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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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Jeevannavar A, Narwani A, Matthews B, Spaak P, Brantschen J, Mächler E, Altermatt F, Tamminen M. Foundation species stabilize an alternative eutrophic state in nutrient-disturbed ponds via selection on microbial community. Front Microbiol 2024; 15:1310374. [PMID: 38628870 PMCID: PMC11019512 DOI: 10.3389/fmicb.2024.1310374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/04/2024] [Indexed: 04/19/2024] Open
Abstract
Eutrophication due to nutrient addition can result in major alterations in aquatic ecosystem productivity. Foundation species, individually and interactively, whether present as invasive species or as instruments of ecosystem management and restoration, can have unwanted effects like stabilizing turbid eutrophic states. In this study, we used whole-pond experimental manipulations to investigate the impacts of disturbance by nutrient additions in the presence and absence of two foundation species: Dreissena polymorpha (a freshwater mussel) and Myriophyllum spicatum (a macrophyte). We tracked how nutrient additions to ponds changed the prokaryotic and eukaryotic communities, using 16S, 18S, and COI amplicon sequencing. The nutrient disturbance and foundation species imposed strong selection on the prokaryotic communities, but not on the microbial eukaryotic communities. The prokaryotic communities changed increasingly over time as the nutrient disturbance intensified. Post-disturbance, the foundation species stabilized the prokaryotic communities as observed by the reduced rate of change in community composition. Our analysis suggests that prokaryotic community change contributed both directly and indirectly to major changes in ecosystem properties, including pH and dissolved oxygen. Our work shows that nutrient disturbance and foundation species strongly affect the prokaryotic community composition and stability, and that the presence of foundation species can, in some cases, promote the emergence and persistence of a turbid eutrophic ecosystem state.
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Affiliation(s)
| | - Anita Narwani
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
| | - Blake Matthews
- Department of Fish Ecology and Evolution, Eawag, Kastanienbaum, Switzerland
| | - Piet Spaak
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
| | - Jeanine Brantschen
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Elvira Mächler
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Florian Altermatt
- Department of Aquatic Ecology, Eawag, Dübendorf, Switzerland
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zürich, Switzerland
| | - Manu Tamminen
- Department of Biology, University of Turku, Turku, Finland
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3
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Monjot A, Bronner G, Courtine D, Cruaud C, Da Silva C, Aury JM, Gavory F, Moné A, Vellet A, Wawrzyniak I, Colombet J, Billard H, Debroas D, Lepère C. Functional diversity of microbial eukaryotes in a meromictic lake: Coupling between metatranscriptomic and a trait-based approach. Environ Microbiol 2023; 25:3406-3422. [PMID: 37916456 DOI: 10.1111/1462-2920.16531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 10/19/2023] [Indexed: 11/03/2023]
Abstract
The advent of high-throughput sequencing has led to the discovery of a considerable diversity of microbial eukaryotes in aquatic ecosystems, nevertheless, their function and contribution to the trophic food web functioning remain poorly characterized especially in freshwater ecosystems. Based on metabarcoding data obtained from a meromictic lake ecosystem (Pavin, France), we performed a morpho-physio-phenological traits-based approach to infer functional groups of microbial eukaryotes. Metatranscriptomic data were also analysed to assess the metabolic potential of these groups across the diel cycle, size fraction, sampling depth, and periods. Our analysis highlights a huge microbial eukaryotic diversity in the monimolimnion characterized by numerous saprotrophs expressing transcripts related to sulfur and nitrate metabolism as well as dissolved and particulate organic matter degradation. We also describe strong seasonal variations of microbial eukaryotes in the mixolimnion, especially for parasites and mixoplankton. It appears that the water mixing (occurring during spring and autumn) which benefits photosynthetic host communities also promotes parasitic fungi dissemination and over-expression of genes involved in the zoospore phototaxis and stage transition in the parasitic cycle. Mixoplanktonic haptophytes over-expressing photosynthesis-, endocytosis- and phagosome-linked genes under nutrient limitation also suggest that phagotrophy may provide them an advantage over non-phagotrophic phytoplankton.
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Affiliation(s)
- Arthur Monjot
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Gisèle Bronner
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Damien Courtine
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Corinne Cruaud
- Genoscope, Institut de Biologie François Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Frederick Gavory
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France
| | - Anne Moné
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Agnès Vellet
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Ivan Wawrzyniak
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jonathan Colombet
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Hermine Billard
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Didier Debroas
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Cécile Lepère
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
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4
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Zhang Z, Li H, Shen W, Du X, Li S, Wei Z, Zhang Z, Feng K, Deng Y. The large-scale spatial patterns of ecological networks between phytoplankton and zooplankton in coastal marine ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 827:154285. [PMID: 35248637 DOI: 10.1016/j.scitotenv.2022.154285] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 11/22/2021] [Accepted: 02/28/2022] [Indexed: 06/14/2023]
Abstract
Although autotrophic phytoplankton and heterotrophic zooplankton both play important roles in the food web of marine ecosystem, their comprehensive interactions and spatial patterns at continental scale remain poorly studied. Here, we collected 251 seawater samples along 13,000 km of Chinese coastline, and microscopically investigated the latitudinal gradients of planktonic diversities. In total, 307 phytoplanktonic and 311 zooplanktonic species were visually identified. Using the newly developed Inter-Domain Ecological Networks (IDENs) approach, the phytoplankton-zooplankton interaction networks were constructed. We found that the phyto-zooplankton network structure was varied across three regions, more complex and numerous connections along the southern coast than in the north. In addition, some particular associations between zooplanktonic and phytoplanktonic groups were found to be localized in specific regions. Furthermore, the seawater temperature and salinity were the major driving force for shaping planktonic interaction networks. These results provide a deeper understanding of planktonic biogeography and phytoplankton-zooplankton interaction patterns.
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Affiliation(s)
- Zheng Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Hongjun Li
- State Environmental Protection Key Laboratory of Coastal Ecosystem, National Marine Environmental Monitoring Center, Dalian, 116023, China
| | - Wenli Shen
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Xiongfeng Du
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shuzhen Li
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education) and Dalian POCT Laboratory, School of Environmental Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Ziyan Wei
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhaojing Zhang
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China
| | - Kai Feng
- CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Ye Deng
- Institute of Marine Science and Technology, Shandong University, Qingdao 266237, China; CAS Key Laboratory for Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China.
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5
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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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6
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FERMANI PAULINA, LAGOMARSINO LEONARDO, TORREMORRELL ANA, ESCARAY ROBERTO, BUSTINGORRY JOSÉ, LLAMES MARÍA, PÉREZ GONZALO, ZAGARESE HORACIO, MATALONI GABRIELA. Divergent dynamics of microbial components in two temperate shallow lakes with contrasting steady states in the Southern Hemisphere. AN ACAD BRAS CIENC 2022; 94:e20191545. [DOI: 10.1590/0001-3765202220191545] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 08/21/2020] [Indexed: 11/22/2022] Open
Affiliation(s)
| | | | | | | | | | - MARÍA LLAMES
- Universidad Nacional de San Martín/UNSAM, Argentina
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7
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Lake Sedimentary DNA Research on Past Terrestrial and Aquatic Biodiversity: Overview and Recommendations. QUATERNARY 2021. [DOI: 10.3390/quat4010006] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The use of lake sedimentary DNA to track the long-term changes in both terrestrial and aquatic biota is a rapidly advancing field in paleoecological research. Although largely applied nowadays, knowledge gaps remain in this field and there is therefore still research to be conducted to ensure the reliability of the sedimentary DNA signal. Building on the most recent literature and seven original case studies, we synthesize the state-of-the-art analytical procedures for effective sampling, extraction, amplification, quantification and/or generation of DNA inventories from sedimentary ancient DNA (sedaDNA) via high-throughput sequencing technologies. We provide recommendations based on current knowledge and best practises.
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Capo E, Ninnes S, Domaizon I, Bertilsson S, Bigler C, Wang XR, Bindler R, Rydberg J. Landscape Setting Drives the Microbial Eukaryotic Community Structure in Four Swedish Mountain Lakes over the Holocene. Microorganisms 2021; 9:microorganisms9020355. [PMID: 33670228 PMCID: PMC7916980 DOI: 10.3390/microorganisms9020355] [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: 01/07/2021] [Revised: 02/03/2021] [Accepted: 02/08/2021] [Indexed: 12/21/2022] Open
Abstract
On the annual and interannual scales, lake microbial communities are known to be heavily influenced by environmental conditions both in the lake and in its terrestrial surroundings. However, the influence of landscape setting and environmental change on shaping these communities over a longer (millennial) timescale is rarely studied. Here, we applied an 18S metabarcoding approach to DNA preserved in Holocene sediment records from two pairs of co-located Swedish mountain lakes. Our data revealed that the microbial eukaryotic communities were strongly influenced by catchment characteristics rather than location. More precisely, the microbial communities from the two bedrock lakes were largely dominated by unclassified Alveolata, while the peatland lakes showed a more diverse microbial community, with Ciliophora, Chlorophyta and Chytrids among the more predominant groups. Furthermore, for the two bedrock-dominated lakes-where the oldest DNA samples are dated to only a few hundred years after the lake formation-certain Alveolata, Chlorophytes, Stramenopiles and Rhizaria taxa were found prevalent throughout all the sediment profiles. Our work highlights the importance of species sorting due to landscape setting and the persistence of microbial eukaryotic diversity over millennial timescales in shaping modern lake microbial communities.
