1
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Mukherjee I, Grujčić V, Salcher MM, Znachor P, Seďa J, Devetter M, Rychtecký P, Šimek K, Shabarova T. Integrating depth-dependent protist dynamics and microbial interactions in spring succession of a freshwater reservoir. ENVIRONMENTAL MICROBIOME 2024; 19:31. [PMID: 38720385 PMCID: PMC11080224 DOI: 10.1186/s40793-024-00574-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/30/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Protists are essential contributors to eukaryotic diversity and exert profound influence on carbon fluxes and energy transfer in freshwaters. Despite their significance, there is a notable gap in research on protistan dynamics, particularly in the deeper strata of temperate lakes. This study aimed to address this gap by integrating protists into the well-described spring dynamics of Římov reservoir, Czech Republic. Over a 2-month period covering transition from mixing to established stratification, we collected water samples from three reservoir depths (0.5, 10 and 30 m) with a frequency of up to three times per week. Microbial eukaryotic and prokaryotic communities were analysed using SSU rRNA gene amplicon sequencing and dominant protistan groups were enumerated by Catalysed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). Additionally, we collected samples for water chemistry, phyto- and zooplankton composition analyses. RESULTS Following the rapid changes in environmental and biotic parameters during spring, protistan and bacterial communities displayed swift transitions from a homogeneous community to distinct strata-specific communities. A prevalence of auto- and mixotrophic protists dominated by cryptophytes was associated with spring algal bloom-specialized bacteria in the epilimnion. In contrast, the meta- and hypolimnion showcased a development of a protist community dominated by putative parasitic Perkinsozoa, detritus or particle-associated ciliates, cercozoans, telonemids and excavate protists (Kinetoplastida), co-occurring with bacteria associated with lake snow. CONCLUSIONS Our high-resolution sampling matching the typical doubling time of microbes along with the combined microscopic and molecular approach and inclusion of all main components of the microbial food web allowed us to unveil depth-specific populations' successions and interactions in a deep lentic ecosystem.
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Affiliation(s)
- Indranil Mukherjee
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic.
| | - Vesna Grujčić
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Michaela M Salcher
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
| | - Petr Znachor
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005, Ceske Budejovice, Czech Republic
| | - Jaromír Seďa
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
| | - Miloslav Devetter
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology and Biogeochemistry, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
| | - Pavel Rychtecký
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
| | - Karel Šimek
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005, Ceske Budejovice, Czech Republic
| | - Tanja Shabarova
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic.
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2
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Šimek K, Mukherjee I, Nedoma J, de Paula CCP, Jezberová J, Sirová D, Vrba J. CARD-FISH and prey tracer techniques reveal the role of overlooked flagellate groups as major bacterivores in freshwater hypertrophic shallow lakes. Environ Microbiol 2022; 24:4256-4273. [PMID: 34933408 PMCID: PMC9788210 DOI: 10.1111/1462-2920.15846] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 11/08/2021] [Accepted: 11/08/2021] [Indexed: 12/30/2022]
Abstract
Heterotrophic nanoflagellates (HNF) and ciliates are major protistan planktonic bacterivores. The term HNF, however, describes a functional guild only and, in contrast to the morphologically distinguishable ciliates, does not reflect the phylogenetic diversity of flagellates in aquatic ecosystems. Associating a function with taxonomic affiliation of key flagellate taxa is currently a major task in microbial ecology. We investigated seasonal changes in the HNF and ciliate community composition as well as taxa-specific bacterivory in four hypertrophic freshwater lakes. Taxa-specific catalyzed reporter deposition-fluorescence in situ hybridization probes assigned taxonomic affiliations to 51%-96% (average ±SD, 75 ± 14%) of total HNF. Ingestion rates of fluorescently labelled bacteria unveiled that HNF contributed to total protist-induced bacterial mortality rates more (56%) than ciliates (44%). Surprisingly, major HNF bacterivores were aplastidic cryptophytes and their Cry1 lineage, comprising on average 53% and 24% of total HNF abundance and 67% and 21% of total HNF bacterivory respectively. Kinetoplastea were important consumers of bacteria during summer phytoplankton blooms, reaching 38% of total HNF. Katablepharidacea (7.5% of total HNF) comprised mainly omnivores, with changing contributions of bacterivorous and algivorous phylotypes. Our results show that aplastidic cryptophytes, accompanied by small omnivorous ciliate genera Halteria/Pelagohalteria, are the major protistan bacterivores in hypertrophic freshwaters.
