankton network, in contrast with reported pathogenic and nutritional interactions between marine phytoplankton and fungi. Compared with the seasonality of bacterial communities in the same samples, the timing, extent, and associated environmental variables for fungi community are unique. These results highlight the fungal seasonal dynamics in coastal water and improve our understanding of the ecology of planktonic fungi.IMPORTANCE Coastal fungal dynamics were long assumed to be due to terrestrial inputs; here, a high-resolution time series reveals strong, repeating annual patterns linked to in situ environmental conditions, arguing for a resident coastal fungal community shaped by environmental factors. These seasonal patterns do, however, differ from those observed in the bacterioplankton at the same site; e.g., fungal diversity peaks in winter, whereas bacterial diversity maxima occur in the spring and fall. While the dynamics of these communities are linked to water temperature and insolation, fungi are also influenced by the carbonate system (pH and DIC). As both fungi and heterotrophic bacteria are thought to be key organic-material metabolizers, differences in their environmental drivers may offer clues as to which group dominates secondary production at this dynamic site. Overall, this study suggests the unique ecological roles of mycoplankton and their potentially broad niche complementarities to other microbial groups in the coastal ocean.
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Wijayawardene NN, Pawłowska J, Letcher PM, Kirk PM, Humber RA, Schüßler A, Wrzosek M, Muszewska A, Okrasińska A, Istel Ł, Gęsiorska A, Mungai P, Lateef AA, Rajeshkumar KC, Singh RV, Radek R, Walther G, Wagner L, Walker C, Wijesundara DSA, Papizadeh M, Dolatabadi S, Shenoy BD, Tokarev YS, Lumyong S, Hyde KD. Notes for genera: basal clades of Fungi (including Aphelidiomycota, Basidiobolomycota, Blastocladiomycota, Calcarisporiellomycota, Caulochytriomycota, Chytridiomycota, Entomophthoromycota, Glomeromycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota, Mucoromycota, Neocallimastigomycota, Olpidiomycota, Rozellomycota and Zoopagomycota). FUNGAL DIVERS 2018. [DOI: 10.1007/s13225-018-0409-5] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Wang Y, Sen B, He Y, Xie N, Wang G. Spatiotemporal Distribution and Assemblages of Planktonic Fungi in the Coastal Waters of the Bohai Sea. Front Microbiol 2018; 9:584. [PMID: 29643845 PMCID: PMC5882831 DOI: 10.3389/fmicb.2018.00584] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Accepted: 03/14/2018] [Indexed: 11/13/2022] Open
Abstract
Fungi play a critical role in the nutrient cycling and ecological function in terrestrial and freshwater ecosystems. Yet, many ecological aspects of their counterparts in coastal ecosystems remain largely elusive. Using high-throughput sequencing, quantitative PCR, and environmental data analyses, we studied the spatiotemporal changes in the abundance and diversity of planktonic fungi and their abiotic and biotic interactions in the coastal waters of three transects along the Bohai Sea. A total of 4362 ITS OTUs were identified and more than 60% of which were unclassified Fungi. Of the classified OTUs three major fungal phyla, Ascomycota, Basidiomycota, and Chytridiomycota were predominant with episodic low dominance phyla Cryptomycota and Mucoromycota (Mortierellales). The estimated average Fungi-specific 18S rRNA gene qPCR abundances varied within 4.28 × 106 and 1.13 × 107copies/L with significantly (P < 0.05) different abundances among the transects suggesting potential influence of the different riverine inputs. The spatiotemporal changes in the OTU abundance of Ascomycota and Basidiomycota phyla coincided significantly (P < 0.05) with nutrients traced to riverine inputs and phytoplankton detritus. Among the eight major fungal orders, the abundance of Hypocreales varied significantly (P < 0.01) across months while Capnodiales, Pleosporales, Eurotiales, and Sporidiobolales varied significantly (P < 0.05) across transects. In addition, our results likely suggest a tripartite interaction model for the association within members of Cryptomycota (hyperparasites), Chytridiomycota (both parasites and saprotrophs), and phytoplankton in the coastal waters. The fungal network featured several hubs and keystone OTUs besides the display of cooperative and competitive relationship within OTUs. These results support the notion that planktonic fungi, hitherto mostly undescribed, play diverse ecological roles in marine habitats and further outline niche processes, tripartite and co-occurrence interaction as the major drivers of their community structure and spatiotemporal distribution in the coastal water column.
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Affiliation(s)
- Yaqiong Wang
- Center for Marine Environmental Ecology, School of Environment Science and Engineering, Tianjin University, Tianjin, China
- School of Ecology, Environment and Resources, Qinghai University for Nationalities, Xining, China
| | - Biswarup Sen
- Center for Marine Environmental Ecology, School of Environment Science and Engineering, Tianjin University, Tianjin, China
| | - Yaodong He
- Center for Marine Environmental Ecology, School of Environment Science and Engineering, Tianjin University, Tianjin, China
| | - Ningdong Xie
- Center for Marine Environmental Ecology, School of Environment Science and Engineering, Tianjin University, Tianjin, China
- Duke Marine Laboratory, Nicholas School of the Environment, Duke University, Durham, NC, United States
| | - Guangyi Wang
- Center for Marine Environmental Ecology, School of Environment Science and Engineering, Tianjin University, Tianjin, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
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50
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Nanoplanktonic diatoms are globally overlooked but play a role in spring blooms and carbon export. Nat Commun 2018; 9:953. [PMID: 29507291 PMCID: PMC5838239 DOI: 10.1038/s41467-018-03376-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 02/08/2018] [Indexed: 12/22/2022] Open
Abstract
Diatoms are one of the major primary producers in the ocean, responsible annually for ~20% of photosynthetically fixed CO2 on Earth. In oceanic models, they are typically represented as large (>20 µm) microphytoplankton. However, many diatoms belong to the nanophytoplankton (2–20 µm) and a few species even overlap with the picoplanktonic size-class (<2 µm). Due to their minute size and difficulty of detection they are poorly characterized. Here we describe a massive spring bloom of the smallest known diatom (Minidiscus) in the northwestern Mediterranean Sea. Analysis of Tara Oceans data, together with literature review, reveal a general oversight of the significance of these small diatoms at the global scale. We further evidence that they can reach the seafloor at high sinking rates, implying the need to revise our classical binary vision of pico- and nanoplanktonic cells fueling the microbial loop, while only microphytoplankton sustain secondary trophic levels and carbon export. Diatoms are major oceanic primary producers, but some species belonging to the nano- and even picoplankton size are poorly characterized. Here the authors describe a massive spring bloom of the smallest known diatom in the Mediterranean Sea and reveal their general oversight at the global scale.
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