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Affiliation(s)
- Eric Capo
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
- Correspondence:
| | - Sofia Ninnes
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
| | - Isabelle Domaizon
- UMR CARRTEL, INRAE, Université Savoie Mont Blanc, 74200 Thonon les Bains, France;
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, SLU, 75007 Uppsala, Sweden;
| | - Christian Bigler
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
| | - Xiao-Ru Wang
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
| | - Richard Bindler
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
| | - Johan Rydberg
- Department of Ecology and Environmental Science, Umeå University, 90187 Umeå, Sweden; (S.N.); (C.B.); (X.-R.W.); (R.B.); (J.R.)
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9
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Jeong M, Kim JI, Nam SW, Shin W. Molecular Phylogeny and Taxonomy of the Genus Spumella (Chrysophyceae) Based on Morphological and Molecular Evidence. FRONTIERS IN PLANT SCIENCE 2021; 12:758067. [PMID: 34764972 PMCID: PMC8577464 DOI: 10.3389/fpls.2021.758067] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/04/2021] [Indexed: 05/08/2023]
Abstract
The genus Spumella, established by Cienkowsky in 1870, is characterized by omnivory, two (rarely three) flagella, a short stick-like structure beneath the flagella, a threadlike stalk, cell division via constriction and cyst formation. Since the first phylogenetic study of Spumella-like flagellates, their paraphyly has consistently been shown, with separation into several genera. More recently, Spumella was carefully investigated using molecular and morphological data to propose seven new species. Classification of this genus and knowledge of its species diversity remain limited because Spumella-like flagellates are extremely difficult to identify based on limited morphological characters. To understand the phylogeny and taxonomy of Spumella, we analyzed molecular and morphological data from 47 strains, including 18 strains isolated from Korean ponds or swamps. Nuclear SSU, ITS and LSU rDNA data were used for maximum likelihood and Bayesian analyses. The molecular data divided the strains into 15 clades, including seven new lineages, each with unique molecular signatures for nuclear SSU rRNA from the E23-2 to E23-5 domains, the spacer between the E23-8 and E23-9 domains of the V4 region and domain 29 of the V5 region. Our results revealed increased species diversity in Spumella. In contrast to the molecular phylogeny results, the taxa showed very similar cell morphologies, suggesting morphological convergence into simple nanoflagellates to enable heterotrophy. Three new species produced stomatocysts in culture. Aspects of stomatocyst morphology, including collar structure, surface ornamentation, and cyst shape, were very useful in differentiating the three species. The general ultrastructure of Spumella bureschii strain Baekdongje012018B8 and S. benthica strain Hwarim032418A5 showed the typical chrysophyte form for the leucoplast, a vestigial chloroplast surrounded by four envelope membranes, supporting the hypothesis that Spumella evolved from a phototroph to a heterotroph via the loss of its photosynthetic ability. Seven new species are proposed: S. benthica, S. communis, S. longicolla, S. oblata, S. rotundata, S. similis, and S. sinechrysos.
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Affiliation(s)
- Minseok Jeong
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Jong Im Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Seung Won Nam
- Nakdonggang National Institute of Biological Resources, Sangju-si, South Korea
| | - Woongghi Shin
- Department of Biology, Chungnam National University, Daejeon, South Korea
- *Correspondence: Woongghi Shin,
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10
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Seasonal Water Level Fluctuation and Concomitant Change of Nutrients Shift Microeukaryotic Communities in a Shallow Lake. WATER 2020. [DOI: 10.3390/w12092317] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Seasonal water level fluctuations (WLFs) impose dramatic influences on lake ecosystems. The influences of WLFs have been well studied for many lake biotas but the microeukaryotic community remains one of the least-explored features. This study employed high-throughput 18S rRNA gene sequencing to investigate the spatiotemporal patterns of microeukaryotic communities in the dry and wet seasons with concomitant change of nutrients in Poyang Lake, which experiences huge seasonal WLFs. The results showed that the dry season and wet season had distinct microeukaryotic community compositions and structures. In the dry season, Ciliophora (13.86–40.98%) and Cryptomonas (3.69–18.64%) were the dominant taxa, and the relative abundance of these taxa were significant higher in the dry season than wet season. Ochrophyta (6.88–45.67%) and Chlorophyta (6.31–22.10%) was the dominant taxa of microeukaryotic communities in the wet season. The seasonal variation of microeukaryotic communities was strongly correlated to seasonal nutrient variations. Microeukaryotic communities responded significantly to dissolved organic carbon, total nitrogen, nitrate, and soluble reactive phosphorus in the dry season, and correlated to nitrate and total phosphorus in the wet season. The microeukaryotic community showed different modular structures in two seasons, and nutrient variations were the key factors influencing seasonal variations of the modular structures. Moreover, microeukaryotic community networks based on different seasons indicated that the microeukaryotic community co-occurrence patterns were not constant but varied largely associating with the nitrogen and phosphorus variations under the effects of WLFs. Our results are important for understanding how microeukaryotic communities respond to nutrient variation under seasonal water level fluctuation.
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11
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Chessa D, Murgia M, Sias E, Deligios M, Mazzarello V, Fiamma M, Rovina D, Carenti G, Ganau G, Pintore E, Fiori M, Kay GL, Ponzeletti A, Cappuccinelli P, Kelvin DJ, Wain J, Rubino S. Metagenomics and microscope revealed T. trichiura and other intestinal parasites in a cesspit of an Italian nineteenth century aristocratic palace. Sci Rep 2020; 10:12656. [PMID: 32728085 PMCID: PMC7391740 DOI: 10.1038/s41598-020-69497-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 07/08/2020] [Indexed: 11/09/2022] Open
Abstract
This study evidenced the presence of parasites in a cesspit of an aristocratic palace of nineteenth century in Sardinia (Italy) by the use of classical paleoparasitological techniques coupled with next-generation sequencing. Parasite eggs identified by microscopy included helminth genera pathogenic for humans and animals: the whipworm Trichuris sp., the roundworm Ascaris sp., the flatworm Dicrocoelium sp. and the fish tapeworm Diphyllobothrium sp. In addition, 18S rRNA metabarcoding and metagenomic sequencing analysis allowed the first description in Sardinia of aDNA of the human specific T. trichiura species and Ascaris genus. Their presence is important for understanding the health conditions, hygiene habits, agricultural practices and the diet of the local inhabitants in the period under study.
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Affiliation(s)
- Daniela Chessa
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Manuela Murgia
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy.
| | - Emanuela Sias
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Massimo Deligios
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Vittorio Mazzarello
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Maura Fiamma
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Daniela Rovina
- Superintendence Archaeology of Sardinia, 07100, Sassari, Italy
| | - Gabriele Carenti
- Department of Nature and Environmental Sciences, University of Sassari, 07100, Sassari, Italy
| | - Giulia Ganau
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - Elisabetta Pintore
- Department of Veterinary Medicine, University of Sassari, 07100, Sassari, Italy
| | | | - Gemma L Kay
- Bob Champion Research and Educational Building, University of East Anglia, Norwich Research Park, Norwich, UK
- The Quadram Institute, Norwich Research Park, Norwich, UK
| | | | - Piero Cappuccinelli
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
| | - David J Kelvin
- Department of Microbiology and Immunology, Dalhousie University, Halifax, NS, Canada
| | - John Wain
- Bob Champion Research and Educational Building, University of East Anglia, Norwich Research Park, Norwich, UK
- The Quadram Institute, Norwich Research Park, Norwich, UK
| | - Salvatore Rubino
- Department of Biomedical Science, University of Sassari, V. le San Pietro 43/B, 07100, Sassari, Italy
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12
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Liu C, Shi X, Wu F, Zhang M, Gao G, Wu Q. Temporal patterns in the interaction between photosynthetic picoeukaryotes and their attached fungi in Lake Chaohu. FEMS Microbiol Ecol 2020; 96:5859481. [DOI: 10.1093/femsec/fiaa123] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 06/17/2020] [Indexed: 12/11/2022] Open
Abstract
ABSTRACT
The combination of flow cytometric sorting and high-throughput sequencing revealed the broad existence of photosynthetic picoeukaryote attached fungi (PPE-attached fungi) in Lake Chaohu. The relative sequence abundance of attached fungi was negatively correlated with that of the photosynthetic picoeukaryotes (PPEs). PPE-attached fungal communities were mainly composed of Basidiomycota, Chytridiomycota and Ascomycota. Temperature, Si and PPE community structure are the most important driving factors for the temporal succession of PPE-attached fungal communities. In particular, PPE-attached fungi can be divided into three groups from high to low temperatures. Phylogenetic molecular ecological network results indicated that the connectivity and the total number of links in the network of the high-temperature group (> 21.82°C) are higher than those in the other two temperature groups (between 9.67 and 21.82°C, and < 9.67°C, respectively). Moreover, the interaction between PPE-attached fungi and the PPEs changed from antagonistic to cooperative, with the decline in temperature. The most abundant operational taxonomic units of PPE-attached fungi were affiliated with the Cladosporium, the most common saprophytic fungus, whereas most fungal hub taxa were Chytridiomycota, the main parasite fungi of phytoplankton.