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Affiliation(s)
- Karel Šimek
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7České Budějovice37005Czech Republic,Faculty of ScienceUniversity of South Bohemia, Branišovská 1760České Budějovice37005Czech Republic
| | - Indranil Mukherjee
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7České Budějovice37005Czech Republic
| | - Jiří Nedoma
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7České Budějovice37005Czech Republic
| | | | - Jitka Jezberová
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7České Budějovice37005Czech Republic
| | - Dagmara Sirová
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7České Budějovice37005Czech Republic
| | - Jaroslav Vrba
- Biology Centre CAS, Institute of Hydrobiology, Na Sádkách 7České Budějovice37005Czech Republic,Faculty of ScienceUniversity of South Bohemia, Branišovská 1760České Budějovice37005Czech Republic
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3
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Chauvet M, Debroas D, Moné A, Dubuffet A, Lepère C. Temporal variations of Microsporidia diversity and discovery of new host-parasite interactions in a lake ecosystem. Environ Microbiol 2022; 24:1672-1686. [PMID: 35246918 DOI: 10.1111/1462-2920.15950] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 02/09/2022] [Accepted: 02/21/2022] [Indexed: 11/29/2022]
Abstract
Microsporidia are a large group of obligate intracellular eukaryotic parasites related to Fungi. Recent studies suggest that their diversity has been greatly underestimated and little is known about their hosts other than metazoans, and thus about their impact on the communities at the base of the food web. In this work, we therefore studied the diversity of Microsporidia over one year and identified potential new hosts in small-sized fractions (<150 μm) in a lake ecosystem using a metabarcoding approach coupled with co-occurrence networks and tyramide signal amplification-fluorescent in situ hybridization. Our analysis shows a great Microsporidia diversity (1 472 OTUs), with an important part of this diversity being unknown. Temporal variations of this diversity have been observed, which might follow temporal variations of their potential hosts such as protists and microzooplankton. New hosts among them were identified as well as associations with phytoplankton. Indeed, repeated infections were observed in Kellicottia (rotifers) with a prevalence of 38% (infected individuals). Microsporidia inside a Stentor (ciliate) were also observed. Finally, potential infections of the diatom Asterionella were identified (prevalence <0.1%). The microsporidian host spectrum could be therefore even more important than previously described, and their role in the functioning of lake ecosystems is undoubtedly largely unknown.
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Affiliation(s)
- Marina Chauvet
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, F-63000, France
| | - Didier Debroas
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, F-63000, France
| | - Anne Moné
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, F-63000, France
| | - Aurore Dubuffet
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, F-63000, France
| | - Cécile Lepère
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, F-63000, France
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4
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Itoïz S, Metz S, Derelle E, Reñé A, Garcés E, Bass D, Soudant P, Chambouvet A. Emerging Parasitic Protists: The Case of Perkinsea. Front Microbiol 2022; 12:735815. [PMID: 35095782 PMCID: PMC8792838 DOI: 10.3389/fmicb.2021.735815] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
The last century has witnessed an increasing rate of new disease emergence across the world leading to permanent loss of biodiversity. Perkinsea is a microeukaryotic parasitic phylum composed of four main lineages of parasitic protists with broad host ranges. Some of them represent major ecological and economical threats because of their geographically invasive ability and pathogenicity (leading to mortality events). In marine environments, three lineages are currently described, the Parviluciferaceae, the Perkinsidae, and the Xcellidae, infecting, respectively, dinoflagellates, mollusks, and fish. In contrast, only one lineage is officially described in freshwater environments: the severe Perkinsea infectious agent infecting frog tadpoles. The advent of high-throughput sequencing methods, mainly based on 18S rRNA assays, showed that Perkinsea is far more diverse than the previously four described lineages especially in freshwater environments. Indeed, some lineages could be parasites of green microalgae, but a formal nature of the interaction needs to be explored. Hence, to date, most of the newly described aquatic clusters are only defined by their environmental sequences and are still not (yet) associated with any host. The unveiling of this microbial black box presents a multitude of research challenges to understand their ecological roles and ultimately to prevent their most negative impacts. This review summarizes the biological and ecological traits of Perkinsea-their diversity, life cycle, host preferences, pathogenicity, and highlights their diversity and ubiquity in association with a wide range of hosts.
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Affiliation(s)
- Sarah Itoïz
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, Plouzané, France
| | | | | | - Albert Reñé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta, Barcelona, Spain
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta, Barcelona, Spain
| | - David Bass
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, United Kingdom
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
- Biosciences, University of Exeter, Exeter, United Kingdom
| | | | - Aurélie Chambouvet
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, Plouzané, France
- Sorbonne Université, CNRS, UMR 7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, Roscoff, France
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5
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Jeon BS, Park MG. A Novel Parasitoid of Marine Dinoflagellates, Pararosarium dinoexitiosum gen. et sp. nov. (Perkinsozoa, Alveolata), Showing Characteristic Beaded Sporocytes. Front Microbiol 2021; 12:748092. [PMID: 34912310 PMCID: PMC8667275 DOI: 10.3389/fmicb.2021.748092] [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] [Received: 07/27/2021] [Accepted: 11/09/2021] [Indexed: 11/13/2022] Open
Abstract
The phylum Perkinsozoa is known as an exclusively parasitic group within alveolates and is widely distributed in various aquatic environments from marine to freshwater environments. Nonetheless, their morphology, life cycle, the identity of the host, and physiological characteristics remain still poorly understood. During intensive sampling along the west coast of Korea in October and November 2017, a new parasitoid, which shares several characteristics with the extant families Perkinsidae and Parviluciferaceae, was discovered and three strains of the new parasitoid were successfully established in cultures. Cross-infection experiments showed that among the examined planktonic groups, only dinoflagellates were susceptible to the new parasitoid, with infections observed in species belonging to eight genera. Even though the new parasitoid shared many morphological and developmental characteristics with other Perkinsozoan parasites, it differed from them by its densely packed trophocyte structure without a large vacuole or hyaline material during the growth stage. These characteristics are common among Parviluciferaceae members. Furthermore, through palintomic extracellular sporogenesis, it produced characteristic interconnected sporocytes resembling a string of beads. Phylogenetic analyses based on the small subunit and large subunit ribosomal DNA sequences revealed that the new parasitoid was distantly related to the family Parviluciferaceae and was more closely related to the families Perkinsidae and Xcellidae. Morphological, ultrastructural, and molecular data on the new parasitoid raised the need to erect a new family, i.e., Pararosariidae, within the phylum Perkinsozoa with Pararosarium dinoexitiosum gen. et sp. nov. as the type species. The isolation and establishment in culture of the new parasitoid outside the family Parviluciferaceae in the present study would contribute to the better understanding of the diversity of Perkinsozoan parasites and provide useful material for comparisons to other parasite species in the further study.