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Affiliation(s)
- 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
| | - Xiaoli Shi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Fan Wu
- 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
| | - Guang Gao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qinglong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
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13
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Abstract
Fungi are phylogenetically and functionally diverse ubiquitous components of almost all ecosystems on Earth, including aquatic environments stretching from high montane lakes down to the deep ocean. Aquatic ecosystems, however, remain frequently overlooked as fungal habitats, although fungi potentially hold important roles for organic matter cycling and food web dynamics. Recent methodological improvements have facilitated a greater appreciation of the importance of fungi in many aquatic systems, yet a conceptual framework is still missing. In this Review, we conceptualize the spatiotemporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic food webs. We focus on currently unexplored fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats.
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14
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Shi X, Li S, Zhang M, Liu C, Wu Q. Temperature mainly determines the temporal succession of the photosynthetic picoeukaryote community in Lake Chaohu, a highly eutrophic shallow lake. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 702:134803. [PMID: 31731125 DOI: 10.1016/j.scitotenv.2019.134803] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 09/30/2019] [Accepted: 10/02/2019] [Indexed: 05/25/2023]
Abstract
Photosynthetic picoeukaryotes (PPEs) are key players in aquatic systems, while their diversity and community composition dynamics remain poorly understood. The monthly composition of PPEs in Lake Chaohu was investigated using a combination of flow cytometry sorting and high throughput sequencing. Results indicated that temperature is the most important factor shaping PPEs community structure. The PPEs community can be categorized into three groups that are dominant at different temperature ranges: high temperature (>21.8 °C), intermediate temperature (between 9.8 °C and 21.8 °C) and low temperature (<9.8 °C). At the supergroup level, Cryptophyta were dominant at the intermediate temperature level, and Bacillariophyta were prevalent at low temperatures. In comparison, Chlorophyta PPEs were sensitive to temperature at the order level. Molecular network analysis using 18S rDNA sequencing results from sorted samples revealed that the Operational Taxonomic Units (OTUs) of PPE from the same taxonomic groups were predominantly positive, implying that they were occupying similar niches. The cooccurrence patterns between PPEs and fungi were mostly negative. In particular, OTU101, which was associated with Chytridiomycota, was negatively related to many OTUs belonging to Chlorophyta and Diatom, indicating that their potential parasitic associations may be not species-specific.
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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; Hunan Institute of Agro-Environment and Ecology, Hunan Academy of Agricultural Sciences, Changsha 410125, China
| | - Min Zhang
- 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
| | - Qinglong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 210008, China
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15
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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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16
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Shi X, Li S, Li H, Chen F, Wu Q. The Community Structure of Picophytoplankton in Lake Fuxian, a Deep and Oligotrophic Mountain Lake. Front Microbiol 2019; 10:2016. [PMID: 31551958 PMCID: PMC6737998 DOI: 10.3389/fmicb.2019.02016] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 08/19/2019] [Indexed: 12/26/2022] Open
Abstract
Spatial and seasonal dynamics of picophytoplankton were investigated by flow cytometry over a year in Lake Fuxian, a deep and oligotrophic mountain lake in southwest China. The contribution of picophytoplankton to the total Chl-a biomass and primary production were 50.1 and 66.1%, respectively. Picophytoplankton were mainly composed of phycoerythrin-rich picocyanobacteria (PE-cells) and photosynthetic picoeukaryotes (PPEs). PPEs were dominant in spring, reaching a maximum cell density of 3.0 × 104 cell mL–1, while PE-cells were prevalent in other seasons. PE-cell abundance was relatively similar throughout the year, except for a decrease in summer during the stratification period, when nutrient concentration was low. High-throughput sequencing results from the sorted samples revealed that Synechococcus was the major PE-cell type, while Chrysophyceae, Dinophyceae, Chlorophyceae, Eustigmatophyceae, and Prymnesiophyceae were equally important PPEs. In spring, PPEs were mainly composed of Chlorophyceae and Trebouxiophyceae, while in summer, their dominance was replaced by that of Chrysophyceae and Prymnesiophyceae. Eustigmatophyceae and Chlorophyceae became the major PPEs in autumn, and Dinophyceae became the most abundant in winter. Single cells of Microcystis were usually detected in summer in the south, suggesting the deterioration of the water quality in Lake Fuxian.
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Affiliation(s)
- Xiaoli Shi
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Shengnan Li
- Hunan Institute of Agro-Environment and Ecology, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Huabing Li
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Feizhou Chen
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Qinglong Wu
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
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17
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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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18
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Rojas-Jimenez K, Wurzbacher C, Bourne EC, Chiuchiolo A, Priscu JC, Grossart HP. Early diverging lineages within Cryptomycota and Chytridiomycota dominate the fungal communities in ice-covered lakes of the McMurdo Dry Valleys, Antarctica. Sci Rep 2017; 7:15348. [PMID: 29127335 PMCID: PMC5681503 DOI: 10.1038/s41598-017-15598-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/30/2017] [Indexed: 01/08/2023] Open
Abstract
Antarctic ice-covered lakes are exceptional sites for studying the ecology of aquatic fungi under conditions of minimal human disturbance. In this study, we explored the diversity and community composition of fungi in five permanently covered lake basins located in the Taylor and Miers Valleys of Antarctica. Based on analysis of the 18S rRNA sequences, we showed that fungal taxa represented between 0.93% and 60.32% of the eukaryotic sequences. Cryptomycota and Chytridiomycota dominated the fungal communities in all lakes; however, members of Ascomycota, Basidiomycota, Zygomycota, and Blastocladiomycota were also present. Of the 1313 fungal OTUs identified, the two most abundant, belonging to LKM11 and Chytridiaceae, comprised 74% of the sequences. Significant differences in the community structure were determined among lakes, water depths, habitat features (i.e., brackish vs. freshwaters), and nucleic acids (DNA vs. RNA), suggesting niche differentiation. Network analysis suggested the existence of strong relationships among specific fungal phylotypes as well as between fungi and other eukaryotes. This study sheds light on the biology and ecology of basal fungi in aquatic systems. To our knowledge, this is the first report showing the predominance of early diverging lineages of fungi in pristine limnetic ecosystems, particularly of the enigmatic phylum Cryptomycota.
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Affiliation(s)
- Keilor Rojas-Jimenez
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, D-16775, Stechlin, Germany.,Universidad Latina de Costa Rica, Campus San Pedro, Apdo, 10138-1000, San Jose, Costa Rica
| | - Christian Wurzbacher
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, D-16775, Stechlin, Germany.,Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straβe 6-8, D-14195, Berlin, Germany
| | - Elizabeth Charlotte Bourne
- Berlin Center for Genomics in Biodiversity Research, Königin-Luise-Straβe 6-8, D-14195, Berlin, Germany.,Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Department of Ecosystem Research, Mϋggelseedamm 301 & 210, D-16775 Stechlin, Berlin, Germany
| | - Amy Chiuchiolo
- Montana State University, Department of Land Resources and Environmental Sciences, 334 Leon Johnson Hall, MT 59717, Bozeman, USA
| | - John C Priscu
- Montana State University, Department of Land Resources and Environmental Sciences, 334 Leon Johnson Hall, MT 59717, Bozeman, USA
| | - Hans-Peter Grossart
- Department of Experimental Limnology, Leibniz-Institute of Freshwater Ecology and Inland Fisheries, Alte Fischerhuette 2, D-16775, Stechlin, Germany. .,Institute for Biochemistry and Biology, Potsdam University, Maulbeerallee 2, 14469, Potsdam, Germany.
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19
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Environmental DNA as a tool for ecological monitoring of fungal communities. UKRAINIAN BOTANICAL JOURNAL 2017. [DOI: 10.15407/ukrbotj74.05.442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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20
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Abstract
The application of environmental DNA techniques and increased genome sequencing of microbial diversity, combined with detailed study of cellular characters, has consistently led to the reexamination of our understanding of the tree of life. This has challenged many of the definitions of taxonomic groups, especially higher taxonomic ranks such as eukaryotic kingdoms. The Fungi is an example of a kingdom which, together with the features that define it and the taxa that are grouped within it, has been in a continual state of flux. In this article we aim to summarize multiple lines of data pertinent to understanding the early evolution and definition of the Fungi. These include ongoing cellular and genomic comparisons that, we will argue, have generally undermined all attempts to identify a synapomorphic trait that defines the Fungi. This article will also summarize ongoing work focusing on taxon discovery, combined with phylogenomic analysis, which has identified novel groups that lie proximate/adjacent to the fungal clade-wherever the boundary that defines the Fungi may be. Our hope is that, by summarizing these data in the form of a discussion, we can illustrate the ongoing efforts to understand what drove the evolutionary diversification of fungi.
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21
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Capo E, Debroas D, Arnaud F, Perga ME, Chardon C, Domaizon I. Tracking a century of changes in microbial eukaryotic diversity in lakes driven by nutrient enrichment and climate warming. Environ Microbiol 2017; 19:2873-2892. [DOI: 10.1111/1462-2920.13815] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Revised: 05/21/2017] [Accepted: 05/30/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Eric Capo
- CARRTEL, INRA, Université de Savoie Mont Blanc; Thonon-les-bains 74200 France
| | - Didier Debroas
- Université Clermont Auvergne, Université Blaise Pascal, Laboratoire «Microorganismes: Génome et Environnement»; BP 10448 Clermont-Ferrand 63000 France
- CNRS, UMR 6023, LMGE; Campus Universitaire des Cézeaux, 63171 Aubière France
| | - Fabien Arnaud
- CNRS, UMR 5204 EDYTEM, Université Savoie Mont Blanc; Le Bourget du Lac Cedex France
| | - Marie-Elodie Perga
- CARRTEL, INRA, Université de Savoie Mont Blanc; Thonon-les-bains 74200 France
| | - Cécile Chardon
- CARRTEL, INRA, Université de Savoie Mont Blanc; Thonon-les-bains 74200 France
| | - Isabelle Domaizon
- CARRTEL, INRA, Université de Savoie Mont Blanc; Thonon-les-bains 74200 France
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22
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Li S, Bronner G, Lepère C, Kong F, Shi X. Temporal and spatial variations in the composition of freshwater photosynthetic picoeukaryotes revealed by MiSeq sequencing from flow cytometry sorted samples. Environ Microbiol 2017; 19:2286-2300. [DOI: 10.1111/1462-2920.13724] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2016] [Accepted: 03/05/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Shengnan Li
- State Key Laboratory of Lake Science and Environment; Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences; Nanjing 210008 China
- College of Resource and Environment, University of Chinese Academy of Sciences; Beijing 100049 China
| | - Gisèle Bronner
- Université Clermont Auvergne CNRS Laboratoire “Microorganismes: Génome et Environnement,”; CLERMONT-FERRAND F-63000 France
| | - Cécile Lepère
- Université Clermont Auvergne CNRS Laboratoire “Microorganismes: Génome et Environnement,”; CLERMONT-FERRAND F-63000 France
| | - Fanxiang Kong
- State Key Laboratory of Lake Science and Environment; Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences; Nanjing 210008 China
| | - Xiaoli Shi
- State Key Laboratory of Lake Science and Environment; Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences; Nanjing 210008 China
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23
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Liu L, Liu M, Wilkinson DM, Chen H, Yu X, Yang J. DNA metabarcoding reveals that 200-μm-size-fractionated filtering is unable to discriminate between planktonic microbial and large eukaryotes. Mol Ecol Resour 2017; 17:991-1002. [PMID: 28063202 DOI: 10.1111/1755-0998.12652] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Revised: 12/29/2016] [Accepted: 01/04/2017] [Indexed: 11/27/2022]
Abstract
Microeukaryotic plankton (0.2-200 μm) are critical components of aquatic ecosystems and key players in global ecological processes. High-throughput sequencing is currently revolutionizing their study on an unprecedented scale. However, it is currently unclear whether we can accurately, effectively and quantitatively depict the microeukaryotic plankton communities using traditional size-fractionated filtering combined with molecular methods. To address this, we analysed the eukaryotic plankton communities both with, and without, prefiltering with a 200 μm pore-size sieve -by using SSU rDNA-based high-throughput sequencing on 16 samples with three replicates in each sample from two subtropical reservoirs sampled from January to October in 2013. We found that ~25% reads were classified as metazoan in both size groups. The species richness, alpha and beta diversity of plankton community and relative abundance of reads in 99.2% eukaryotic OTUs showed no significant changes after prefiltering with a 200 μm pore-size sieve. We further found that both >0.2 μm and 0.2-200 μm eukaryotic plankton communities, especially the abundant plankton subcommunities, exhibited very similar, and synchronous, spatiotemporal patterns and processes associated with almost identical environmental drivers. The lack of an effect on community structure from prefiltering suggests that environmental DNA from larger metazoa is introduced into the smaller size class. Therefore, size-fractionated filtering with 200 μm is insufficient to discriminate between the eukaryotic plankton size groups in metabarcoding approaches. Our results also highlight the importance of sequencing depth, and strict quality filtering of reads, when designing studies to characterize microeukaryotic plankton communities.
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Affiliation(s)
- Lemian Liu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Min Liu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - David M Wilkinson
- School of Natural Science and Psychology, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF, UK.,School of Life Sciences, University of Lincoln, Lincoln, LN6 7TS, UK
| | - Huihuang Chen
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Xiaoqing Yu
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Jun Yang
- Aquatic EcoHealth Group, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
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24
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Capo E, Debroas D, Arnaud F, Guillemot T, Bichet V, Millet L, Gauthier E, Massa C, Develle AL, Pignol C, Lejzerowicz F, Domaizon I. Long-term dynamics in microbial eukaryotes communities: a palaeolimnological view based on sedimentary DNA. Mol Ecol 2016; 25:5925-5943. [DOI: 10.1111/mec.13893] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Revised: 09/08/2016] [Accepted: 10/07/2016] [Indexed: 01/21/2023]
Affiliation(s)
- Eric Capo
- CARRTEL; INRA; Université de Savoie Mont Blanc; 74200 Thonon-les-bains France
| | - Didier Debroas
- Université Clermont Auvergne; Laboratoire “Microorganismes: Génome et Environnement”; Université Blaise Pascal; BP 10448 F-63000 Clermont-Ferrand France
- CNRS; UMR 6023; LMGE; Campus Universitaire des Cézeaux 63171 Aubière France
| | - Fabien Arnaud
- CNRS; UMR 5204 EDYTEM; Université Savoie Mont Blanc; 5 Boulevard de la mer Caspienne, 73376 Le Bourget du Lac Cedex France
| | - Typhaine Guillemot
- Laboratoire Chrono-Environnement; UMR 6249 CNRS; Université de Bourgogne Franche-Comté; 16 Route de Gray, 25000 Besançon France
| | - Vincent Bichet
- Laboratoire Chrono-Environnement; UMR 6249 CNRS; Université de Bourgogne Franche-Comté; 16 Route de Gray, 25000 Besançon France
| | - Laurent Millet
- Laboratoire Chrono-Environnement; UMR 6249 CNRS; Université de Bourgogne Franche-Comté; 16 Route de Gray, 25000 Besançon France
| | - Emilie Gauthier
- Laboratoire Chrono-Environnement; UMR 6249 CNRS; Université de Bourgogne Franche-Comté; 16 Route de Gray, 25000 Besançon France
| | - Charly Massa
- Laboratoire Chrono-Environnement; UMR 6249 CNRS; Université de Bourgogne Franche-Comté; 16 Route de Gray, 25000 Besançon France
| | - Anne-Lise Develle
- CNRS; UMR 5204 EDYTEM; Université Savoie Mont Blanc; 5 Boulevard de la mer Caspienne, 73376 Le Bourget du Lac Cedex France
| | - Cécile Pignol
- CNRS; UMR 5204 EDYTEM; Université Savoie Mont Blanc; 5 Boulevard de la mer Caspienne, 73376 Le Bourget du Lac Cedex France
| | - Franck Lejzerowicz
- Department of Genetics and Evolution; University of Geneva; 4 Boulevard d'Yvoy, 1205 Geneva Switzerland
| | - Isabelle Domaizon
- CARRTEL; INRA; Université de Savoie Mont Blanc; 74200 Thonon-les-bains France
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25
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Sun Y, Shen D, Zhou X, Shi N, Tian Y. Microbial diversity and community structure of denitrifying biological filters operated with different carbon sources. SPRINGERPLUS 2016; 5:1752. [PMID: 27795895 PMCID: PMC5055511 DOI: 10.1186/s40064-016-3451-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 09/29/2016] [Indexed: 11/24/2022]
Abstract
The treatment performance and spatial microbial community structure of three parallel denitrifying biological filters (DNBFs) operated with methanol, ethanol and acetate, respectively, were explored. The acetate-fed DNBF presented the highest denitrification rate and NOx-N (NO2-N and NO3-N) removal efficiency, while the methanol-fed DNBF showed the lowest carbon consumption and NOx-N removal efficiency. Distinct spatial distribution patterns of terminal restriction fragment length polymorphism fingerprints were observed among the DNBFs. The ethanol enhanced captured biofilms throughout the flowpath of DNBF had the highest diversity and evenness. The methanol-enhanced attached biofilm along the flowpath presented the highest evenness, but lowest richness and limited diversity. β-Proteobacteria was dominant in the microbial community in all of methanol, ethanol and acetate enhanced biofilm; however, different external carbon sources resulted in different dominant genera species. Thauera was dominant in the acetate enhanced bacterial community, while both Dechloromonas and Thauera were dominant in that of ethanol fed. However, methylotrophic bacteria (Methyloversatilis and Methylotenera) dominated exclusively in the methanol enhanced bacterial community throughout of the DNBF.