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Affiliation(s)
- Boo Seong Jeon
- LOHABE, Department of Oceanography, Chonnam National University, Gwangju, South Korea
| | - Myung Gil Park
- LOHABE, Department of Oceanography, Chonnam National University, Gwangju, South Korea
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6
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Piwosz K, Mukherjee I, Salcher MM, Grujčić V, Šimek K. CARD-FISH in the Sequencing Era: Opening a New Universe of Protistan Ecology. Front Microbiol 2021; 12:640066. [PMID: 33746931 PMCID: PMC7970053 DOI: 10.3389/fmicb.2021.640066] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 02/09/2021] [Indexed: 12/12/2022] Open
Abstract
Phagotrophic protists are key players in aquatic food webs. Although sequencing-based studies have revealed their enormous diversity, ecological information on in situ abundance, feeding modes, grazing preferences, and growth rates of specific lineages can be reliably obtained only using microscopy-based molecular methods, such as Catalyzed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). CARD-FISH is commonly applied to study prokaryotes, but less so to microbial eukaryotes. Application of this technique revealed that Paraphysomonas or Spumella-like chrysophytes, considered to be among the most prominent members of protistan communities in pelagic environments, are omnipresent but actually less abundant than expected, in contrast to little known groups such as heterotrophic cryptophyte lineages (e.g., CRY1), cercozoans, katablepharids, or the MAST lineages. Combination of CARD-FISH with tracer techniques and application of double CARD-FISH allow visualization of food vacuole contents of specific flagellate groups, thus considerably challenging our current, simplistic view that they are predominantly bacterivores. Experimental manipulations with natural communities revealed that larger flagellates are actually omnivores ingesting both prokaryotes and other protists. These new findings justify our proposition of an updated model of microbial food webs in pelagic environments, reflecting more authentically the complex trophic interactions and specific roles of flagellated protists, with inclusion of at least two additional trophic levels in the nanoplankton size fraction. Moreover, we provide a detailed CARD-FISH protocol for protists, exemplified on mixo- and heterotrophic nanoplanktonic flagellates, together with tips on probe design, a troubleshooting guide addressing most frequent obstacles, and an exhaustive list of published probes targeting protists.
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Affiliation(s)
- Kasia Piwosz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Gdynia, Poland
- Centre ALGATECH, Institute of Microbiology of the Czech Academy of Sciences, Třeboň, Czechia
| | - Indranil Mukherjee
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czechia
| | - Michaela M. Salcher
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czechia
| | - Vesna Grujčić
- Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Karel Šimek
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, České Budějovice, Czechia
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7
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Cruaud P, Vigneron A, Fradette MS, Dorea CC, Culley AI, Rodriguez MJ, Charette SJ. Annual Protist Community Dynamics in a Freshwater Ecosystem Undergoing Contrasted Climatic Conditions: The Saint-Charles River (Canada). Front Microbiol 2019; 10:2359. [PMID: 31681222 PMCID: PMC6805768 DOI: 10.3389/fmicb.2019.02359] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 09/27/2019] [Indexed: 11/23/2022] Open
Abstract
Protists are key stone components of aquatic ecosystems, sustaining primary productivity and aquatic food webs. However, their diversity, ecology and structuring factors shaping their temporal distribution remain strongly misunderstood in freshwaters. Using high-throughput sequencing on water samples collected over 16 different months (including two summer and two winter periods), combined with geochemical measurements and climate monitoring, we comprehensively determined the pico- and nanoeukaryotic community composition and dynamics in a Canadian river undergoing prolonged ice-cover winters. Our analysis revealed a large protist diversity in this fluctuating ecosystem and clear seasonal patterns demonstrating a direct and/or indirect selective role of abiotic factors, such as water temperature or nitrogen concentrations, in structuring the eukaryotic microbial community. Nonetheless, our results also revealed that primary productivity, predatory as well as parasitism lifestyles, inferred from fine phylogenetic placements, remained potentially present over the annual cycle, despite the large seasonal fluctuations and the remodeling of the community composition under ice. In addition, potential interplays with the bacterial community composition were identified supporting a possible contribution of the bacterial community to the temporal dynamics of the protist community structure. Our results illustrate the complexity of the eukaryotic microbial community and provide a substantive and useful dataset to better understand the global freshwater ecosystem functioning.