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Affiliation(s)
- Yingxue Sun
- Department of Environmental Science and Engineering, Beijing Technology and Business University, No. 11 Fucheng Road, HaiDian District, Beijing, 100048 People's Republic of China
| | - Dandan Shen
- Department of Environmental Science and Engineering, Beijing Technology and Business University, No. 11 Fucheng Road, HaiDian District, Beijing, 100048 People's Republic of China ; State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing, 100084 People's Republic of China
| | - Xiaoli Zhou
- Department of Environmental Science and Engineering, Beijing Technology and Business University, No. 11 Fucheng Road, HaiDian District, Beijing, 100048 People's Republic of China
| | - Na Shi
- Department of Environmental Science and Engineering, Beijing Technology and Business University, No. 11 Fucheng Road, HaiDian District, Beijing, 100048 People's Republic of China ; State Environmental Protection Key Laboratory of Microorganism Application and Risk Control (SMARC), School of Environment, Tsinghua University, Beijing, 100084 People's Republic of China
| | - Yuan Tian
- Department of Environmental Science and Engineering, Beijing Technology and Business University, No. 11 Fucheng Road, HaiDian District, Beijing, 100048 People's Republic of China
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Rocke E, Jing H, Xia X, Liu H. Effects of Hypoxia on the Phylogenetic Composition and Species Distribution of Protists in a Subtropical Harbor. MICROBIAL ECOLOGY 2016; 72:96-105. [PMID: 26979838 DOI: 10.1007/s00248-016-0751-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Accepted: 03/02/2016] [Indexed: 06/05/2023]
Abstract
Tolo Harbor, a subtropical semi-enclosed coastal water body, is surrounded by an expanding urban community, which contributes to large concentrations of nutrient runoff, leading to algal blooms and localized hypoxic episodes. Present knowledge of protist distributions in subtropical waters during hypoxic conditions is very limited. In this study, therefore, we combined parallel 454 pyrosequencing technology and denaturing gradient gel electrophoresis (DGGE) fingerprint analyses to reveal the protist community shifts before, during, and after a 2-week hypoxic episode during the summer of 2011. Hierarchical clustering for DGGE demonstrated similar grouping of hypoxic samples separately from oxic samples. Dissolved oxygen (DO) concentration and dissolved inorganic nitrogen:phosphate (DIN:PO4) concentrations significantly affected OTU distribution in 454 sequenced samples, and a shift toward a ciliate and marine alveolate clade II (MALV II) species composition occurred as waters shifted from oxic to hypoxic. These results suggest that protist community shifts toward heterotrophic and parasitic tendencies as well as decreased diversity and richness in response to hypoxic outbreaks.
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Affiliation(s)
- Emma Rocke
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hongmei Jing
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
- Sanya Institute of Deep-Sea Science and Engineering, Chinese Academy of Sciences, Sanya, 572000, China
| | - Xiaomin Xia
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hongbin Liu
- Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.
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27
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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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28
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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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29
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Grossmann L, Bock C, Schweikert M, Boenigk J. Small but Manifold - Hidden Diversity in "Spumella-like Flagellates". J Eukaryot Microbiol 2016; 63:419-39. [PMID: 26662881 PMCID: PMC5066751 DOI: 10.1111/jeu.12287] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Revised: 10/16/2015] [Accepted: 11/09/2015] [Indexed: 11/27/2022]
Abstract
Colourless, nonscaled chrysophytes comprise morphologically similar or even indistinguishable flagellates which are important bacterivors in water and soil crucial for ecosystem functioning. However, phylogenetic analyses indicate a multiple origin of such colourless, nonscaled flagellate lineages. These flagellates are often referred to as “Spumella‐like flagellates” in ecological and biogeographic studies. Although this denomination reflects an assumed polyphyly, it obscures the phylogenetic and taxonomic diversity of this important flagellate group and, thus, hinders progress in lineage‐ and taxon‐specific ecological surveys. The smallest representatives of colourless chrysophytes have been addressed in very few taxonomic studies although they are among the dominant flagellates in field communities. To overcome the blurred picture and set the field for further investigation in biogeography and ecology of the organisms in question, we studied a set of strains of specifically small, colourless, nonscaled chrysomonad flagellates by means of electron microscopy and molecular analyses. They were isolated by a filtration‐acclimatisation approach focusing on flagellates of around 5 μm. We present the phylogenetic position of eight different lineages on both the ordinal and the generic level. Accordingly, we describe the new genera Apoikiospumella, Chromulinospumella, Segregatospumella, Cornospumella and Acrispumella Boenigk et Grossmann n. g. and different species within them.
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Affiliation(s)
- Lars Grossmann
- Department of Biodiversity, University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
| | - Christina Bock
- Department of Biodiversity, University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
| | - Michael Schweikert
- Department of Zoology, University of Stuttgart, Pfaffenwaldring 57, 70550, Stuttgart, Germany
| | - Jens Boenigk
- Department of Biodiversity, University of Duisburg-Essen, Universitätsstrasse 5, 45141, Essen, Germany
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30
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Simon M, López-García P, Deschamps P, Moreira D, Restoux G, Bertolino P, Jardillier L. Marked seasonality and high spatial variability of protist communities in shallow freshwater systems. ISME JOURNAL 2015; 9:1941-53. [PMID: 25853803 DOI: 10.1038/ismej.2015.6] [Citation(s) in RCA: 92] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 12/02/2014] [Accepted: 12/11/2014] [Indexed: 11/09/2022]
Abstract
Small eukaryotes have key roles in aquatic ecosystems, influencing their local environment, global biogeochemical cycles and climate. Their impact depends on community structure, which varies along time. However, very few studies take into account temporal variation. This is especially true for small, shallow freshwater systems, which remain largely understudied despite their wide variety, global surface and intense microbial activity. We have monthly followed changes in the community structure of small microbial eukaryotes (0.2-5 μm cell diameter) for 2 years in four ponds and one brook located in North-Western France based on massive 18S rDNA amplicon 454 pyrosequencing. We detected a total of 3742 stringently defined operational taxonomic units (OTUs) encompassing all recognized eukaryotic supergroups and lineages of uncertain affiliation. Although geographically close, protist communities in the five ecosystems were contrasting, with very few shared OTUs, suggesting that environmental selection mainly drives community structure. The temporal dynamics of different high-rank taxa appeared complex and rapid at monthly scales. Despite this, a clear and reproducible seasonality was observed. As expected, low-abundance OTUs dominated the community. Although some of them appeared sporadically or remained at low frequencies during the survey, others occasionally reached relatively high abundances, sometimes recurrently. This shows that at least a fraction of low-abundance eukaryotes constitutes a seed bank. The annual proportion of primary producers, free-living heterotrophs and parasites appeared remarkably constant among the different ecosystems, suggesting underlying trends of ecosystem carrying capacity for these functional groups.
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Affiliation(s)
- Marianne Simon
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France
| | | | - Philippe Deschamps
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France
| | - Gwendal Restoux
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France
| | - Paola Bertolino
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France
| | - Ludwig Jardillier
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France
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31
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Oikonomou A, Filker S, Breiner HW, Stoeck T. Protistan diversity in a permanently stratified meromictic lake (Lake Alatsee, SW Germany). Environ Microbiol 2014; 17:2144-57. [PMID: 25330396 DOI: 10.1111/1462-2920.12666] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2014] [Revised: 09/26/2014] [Accepted: 10/08/2014] [Indexed: 11/28/2022]
Abstract
Protists play a crucial role for ecosystem function(ing) and oxygen is one of the strongest barriers against their local dispersal. However, protistan diversity in freshwater habitats with oxygen gradients received very little attention. We applied high-throughput sequencing of the V9 region (18S rRNA gene) to provide a hitherto unique spatiotemporal analysis of protistan diversity along the oxygen gradient of a freshwater meromictic lake (Lake Alatsee, SW Germany). In the mixolimnion, the communities experienced most seasonal structural changes, with Stramenopiles dominating in autumn and Dinoflagellata in summer. The suboxic interface supported the highest diversity, but only 23 OTUs95% (mainly Euglenozoa, after quality check and removal of operational taxonomic units (OTUs) with less than three sequences) were exclusively associated with this habitat. Eukaryotic communities in the anoxic monimolimnion showed the most stable seasonal pattern, with Chrysophyta and Bicosoecida being the dominant taxa. Our data pinpoint to the ecological role of the interface as a short-term 'meeting point' for protists, contributing to the coupling of the mixolimnion and the monimolimnion. Our analyses of divergent genetic diversity suggest a high degree of previously undescribed OTUs. Future research will have to reveal if this result actually points to a high number of undescribed species in such freshwater habitats.
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Affiliation(s)
- Andreas Oikonomou
- Department of Ecology, University of Kaiserslautern, Erwin Schroedinger Str. 14, D-67663, Kaiserslautern, Germany
| | - Sabine Filker
- Department of Ecology, University of Kaiserslautern, Erwin Schroedinger Str. 14, D-67663, Kaiserslautern, Germany
| | - Hans-Werner Breiner
- Department of Ecology, University of Kaiserslautern, Erwin Schroedinger Str. 14, D-67663, Kaiserslautern, Germany
| | - Thorsten Stoeck
- Department of Ecology, University of Kaiserslautern, Erwin Schroedinger Str. 14, D-67663, Kaiserslautern, Germany
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32
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Boopathi T, Faria DG, Lee MD, Lee J, Chang M, Ki JS. A molecular survey of freshwater microeukaryotes in an Arctic reservoir (Svalbard, 79°N) in summer by using next-generation sequencing. Polar Biol 2014. [DOI: 10.1007/s00300-014-1576-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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33
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Simon M, Jardillier L, Deschamps P, Moreira D, Restoux G, Bertolino P, López-García P. Complex communities of small protists and unexpected occurrence of typical marine lineages in shallow freshwater systems. Environ Microbiol 2014; 17:3610-27. [PMID: 25115943 DOI: 10.1111/1462-2920.12591] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Accepted: 08/05/2014] [Indexed: 12/11/2022]
Abstract
Although inland water bodies are more heterogeneous and sensitive to environmental variation than oceans, the diversity of small protists in these ecosystems is much less well known. Some molecular surveys of lakes exist, but little information is available from smaller, shallower and often ephemeral freshwater systems, despite their global distribution and ecological importance. We carried out a comparative study based on massive pyrosequencing of amplified 18S rRNA gene fragments of protists in the 0.2-5 μm size range in one brook and four shallow ponds located in the Natural Regional Park of the Chevreuse Valley, France. Our study revealed a wide diversity of small protists, with 812 stringently defined operational taxonomic units (OTUs) belonging to the recognized eukaryotic supergroups (SAR--Stramenopiles, Alveolata, Rhizaria--Archaeplastida, Excavata, Amoebozoa, Opisthokonta) and to groups of unresolved phylogenetic position (Cryptophyta, Haptophyta, Centrohelida, Katablepharida, Telonemida, Apusozoa). Some OTUs represented deep-branching lineages (Cryptomycota, Aphelida, Colpodellida, Tremulida, clade-10 Cercozoa, HAP-1 Haptophyta). We identified several lineages previously thought to be marine including, in addition to MAST-2 and MAST-12, already detected in freshwater, MAST-3 and possibly MAST-6. Protist community structures were different in the five ecosystems. These differences did not correlate with geographical distances, but seemed to be influenced by environmental parameters.
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Affiliation(s)
- Marianne Simon
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, 91405, Orsay, France
| | - Ludwig Jardillier
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, 91405, Orsay, France
| | - Philippe Deschamps
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, 91405, Orsay, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, 91405, Orsay, France
| | - Gwendal Restoux
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, 91405, Orsay, France
| | - Paola Bertolino
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, 91405, Orsay, France
| | - Purificación López-García
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, 91405, Orsay, France
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34
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Rocke E, Liu H. Respiration, growth and grazing rates of three ciliate species in hypoxic conditions. MARINE POLLUTION BULLETIN 2014; 85:410-417. [PMID: 24874506 DOI: 10.1016/j.marpolbul.2014.04.050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2013] [Revised: 04/28/2014] [Accepted: 04/30/2014] [Indexed: 06/03/2023]
Abstract
Marine hypoxic episodes are affecting both marine and freshwater bodies all over the world. Yet, limited data exists with regard to the effects of decreasing oxygen on protist metabolism. Three ciliate species were therefore isolated from Hong Kong coastal waters. Controlled hypoxic conditions were simulated in the lab environment, during which time growth, respiration and grazing rates were measured. Euplotes sp. and a Oxytrichidae-like ciliate showed decreased growth and respiration below 2.5 mg O2 L(-1), however Uronema marinum kept steady growth and respiration until below 1.5 mg O2 L(-1). Euplotes sp. and the Oxytrichidae-like ciliate had the highest ingestion rate, which dropped significantly below 3.0 mg O2 L(-1). U.marinum grazing rates were affected at and below 1.5 mg O2 L(-1), correlating with their drop in growth and respiration at this lower concentration. This study illustrates the slowing metabolism of key grazing protists, as well as species-specific tolerance in response to hypoxia.
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Affiliation(s)
- Emma Rocke
- Hong Kong University of Science and Technology, Division of Life Science, Clear Water Bay, Kowloon, Hong Kong
| | - Hongbin Liu
- Hong Kong University of Science and Technology, Division of Life Science, Clear Water Bay, Kowloon, Hong Kong.
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35
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Patterns in the composition of microbial communities from a subtropical river: effects of environmental, spatial and temporal factors. PLoS One 2013; 8:e81232. [PMID: 24244735 PMCID: PMC3828266 DOI: 10.1371/journal.pone.0081232] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Accepted: 10/10/2013] [Indexed: 11/21/2022] Open
Abstract
Microbes are key components of aquatic ecosystems and play crucial roles in global biogeochemical cycles. However, the spatiotemporal dynamics of planktonic microbial community composition in riverine ecosystems are still poorly understood. In this study, we used denaturing gradient gel electrophoresis of PCR-amplified 16S and 18S rRNA gene fragments and multivariate statistical methods to explore the spatiotemporal patterns and driving factors of planktonic bacterial and microbial eukaryotic communities in the subtropical Jiulong River, southeast China. Both bacterial and microbial eukaryotic communities varied significantly in time and were spatially structured according to upper stream, middle-lower stream and estuary. Among all the environmental factors measured, water temperature, conductivity, PO4-P and TN/TP were best related to the spatiotemporal distribution of bacterial community, while water temperature, conductivity, NOx-N and transparency were closest related to the variation of eukaryotic community. Variation partitioning, based on partial RDA, revealed that environmental factors played the most important roles in structuring the microbial assemblages by explaining 11.3% of bacterial variation and 17.5% of eukaryotic variation. However, pure spatial factors (6.5% for bacteria and 9.6% for eukaryotes) and temporal factors (3.3% for bacteria and 5.5% for eukaryotes) also explained some variation in microbial distribution, thus inherent spatial and temporal variation of microbial assemblages should be considered when assessing the impact of environmental factors on microbial communities.
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36
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Kim DY, Countway PD, Jones AC, Schnetzer A, Yamashita W, Tung C, Caron DA. Monthly to interannual variability of microbial eukaryote assemblages at four depths in the eastern North Pacific. ISME JOURNAL 2013; 8:515-530. [PMID: 24173457 DOI: 10.1038/ismej.2013.173] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Revised: 08/15/2012] [Accepted: 08/17/2013] [Indexed: 11/09/2022]
Abstract
The monthly, seasonal and interannual variability of microbial eukaryote assemblages were examined at 5 m, the deep chlorophyll maximum, 150 m and 500 m at the San Pedro Ocean Time-series station (eastern North Pacific). The depths spanned transitions in temperature, light, nutrients and oxygen, and included a persistently hypoxic environment at 500 m. Terminal restriction fragment length polymorphism was used for the analysis of 237 samples that were collected between September 2000 and December 2010. Spatiotemporal variability patterns of microeukaryote assemblages indicated the presence of distinct shallow and deep communities at the SPOT station, presumably reflecting taxa that were specifically adapted for the conditions in those environments. Community similarity values between assemblages collected 1 month apart at each depth ranged between ∼20% and ∼84% (averages were ∼50-59%). The assemblage at 5 m was temporally more dynamic than deeper assemblages and also displayed substantial interannual variability during the first ∼3 years of the study. Evidence of seasonality was detected for the microbial eukaryote assemblage at 5 m between January 2008 and December 2010 and at 150 m between September 2000 and December 2003. Seasonality was not detected for assemblages at the deep chlorophyll a maximum, which varied in depth seasonally, or at 500 m. Microbial eukaryote assemblages exhibited cyclical patterns in at least 1 year at each depth, implying an annual resetting of communities. Substantial interannual variability was detected for assemblages at all depths and represented the largest source of temporal variability in this temperate coastal ecosystem.