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Affiliation(s)
- Perrine Cruaud
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada.,Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC, Canada.,CRAD, Université Laval, Québec City, QC, Canada
| | - Adrien Vigneron
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada.,Centre D'Études Nordiques, Université Laval, Québec City, QC, Canada.,Département de Biologie, Université Laval, Québec City, QC, Canada
| | - Marie-Stéphanie Fradette
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada.,Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC, Canada.,CRAD, Université Laval, Québec City, QC, Canada
| | - Caetano C Dorea
- Department of Civil Engineering, University of Victoria, Victoria, BC, Canada
| | - Alexander I Culley
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada.,Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC, Canada.,Groupe de Recherche en Ecologie Buccale, Faculté de Médecine Dentaire, Université Laval, Québec City, QC, Canada
| | - Manuel J Rodriguez
- CRAD, Université Laval, Québec City, QC, Canada.,École Supérieure D'aménagement du Territoire et de Développement Régional (ESAD), Université Laval, Québec City, QC, Canada
| | - Steve J Charette
- Institut de Biologie Intégrative et des Systèmes, Université Laval, Québec City, QC, Canada.,Département de Biochimie, de Microbiologie et de Bio-Informatique, Faculté des Sciences et de Génie, Université Laval, Québec City, QC, Canada.,Centre de Recherche de l'Institut Universitaire de Cardiologie et de Pneumologie de Québec, Québec City, QC, Canada
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8
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Lepère C, Domaizon I, Humbert JF, Jardillier L, Hugoni M, Debroas D. Diversity, spatial distribution and activity of fungi in freshwater ecosystems. PeerJ 2019; 7:e6247. [PMID: 30809429 PMCID: PMC6387782 DOI: 10.7717/peerj.6247] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/30/2018] [Indexed: 12/31/2022] Open
Abstract
High-throughput sequencing has given new insights into aquatic fungal community ecology over the last 10 years. Based on 18S ribosomal RNA gene sequences publicly available, we investigated fungal richness and taxonomic composition among 25 lakes and four rivers. We used a single pipeline to process the reads from raw data to the taxonomic affiliation. In addition, we studied, for a subset of lakes, the active fraction of fungi through the 18S rRNA transcripts level. These results revealed a high diversity of fungi that can be captured by 18S rRNA primers. The most OTU-rich groups were Dikarya (47%), represented by putative filamentous fungi more diverse and abundant in freshwater habitats than previous studies have suggested, followed by Cryptomycota (17.6%) and Chytridiomycota (15.4%). The active fraction of the community showed the same dominant groups as those observed at the 18S rRNA genes level. On average 13.25% of the fungal OTUs were active. The small number of OTUs shared among aquatic ecosystems may result from the low abundances of those microorganisms and/or they constitute allochthonous fungi coming from other habitats (e.g., sediment or catchment areas). The richness estimates suggest that fungi have been overlooked and undersampled in freshwater ecosystems, especially rivers, though they play key roles in ecosystem functioning as saprophytes and parasites.
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Affiliation(s)
- Cécile Lepère
- Laboratoire: Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Isabelle Domaizon
- CARRTEL, Université Savoie Mont Blanc, INRA, Thonon Les Bains, France
| | | | - Ludwig Jardillier
- Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Mylène Hugoni
- CNRS, UMR5557, Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, Villeurbanne Cedex, France
| | - Didier Debroas
- Laboratoire: Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
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9
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What has happened to the “aquatic phycomycetes” (sensu Sparrow)? Part II: Shared properties of zoosporic true fungi and fungus-like microorganisms. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2017.09.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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10
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Shi X, Li S, Liu C, Zhang M, Liu M. Community structure of photosynthetic picoeukaryotes differs in lakes with different trophic statuses along the middle-lower reaches of the Yangtze River. FEMS Microbiol Ecol 2018; 94:4817532. [DOI: 10.1093/femsec/fiy011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2017] [Accepted: 01/18/2018] [Indexed: 02/04/2023] Open
Affiliation(s)
- Xiaoli Shi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Shengnan Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Changqing Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Zhang
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Mixue Liu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Gleason FH, Marano AV, Lilje O, Lange L. What has happened to the “aquatic phycomycetes” (sensu Sparrow)? Part I: A brief historical perspective. FUNGAL BIOL REV 2018. [DOI: 10.1016/j.fbr.2017.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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12
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Wurzbacher C, Grossart HP. Improved detection and identification of aquatic fungi and chitin in aquatic environments. Mycologia 2017; 104:1267-71. [DOI: 10.3852/11-225] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
| | - Hans-Peter Grossart
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries (IGB), Dept. Limnology of Stratified Lakes, Alte Fischerhuette 2, 16775 Stechlin, Germany
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13
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Lepère C, Ostrowski M, Hartmann M, Zubkov MV, Scanlan DJ. In situ associations between marine photosynthetic picoeukaryotes and potential parasites - a role for fungi? ENVIRONMENTAL MICROBIOLOGY REPORTS 2016; 8:445-51. [PMID: 26420747 DOI: 10.1111/1758-2229.12339] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 09/23/2015] [Accepted: 09/25/2015] [Indexed: 05/25/2023]
Abstract
Photosynthetic picoeukaryotes (PPEs) are important components of the marine picophytoplankton community playing a critical role in CO2 fixation but also as bacterivores, particularly in the oligotrophic gyres. Despite an increased interest in these organisms and an improved understanding of the genetic diversity of this group, we still know little of the environmental factors controlling the abundance of these organisms. Here, we investigated the quantitative importance of eukaryotic parasites in the free-living fraction as well as in associations with PPEs along a transect in the South Atlantic. Using tyramide signal amplification-fluorescence in situ hybridization (TSA-FISH), we provide quantitative evidence of the occurrence of free-living fungi in open ocean marine systems, while the Perkinsozoa and Syndiniales parasites were not abundant in these waters. Using flow cytometric cell sorting of different PPE populations followed by a dual-labelled TSA-FISH approach, we also demonstrate fungal associations, potentially parasitic, occurring with both pico-Prymnesiophyceae and pico-Chrysophyceae. These data highlight the necessity for further work investigating the specific role of marine fungi as parasites of phytoplankton to improve understanding of carbon flow in marine ecosystems.
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Affiliation(s)
- Cécile Lepère
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
- Université Clermont Auvergne, Université Blaise Pascal, Laboratoire 'Microorganismes : Génome et Environnement', BP 10448, Clermont-Ferrand, F-63000, France
- CNRS, UMR 6023, LMGE, Aubière, F-63171, France
| | - Martin Ostrowski
- Department of Chemistry and Biomolecular Sciences, Macquarie University, North Ryde, NSW, 2109, Australia
| | | | | | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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Nagahama T, Nagano Y. Cultured and uncultured fungal diversity in deep-sea environments. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2016; 53:173-87. [PMID: 22222832 DOI: 10.1007/978-3-642-23342-5_9] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The importance of fungi found in deep-sea extreme environments is becoming increasingly recognized. In this chapter, current scientific findings on the fungal diversity in several deep-sea environments by conventional culture and culture-independent methods are reviewed and discussed, primarily focused on culture-independent approaches. Fungal species detected by conventional culture methods mostly belonged to Ascomycota and Basidiomycota phyla. Culture-independent approaches have revealed the presence of highly novel fungal phylotypes, including new taxonomic groups placed in deep branches within the phylum Chytridiomycota and unknown ancient fungal groups. Future attempts to culture these unknown fungal groups may provide key insights into the early evolution of fungi and their ecological and physiological significance in deep-sea environments.
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Affiliation(s)
- Takahiko Nagahama
- Department of Food and Nutrition, Higashi-Chikushi Junior College, 5-1-1 Shimoitozu, Kokurakita-ku, Kitakyusyu, Fukuoka, 800-0351, Japan,
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Lepère C, Domaizon I, Hugoni M, Vellet A, Debroas D. Diversity and Dynamics of Active Small Microbial Eukaryotes in the Anoxic Zone of a Freshwater Meromictic Lake (Pavin, France). Front Microbiol 2016; 7:130. [PMID: 26904006 PMCID: PMC4748746 DOI: 10.3389/fmicb.2016.00130] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Accepted: 01/25/2016] [Indexed: 11/13/2022] Open
Abstract
Microbial eukaryotes play a crucial role in ecosystem functioning and oxygen is considered to be one of the strongest barriers against their local dispersal. However, diversity of microbial eukaryotes in freshwater habitats with oxygen gradients has previously received very little attention. We applied high-throughput sequencing (V4 region of the 18S rRNA gene) in conjunction with quantitative PCR (DNA and RNA) and fluorescent in situ hybridization (FISH) analyses, to provide an unique spatio-temporal analysis of microbial eukaryotes diversity and potential activity in a meromictic freshwater lake (lake Pavin). This study revealed a high genetic diversity of unicellular eukaryotes in the permanent anoxic zone of lake Pavin and allowed the discrimination of active vs. inactive components. Forty-two percent of the OTUs (Operational Taxonomic Units) are exclusively present in the monimolimnion, where Alveolata (Ciliophora and Dinophyceae) and Fungi (Dikarya and Chytrids) are the most active phyla and are probably represented by species capable of anaerobic metabolism. Pigmented eukaryotes (Haptophyceae and Chlorophyceae) are also present and active in this zone, which opens up questions regarding their metabolism.
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Affiliation(s)
- Cécile Lepère
- Laboratoire "Microorganismes: Génome et Environnement", Clermont Université, Université Blaise PascalClermont-Ferrand, France; Centre National de la Recherche Scientifique, UMR 6023, LMGEAubière, France
| | - Isabelle Domaizon
- Institut National de la Recherche Agronomique, UMR 42 CARRTELThonon-les-Bains, France; Université Savoie MontBlancChambéry, France
| | - Mylène Hugoni
- Laboratoire "Microorganismes: Génome et Environnement", Clermont Université, Université Blaise PascalClermont-Ferrand, France; Centre National de la Recherche Scientifique, UMR 6023, LMGEAubière, France
| | - Agnès Vellet
- Laboratoire "Microorganismes: Génome et Environnement", Clermont Université, Université Blaise PascalClermont-Ferrand, France; Centre National de la Recherche Scientifique, UMR 6023, LMGEAubière, France
| | - Didier Debroas
- Laboratoire "Microorganismes: Génome et Environnement", Clermont Université, Université Blaise PascalClermont-Ferrand, France; Centre National de la Recherche Scientifique, UMR 6023, LMGEAubière, France
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Capo E, Debroas D, Arnaud F, Domaizon I. Is Planktonic Diversity Well Recorded in Sedimentary DNA? Toward the Reconstruction of Past Protistan Diversity. MICROBIAL ECOLOGY 2015; 70:865-75. [PMID: 26022714 DOI: 10.1007/s00248-015-0627-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Accepted: 05/12/2015] [Indexed: 05/25/2023]
Abstract
Studies based on the coupling of a paleolimnological approach and molecular tools (e.g., sequencing of sedimentary DNA) present a promising opportunity to obtain long-term data on past lacustrine biodiversity. However, certain validations are still required, such as the evaluation of DNA preservation in sediments for various planktonic taxa that do not leave any morphological diagnostic features. In this study, we focused on the diversity of planktonic unicellular eukaryotes and verified the presence of their DNA in sediment archives. We compared the molecular inventories (high-throughput sequencing of 18S ribosomal DNA) obtained from monitoring the water column with those obtained for DNA archived in the first 30 cm of sediment. Seventy-one percent of taxonomic units found in the water samples were detected in sediment samples, including pigmented taxa, such as Chlorophyta, Dinophyceae, and Chrysophyceae, phagotrophic taxa, such as Ciliophora, parasitic taxa, such as Apicomplexa and Chytridiomycota, and saprotrophs, such as Cryptomycota. Parallel analysis of 18S ribosomal RNA (rRNA) transcripts revealed the presence of living eukaryotic taxa only in the top 2 cm of sediment; although some limits exist in using RNA/DNA ratio as indicator of microbial activity, these results suggested that the sedimentary DNA mostly represented DNA from past and inactive communities. Only the diversity of a few groups, such as Cryptophyta and Haptophyta, seemed to be poorly preserved in sediments. Our overall results showed that the application of sequencing techniques to sedimentary DNA could be used to reconstruct past diversity for numerous planktonic eukaryotic groups.