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Affiliation(s)
- Diane Y Kim
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA.
| | - Peter D Countway
- Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine, USA
| | - Adriane C Jones
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Astrid Schnetzer
- Marine, Earth and Atmospheric Sciences, North Carolina State University, Raleigh, NC, USA
| | - Warren Yamashita
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Christine Tung
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - David A Caron
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
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37
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Bachy C, Moreira D, Dolan JR, López-García P. Seasonal dynamics of free-living tintinnid ciliate communities revealed by environmental sequences from the North-West Mediterranean Sea. FEMS Microbiol Ecol 2013; 87:330-42. [DOI: 10.1111/1574-6941.12224] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/13/2013] [Accepted: 09/16/2013] [Indexed: 01/23/2023] Open
Affiliation(s)
- Charles Bachy
- Unité d'Ecologie; Systématique et Evolution; CNRS UMR 8079; Université Paris-Sud; Orsay Cedex France
| | - David Moreira
- Unité d'Ecologie; Systématique et Evolution; CNRS UMR 8079; Université Paris-Sud; Orsay Cedex France
| | - John R. Dolan
- Laboratoire d'Océanographie de Villefranche, Marine Microbial Ecology; UMR 7093; Université Pierre et Marie Curie and Centre National de la Recherche Scientifique (CNRS); Villefranche-sur-Mer France
| | - Purificación López-García
- Unité d'Ecologie; Systématique et Evolution; CNRS UMR 8079; Université Paris-Sud; Orsay Cedex France
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Lepère C, Domaizon I, Taïb N, Mangot JF, Bronner G, Boucher D, Debroas D. Geographic distance and ecosystem size determine the distribution of smallest protists in lacustrine ecosystems. FEMS Microbiol Ecol 2013; 85:85-94. [DOI: 10.1111/1574-6941.12100] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 02/18/2013] [Accepted: 02/18/2013] [Indexed: 01/01/2023] Open
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Taib N, Mangot JF, Domaizon I, Bronner G, Debroas D. Phylogenetic affiliation of SSU rRNA genes generated by massively parallel sequencing: new insights into the freshwater protist diversity. PLoS One 2013; 8:e58950. [PMID: 23516585 PMCID: PMC3597552 DOI: 10.1371/journal.pone.0058950] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 02/11/2013] [Indexed: 12/23/2022] Open
Abstract
Recent advances in next-generation sequencing (NGS) technologies spur progress in determining the microbial diversity in various ecosystems by highlighting, for example, the rare biosphere. Currently, high-throughput pyrotag sequencing of PCR-amplified SSU rRNA gene regions is mainly used to characterize bacterial and archaeal communities, and rarely to characterize protist communities. In addition, although taxonomic assessment through phylogeny is considered as the most robust approach, similarity and probabilistic approaches remain the most commonly used for taxonomic affiliation. In a first part of this work, a tree-based method was compared with different approaches of taxonomic affiliation (BLAST and RDP) of 18S rRNA gene sequences and was shown to be the most accurate for near full-length sequences and for 400 bp amplicons, with the exception of amplicons covering the V5-V6 region. Secondly, the applicability of this method was tested by running a full scale test using an original pyrosequencing dataset of 18S rRNA genes of small lacustrine protists (0.2-5 µm) from eight freshwater ecosystems. Our results revealed that i) fewer than 5% of the operational taxonomic units (OTUs) identified through clustering and phylogenetic affiliation had been previously detected in lakes, based on comparison to sequence in public databases; ii) the sequencing depth provided by the NGS coupled with a phylogenetic approach allowed to shed light on clades of freshwater protists rarely or never detected with classical molecular ecology approaches; and iii) phylogenetic methods are more robust in describing the structuring of under-studied or highly divergent populations. More precisely, new putative clades belonging to Mamiellophyceae, Foraminifera, Dictyochophyceae and Euglenida were detected. Beyond the study of protists, these results illustrate that the tree-based approach for NGS based diversity characterization allows an in-depth description of microbial communities including taxonomic profiling, community structuring and the description of clades of any microorganisms (protists, Bacteria and Archaea).
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Affiliation(s)
- Najwa Taib
- Clermont Université, Université Blaise-Pascal, Laboratoire "Microorganismes: Génome et Environnement", BP 10448, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubiere, France
| | - Jean-François Mangot
- Clermont Université, Université Blaise-Pascal, Laboratoire "Microorganismes: Génome et Environnement", BP 10448, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubiere, France
- INRA, UMR 42 CARRTEL, Thonon les Bains, France
- Université de Savoie, UMR 42 CARRTEL, Le Bourget du Lac, France
| | - Isabelle Domaizon
- INRA, UMR 42 CARRTEL, Thonon les Bains, France
- Université de Savoie, UMR 42 CARRTEL, Le Bourget du Lac, France
| | - Gisèle Bronner
- Clermont Université, Université Blaise-Pascal, Laboratoire "Microorganismes: Génome et Environnement", BP 10448, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubiere, France
| | - Didier Debroas
- Clermont Université, Université Blaise-Pascal, Laboratoire "Microorganismes: Génome et Environnement", BP 10448, Clermont-Ferrand, France
- CNRS, UMR 6023, LMGE, Aubiere, France
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Domaizon I, Lepère C, Debroas D, Bouvy M, Ghiglione JF, Jacquet S, Bettarel Y, Bouvier C, Torréton JP, Vidussi F, Mostajir B, Kirkham A, Lefloc'h E, Fouilland E, Montanié H, Bouvier T. Short-term responses of unicellular planktonic eukaryotes to increases in temperature and UVB radiation. BMC Microbiol 2012; 12:202. [PMID: 22966751 PMCID: PMC3478981 DOI: 10.1186/1471-2180-12-202] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 08/27/2012] [Indexed: 11/18/2022] Open
Abstract
Background Small size eukaryotes play a fundamental role in the functioning of coastal ecosystems, however, the way in which these micro-organisms respond to combined effects of water temperature, UVB radiations (UVBR) and nutrient availability is still poorly investigated. Results We coupled molecular tools (18S rRNA gene sequencing and fingerprinting) with microscope-based identification and counting to experimentally investigate the short-term responses of small eukaryotes (<6 μm; from a coastal Mediterranean lagoon) to a warming treatment (+3°C) and UVB radiation increases (+20%) at two different nutrient levels. Interestingly, the increase in temperature resulted in higher pigmented eukaryotes abundances and in community structure changes clearly illustrated by molecular analyses. For most of the phylogenetic groups, some rearrangements occurred at the OTUs level even when their relative proportion (microscope counting) did not change significantly. Temperature explained almost 20% of the total variance of the small eukaryote community structure (while UVB explained only 8.4%). However, complex cumulative effects were detected. Some antagonistic or non additive effects were detected between temperature and nutrients, especially for Dinophyceae and Cryptophyceae. Conclusions This multifactorial experiment highlights the potential impacts, over short time scales, of changing environmental factors on the structure of various functional groups like small primary producers, parasites and saprotrophs which, in response, can modify energy flow in the planktonic food webs.
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Colombet J, Sime-Ngando T. Seasonal depth-related gradients in virioplankton: lytic activity and comparison with protistan grazing potential in Lake Pavin (France). MICROBIAL ECOLOGY 2012; 64:67-78. [PMID: 22391799 DOI: 10.1007/s00248-012-0032-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Accepted: 02/17/2012] [Indexed: 05/31/2023]
Abstract
This study presents an original depth-related survey of virioplankton lytic activity in relation to prokaryotic production and potential protistan bacterivory in the deep (Z(max) = 92 m) meromictic volcanic Lake Pavin (Massif Central, France). The sampling strategy was designed to be representative of the physico-chemical gradients of the water column of the lake, and of the seasonal variability as well, i.e. 12 different depths sampled in triplicates from April to December 2005. In the space, viral lytic activity estimated from the frequency of visibly infected prokaryotic cells and from burst size over the study period generally decreased with depth. This was viewed as a paradox compared to the abundances of viruses and prokaryotes and to the prokaryotic production which increased with depth. The seasonal variability in viral lytic activity was correlated with prokaryotic variables (abundance and production) in the deepest waters, i.e. from the hypolimnion downwards. Compared to previous studies known from the mixolimnion, we conclude that the deep waters in Lake Pavin represent an exclusive environment for heterotrophic prokaryotes whose seasonal activity offers an optimal and unique resource for thriving viral communities, some of which may be typical, endemic to the ambient dark, cold and stable deep water masses. Overall, the main findings in the present study get well around a previous statement that the ecology of the deepest waters of Lake Pavin is essentially driven by the dark viral loop (dissolved organic matter-prokaryotes-viruses) processes, which can sequester organic matters and nutrients for a long-lived turnover time. This is in agreement with recent demonstrations from marine systems that meso- and bathypelagic waters are optimal environments for viral survival and proliferation.