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Affiliation(s)
- Eric Capo
- INRA, UMR 42 CARRTEL, 74203, Thonon-les-bains Cedex, France
- Université Savoie Mont Blanc, UMR 42 CARRTEL, 73379, Le Bourget du Lac, France
| | - Didier Debroas
- Clermont Université, Université Blaise Pascal, CNRS, UMR 6023 LMGE, 63171, Aubière, France
| | - Fabien Arnaud
- CNRS, UMR 5204 EDYTEM, Université Savoie Mont Blanc, 73379, Le Bourget du Lac Cedex, France
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Cryptic infection of a broad taxonomic and geographic diversity of tadpoles by Perkinsea protists. Proc Natl Acad Sci U S A 2015; 112:E4743-51. [PMID: 26261337 DOI: 10.1073/pnas.1500163112] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The decline of amphibian populations, particularly frogs, is often cited as an example in support of the claim that Earth is undergoing its sixth mass extinction event. Amphibians seem to be particularly sensitive to emerging diseases (e.g., fungal and viral pathogens), yet the diversity and geographic distribution of infectious agents are only starting to be investigated. Recent work has linked a previously undescribed protist with mass-mortality events in the United States, in which infected frog tadpoles have an abnormally enlarged yellowish liver filled with protist cells of a presumed parasite. Phylogenetic analyses revealed that this infectious agent was affiliated with the Perkinsea: a parasitic group within the alveolates exemplified by Perkinsus sp., a "marine" protist responsible for mass-mortality events in commercial shellfish populations. Using small subunit (SSU) ribosomal DNA (rDNA) sequencing, we developed a targeted PCR protocol for preferentially sampling a clade of the Perkinsea. We tested this protocol on freshwater environmental DNA, revealing a wide diversity of Perkinsea lineages in these environments. Then, we used the same protocol to test for Perkinsea-like lineages in livers of 182 tadpoles from multiple families of frogs. We identified a distinct Perkinsea clade, encompassing a low level of SSU rDNA variation different from the lineage previously associated with tadpole mass-mortality events. Members of this clade were present in 38 tadpoles sampled from 14 distinct genera/phylogroups, from five countries across three continents. These data provide, to our knowledge, the first evidence that Perkinsea-like protists infect tadpoles across a wide taxonomic range of frogs in tropical and temperate environments, including oceanic islands.
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Mukherjee I, Hodoki Y, Nakano SI. Kinetoplastid flagellates overlooked by universal primers dominate in the oxygenated hypolimnion of Lake Biwa, Japan. FEMS Microbiol Ecol 2015; 91:fiv083. [PMID: 26187480 DOI: 10.1093/femsec/fiv083] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2015] [Indexed: 11/12/2022] Open
Abstract
Kinetoplastid flagellates, microscopically often detected from various aquatic environments and considered ubiquitous are seldom reported in molecular diversity studies with universal eukaryote DNA primers. To investigate this inconsistency, we examined nanoflagellate diversity in Lake Biwa, Japan by 18S rRNA gene clone libraries using universal eukaryote and kinetoplastid-specific primers. We also examined the abundance of kinetoplastids by Catalyzed Reporter Deposition-Fluorescence In Situ Hybridization. No, kinetoplastid sequences were detected in the universal eukaryote primers library from epilimnion and hypolimnion in different seasons. However, kinetoplastid flagellates were detected with kinetoplastid-specific probe from all of the seasons and contributed up to 11.9 and 36.0% of total eukaryotes in the epilimnion and hypolimnion, respectively. Thus, kinetoplastids probably are a significant, sometimes dominant, group in the hypolimnion, contributing up to 43.7% of the total flagellates. Using group-specific primers, kinetoplastid sequences were also obtained from both epilimnion and hypolimnion library. Therefore, we attributed the inconsistency to the divergent nature of 18S rRNA gene of kinetoplastids, which lead to their undetection in the universal eukaryote primer libraries. This study revealed that kinetoplastids have significant ecological importance in the hypolimnion of Lake Biwa, suggesting that these flagellates have been overlooked in other studies using universal eukaryote primers.
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Affiliation(s)
- Indranil Mukherjee
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
| | - Yoshikuni Hodoki
- Department of Biology, Keio University, Yokohama, Kanagawa 223-8521, Japan
| | - Shin-Ichi Nakano
- Center for Ecological Research, Kyoto University, Otsu, Shiga 520-2113, Japan
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Gleason FH, Chambouvet A, Sullivan BK, Lilje O, Rowley JJ. Multiple zoosporic parasites pose a significant threat to amphibian populations. FUNGAL ECOL 2014. [DOI: 10.1016/j.funeco.2014.04.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Chambouvet A, Berney C, Romac S, Audic S, Maguire F, De Vargas C, Richards TA. Diverse molecular signatures for ribosomally 'active' Perkinsea in marine sediments. BMC Microbiol 2014; 14:110. [PMID: 24779375 PMCID: PMC4044210 DOI: 10.1186/1471-2180-14-110] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 04/03/2014] [Indexed: 01/09/2023] Open
Abstract
Background Perkinsea are a parasitic lineage within the eukaryotic superphylum Alveolata. Recent studies making use of environmental small sub-unit ribosomal RNA gene (SSU rDNA) sequencing methodologies have detected a significant diversity and abundance of Perkinsea-like phylotypes in freshwater environments. In contrast only a few Perkinsea environmental sequences have been retrieved from marine samples and only two groups of Perkinsea have been cultured and morphologically described and these are parasites of marine molluscs or marine protists. These two marine groups form separate and distantly related phylogenetic clusters, composed of closely related lineages on SSU rDNA trees. Here, we test the hypothesis that Perkinsea are a hitherto under-sampled group in marine environments. Using 454 diversity ‘tag’ sequencing we investigate the diversity and distribution of these protists in marine sediments and water column samples taken from the Deep Chlorophyll Maximum (DCM) and sub-surface using both DNA and RNA as the source template and sampling four European offshore locations. Results We detected the presence of 265 sequences branching with known Perkinsea, the majority of them recovered from marine sediments. Moreover, 27% of these sequences were sampled from RNA derived cDNA libraries. Phylogenetic analyses classify a large proportion of these sequences into 38 cluster groups (including 30 novel marine cluster groups), which share less than 97% sequence similarity suggesting this diversity encompasses a range of biologically and ecologically distinct organisms. Conclusions These results demonstrate that the Perkinsea lineage is considerably more diverse than previously detected in marine environments. This wide diversity of Perkinsea-like protists is largely retrieved in marine sediment with a significant proportion detected in RNA derived libraries suggesting this diversity represents ribosomally ‘active’ and intact cells. Given the phylogenetic range of hosts infected by known Perkinsea parasites, these data suggest that Perkinsea either play a significant but hitherto unrecognized role as parasites in marine sediments and/or members of this group are present in the marine sediment possibly as part of the ‘seed bank’ microbial community.
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Affiliation(s)
- Aurélie Chambouvet
- Life Sciences, The Natural History Museum, Cromwell Road, London SW7 5BD, UK.
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21
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Spatial structure of eukaryotic ultraplankton community in the northern South China Sea. Biologia (Bratisl) 2014. [DOI: 10.2478/s11756-014-0361-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Zhong X, Jacquet S. Contrasting diversity of phycodnavirus signature genes in two large and deep western European lakes. Environ Microbiol 2013; 16:759-73. [DOI: 10.1111/1462-2920.12201] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2013] [Revised: 05/14/2013] [Accepted: 06/22/2013] [Indexed: 01/11/2023]
Affiliation(s)
- Xu Zhong
- INRA; UMR CARRTEL; 75 Avenue de Corzent 74203 Thonon-les-Bains cx France
| | - Stéphan Jacquet
- INRA; UMR CARRTEL; 75 Avenue de Corzent 74203 Thonon-les-Bains cx France
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Seenivasan R, Sausen N, Medlin LK, Melkonian M. Picomonas judraskeda gen. et sp. nov.: the first identified member of the Picozoa phylum nov., a widespread group of picoeukaryotes, formerly known as 'picobiliphytes'. PLoS One 2013; 8:e59565. [PMID: 23555709 PMCID: PMC3608682 DOI: 10.1371/journal.pone.0059565] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2012] [Accepted: 02/19/2013] [Indexed: 01/21/2023] Open
Abstract
In 2007, a novel, putatively photosynthetic picoeukaryotic lineage, the ‘picobiliphytes’, with no known close eukaryotic relatives, was reported from 18S environmental clone library sequences and fluorescence in situ hybridization. Although single cell genomics later showed these organisms to be heterotrophic rather than photosynthetic, until now this apparently widespread group of pico-(or nano-)eukaryotes has remained uncultured and the organisms could not be formally recognized. Here, we describe Picomonas judraskeda gen. et sp. nov., from marine coastal surface waters, which has a ‘picobiliphyte’ 18S rDNA signature. Using vital mitochondrial staining and cell sorting by flow cytometry, a single cell-derived culture was established. The cells are biflagellate, 2.5–3.8×2–2.5 µm in size, lack plastids and display a novel stereotypic cycle of cell motility (described as the “jump, drag, and skedaddle”-cycle). They consist of two hemispherical parts separated by a deep cleft, an anterior part that contains all major cell organelles including the flagellar apparatus, and a posterior part housing vacuoles/vesicles and the feeding apparatus, both parts separated by a large vacuolar cisterna. From serial section analyses of cells, fixed at putative stages of the feeding cycle, it is concluded that cells are not bacterivorous, but feed on small marine colloids of less than 150 nm diameter by fluid-phase, bulk flow endocytosis. Based on the novel features of cell motility, ultrastructure and feeding, and their isolated phylogenetic position, we establish a new phylum, Picozoa, for Picomonas judraskeda, representing an apparently widespread and ecologically important group of heterotrophic picoeukaryotes, formerly known as ‘picobiliphytes’.
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Affiliation(s)
- Ramkumar Seenivasan
- Department of Botany, Cologne Biocenter, University of Cologne, Cologne, Germany.
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Mangot JF, Domaizon I, Taib N, Marouni N, Duffaud E, Bronner G, Debroas D. Short-term dynamics of diversity patterns: evidence of continual reassembly within lacustrine small eukaryotes. Environ Microbiol 2013; 15:1745-58. [DOI: 10.1111/1462-2920.12065] [Citation(s) in RCA: 95] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 10/03/2012] [Accepted: 11/22/2012] [Indexed: 12/20/2022]
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Parveen B, Mary I, Vellet A, Ravet V, Debroas D. Temporal dynamics and phylogenetic diversity of free-living and particle-associatedVerrucomicrobiacommunities in relation to environmental variables in a mesotrophic lake. FEMS Microbiol Ecol 2012; 83:189-201. [DOI: 10.1111/j.1574-6941.2012.01469.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2011] [Revised: 07/25/2012] [Accepted: 07/26/2012] [Indexed: 11/28/2022] Open
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Weber F, del Campo J, Wylezich C, Massana R, Jürgens K. Unveiling trophic functions of uncultured protist taxa by incubation experiments in the brackish Baltic Sea. PLoS One 2012; 7:e41970. [PMID: 22860041 PMCID: PMC3408427 DOI: 10.1371/journal.pone.0041970] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Accepted: 06/28/2012] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Our knowledge of the phylogeny and diversity of aquatic protists is rapidly increasing due to molecular surveys and next-generation sequencing approaches. This has led to a considerable discrepancy between the taxa known from cultures and those known from environmental 18S rRNA gene sequences. Hence, it is generally difficult to assign ecological functions to new taxa detected by culture-independent molecular approaches. METHODOLOGY/PRINCIPAL FINDINGS A combination of unamended dark incubations and 18S rRNA sequencing was chosen to link molecular diversity data of uncultured protists with heterotrophic, presumably bacterivorous, growth. The incubations, conducted with Baltic Sea brackish water, resulted in a consistent shift from a protistan community dominated by phototrophs to one in which heterotrophs predominated. This was determined on the basis of cell abundance and 18S rRNA sequences derived from fingerprint analysis and clone libraries. The bulk of enriched phylotypes after incubation were related to hitherto uncultured marine taxa within chrysophytes, ochrophytes, choanoflagellates, cercozoans, and picobiliphytes, mostly represented in recently established or here defined environmental clades. Their growth in the dark, together with coinciding results from studies with a similar objective, provides evidence that these uncultured taxa represent heterotrophic or mixotrophic species. CONCLUSIONS/SIGNIFICANCE These findings shed some light into the trophic role of diverse uncultured protists especially within functionally heterogeneous groups (e.g., chrysophytes, ochrophytes) and groups that appear to be puzzling with regard to their nutrition (picobiliphytes). Additionally, our results indicate that the heterotrophic flagellate community in the southwestern Baltic Sea is dominated by species of marine origin. The combination of unamended incubations with molecular diversity analysis is thus confirmed as a promising approach to explore the trophic mode of environmentally relevant protist taxa for which only sequence data are currently available.
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Affiliation(s)
- Felix Weber
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany.
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Nagahama T, Takahashi E, Nagano Y, Abdel-Wahab MA, Miyazaki M. Molecular evidence that deep-branching fungi are major fungal components in deep-sea methane cold-seep sediments. Environ Microbiol 2011; 13:2359-70. [PMID: 21605311 DOI: 10.1111/j.1462-2920.2011.02507.x] [Citation(s) in RCA: 111] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The motile cells of chytrids were once believed to be relics from the time before the colonization of land by fungi. However, the majority of chytrids had not been found in marine but freshwater environments. We investigated fungal diversity by a fungal-specific PCR-based analysis of environmental DNA in deep-sea methane cold-seep sediments, identifying a total of 35 phylotypes, 12 of which were early diverging fungi (basal fungi, ex 'lower fungi'). The basal fungi occupied a major portion of fungal clones. These were phylogenetically placed into a deep-branching clade of fungi and the LKM11 clade that was a divergent group comprised of only environmental clones from aquatic environments. As suggested by Lara and colleagues, species of the endoparasitic genus Rozella, being recently considered of the earliest branching taxa of fungi, were nested within the LKM11 clade. In the remaining 23 phylotypes identified as the Dikarya, the majority of which were similar to those which appeared in previously deep-sea studies, but also highly novel lineages associated with Soil Clone Group I (SCGI), Entorrhiza sp. and the agaricomycetous fungi were recorded. The fungi of the Dikarya may play a role in the biodegradation of lignin and lignin-derived materials in deep-sea, because the characterized fungal species related to the frequent phylotypes within the Dikarya have been reported to possess an ability to degrade lignin.
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Affiliation(s)
- Takahiko Nagahama
- Department of Foods and Human Nutrition, Higashi-Chikushi Junior College, 5-1-1 Shimoitozu, Kokurakita-ku, Kitakyusyu, 803-8511, Japan.
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Jones MDM, Forn I, Gadelha C, Egan MJ, Bass D, Massana R, Richards TA. Discovery of novel intermediate forms redefines the fungal tree of life. Nature 2011; 474:200-3. [DOI: 10.1038/nature09984] [Citation(s) in RCA: 334] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2009] [Accepted: 03/07/2011] [Indexed: 11/09/2022]
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Gachon CMM, Sime-Ngando T, Strittmatter M, Chambouvet A, Kim GH. Algal diseases: spotlight on a black box. TRENDS IN PLANT SCIENCE 2010; 15:633-40. [PMID: 20833575 DOI: 10.1016/j.tplants.2010.08.005] [Citation(s) in RCA: 112] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 08/06/2010] [Accepted: 08/14/2010] [Indexed: 05/25/2023]
Abstract
Like any other living organisms, algae are plagued by diseases caused by fungi, protists, bacteria or viruses. As aquaculture continues to rise worldwide, pathogens of nori or biofuel sources are becoming a significant economic burden. Parasites are also increasingly being considered of equal importance with predators for ecosystem functioning. Altered disease patterns in disturbed environments are blamed for sudden extinctions, regime shifts, and spreading of alien species. Here we review the biodiversity and impact of pathogens and parasites of aquatic primary producers in freshwater and marine systems. We also cover recent advances on algal defence reactions, and discuss how emerging technologies can be used to reassess the profound, multi-faceted, and so far broadly-overlooked influence of algal diseases on ecosystem properties.
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Affiliation(s)
- Claire M M Gachon
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, PA37 1QA, United Kingdom.
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Lepère C, Masquelier S, Mangot JF, Debroas D, Domaizon I. Vertical structure of small eukaryotes in three lakes that differ by their trophic status: a quantitative approach. ISME JOURNAL 2010; 4:1509-19. [DOI: 10.1038/ismej.2010.83] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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