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Affiliation(s)
- Jonathan Colombet
- Laboratoire Microorganismes: Génome et Environnement, Clermont Université Blaise Pascal, UMR CNRS 6023, Aubière, France
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Monchy S, Grattepanche JD, Breton E, Meloni D, Sanciu G, Chabé M, Delhaes L, Viscogliosi E, Sime-Ngando T, Christaki U. Microplanktonic community structure in a coastal system relative to a Phaeocystis bloom inferred from morphological and tag pyrosequencing methods. PLoS One 2012; 7:e39924. [PMID: 22792138 PMCID: PMC3389043 DOI: 10.1371/journal.pone.0039924] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Accepted: 05/29/2012] [Indexed: 11/18/2022] Open
Abstract
Background Massive phytoplankton blooms, like the recurrent Phaeocystis proliferation observed every year in the Eastern English Channel (EEC), have a significant influence on the overall planktonic community structure and their food web dynamics. As well as being an important area for local fisheries, the EEC is an ideal ecosystem for work on microbial diversity. This is because, although its environmental context is relatively complex, it is reasonably well understood due to several years of monitoring and morphological observations of its planktonic organisms. The objective of our study was to better understand the under-explored microbial eukaryotic diversity relative to the Phaeocystis bloom. Methodology and Principal Findings The community structure of microplankton (diatoms, haptophytes, ciliates and dinoflagellates) was studied through morphological observations and tag pyrosequencing. During the annual Phaeocystis spring bloom, the phytoplankton biomass increased by 34-fold, while the microzooplankton biomass showed a 4-fold increase, representing on average about 4.6% of the biomass of their phytoplankton prey. Tag pyrosequencing unveiled an extensive diversity of Gymnodiniaceae, with G. spirale and G. fusiformis representing the most abundant reads. An extended diversity of Phaeocystales, with partial 18S rDNA genes sequence identity as low as 85% was found, with taxa corresponding to P. globosa, but also to unknown Phaeocystaceae. Conclusions Morphological analyses and pyrosequencing were generally in accordance with capturing frequency shifts of abundant taxa. Tag pyrosequencing allowed highlighting the maintenance of microplankton diversity during the Phaeocystis bloom and the increase of the taxa presenting low number of reads (minor taxa) along with the dominant ones in response to biotic and/or abiotic changing conditions. Although molecular approaches have enhanced our perception on diversity, it has come to light that the challenge of modelling and predicting ecological change requires the use of different complementary approaches, to link taxonomic data with the functional roles of microbes in biogeochemical cycles.
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Affiliation(s)
- Sébastien Monchy
- Laboratoire d'Océanologie et Géoscience (LOG), UMR CNRS 8187, Université du Littoral Côte d'Opale, Université Lille Nord, Wimereux, France.
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Gonçalves VN, Vaz AB, Rosa CA, Rosa LH. Diversity and distribution of fungal communities in lakes of Antarctica. FEMS Microbiol Ecol 2012; 82:459-71. [DOI: 10.1111/j.1574-6941.2012.01424.x] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2011] [Revised: 05/03/2012] [Accepted: 05/25/2012] [Indexed: 11/29/2022] Open
Affiliation(s)
- Vívian N. Gonçalves
- Departamento de Microbiologia; Instituto de Ciências Biológicas; Universidade Federal de Minas Gerais; Belo Horizonte; MG; Brazil
| | - Aline B.M. Vaz
- Departamento de Microbiologia; Instituto de Ciências Biológicas; Universidade Federal de Minas Gerais; Belo Horizonte; MG; Brazil
| | - Carlos A. Rosa
- Departamento de Microbiologia; Instituto de Ciências Biológicas; Universidade Federal de Minas Gerais; Belo Horizonte; MG; Brazil
| | - Luiz H. Rosa
- Departamento de Microbiologia; Instituto de Ciências Biológicas; Universidade Federal de Minas Gerais; Belo Horizonte; MG; Brazil
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Jobard M, Rasconi S, Solinhac L, Cauchie HM, Sime-Ngando T. Molecular and morphological diversity of fungi and the associated functions in three European nearby lakes. Environ Microbiol 2012; 14:2480-94. [DOI: 10.1111/j.1462-2920.2012.02771.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Composition of the summer photosynthetic pico and nanoplankton communities in the Beaufort Sea assessed by T-RFLP and sequences of the 18S rRNA gene from flow cytometry sorted samples. ISME JOURNAL 2012; 6:1480-98. [PMID: 22278671 DOI: 10.1038/ismej.2011.213] [Citation(s) in RCA: 110] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The composition of photosynthetic pico and nanoeukaryotes was investigated in the North East Pacific and the Arctic Ocean with special emphasis on the Beaufort Sea during the MALINA cruise in summer 2009. Photosynthetic populations were sorted using flow cytometry based on their size and pigment fluorescence. Diversity of the sorted photosynthetic eukaryotes was determined using terminal-restriction fragment length polymorphism analysis and cloning/sequencing of the 18S ribosomal RNA gene. Picoplankton was dominated by Mamiellophyceae, a class of small green algae previously included in the prasinophytes: in the North East Pacific, the contribution of an Arctic Micromonas ecotype increased steadily northward becoming the only taxon occurring at most stations throughout the Beaufort Sea. In contrast, nanoplankton was more diverse: North Pacific stations were dominated by Pseudo-nitzschia sp. whereas those in the Beaufort Sea were dominated by two distinct Chaetoceros species as well as by Chrysophyceae, Pelagophyceae and Chrysochromulina spp.. This study confirms the importance of Arctic Micromonas within picoplankton throughout the Beaufort Sea and demonstrates that the photosynthetic picoeukaryote community in the Arctic is much less diverse than at lower latitudes. Moreover, in contrast to what occurs in warmer waters, most of the key pico- and nanoplankton species found in the Beaufort Sea could be successfully established in culture.
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Richards TA, Jones MDM, Leonard G, Bass D. Marine fungi: their ecology and molecular diversity. ANNUAL REVIEW OF MARINE SCIENCE 2012; 4:495-522. [PMID: 22457985 DOI: 10.1146/annurev-marine-120710-100802] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Fungi appear to be rare in marine environments. There are relatively few marine isolates in culture, and fungal small subunit ribosomal DNA (SSU rDNA) sequences are rarely recovered in marine clone library experiments (i.e., culture-independent sequence surveys of eukaryotic microbial diversity from environmental DNA samples). To explore the diversity of marine fungi, we took a broad selection of SSU rDNA data sets and calculated a summary phylogeny. Bringing these data together identified a diverse collection of marine fungi, including sequences branching close to chytrids (flagellated fungi), filamentous hypha-forming fungi, and multicellular fungi. However, the majority of the sequences branched with ascomycete and basidiomycete yeasts. We discuss evidence for 36 novel marine lineages, the majority and most divergent of which branch with the chytrids. We then investigate what these data mean for the evolutionary history of the Fungi and specifically marine-terrestrial transitions. Finally, we discuss the roles of fungi in marine ecosystems.
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Affiliation(s)
- Thomas A Richards
- Department of Zoology, Natural History Museum, London SW7 5BD, United Kingdom.
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Couradeau E, Benzerara K, Moreira D, Gérard E, Kaźmierczak J, Tavera R, López-García P. Prokaryotic and eukaryotic community structure in field and cultured microbialites from the alkaline Lake Alchichica (Mexico). PLoS One 2011; 6:e28767. [PMID: 22194908 PMCID: PMC3237500 DOI: 10.1371/journal.pone.0028767] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 11/14/2011] [Indexed: 11/18/2022] Open
Abstract
The geomicrobiology of crater lake microbialites remains largely unknown despite their evolutionary interest due to their resemblance to some Archaean analogs in the dominance of in situ carbonate precipitation over accretion. Here, we studied the diversity of archaea, bacteria and protists in microbialites of the alkaline Lake Alchichica from both field samples collected along a depth gradient (0-14 m depth) and long-term-maintained laboratory aquaria. Using small subunit (SSU) rRNA gene libraries and fingerprinting methods, we detected a wide diversity of bacteria and protists contrasting with a minor fraction of archaea. Oxygenic photosynthesizers were dominated by cyanobacteria, green algae and diatoms. Cyanobacterial diversity varied with depth, Oscillatoriales dominating shallow and intermediate microbialites and Pleurocapsales the deepest samples. The early-branching Gloeobacterales represented significant proportions in aquaria microbialites. Anoxygenic photosynthesizers were also diverse, comprising members of Alphaproteobacteria and Chloroflexi. Although photosynthetic microorganisms dominated in biomass, heterotrophic lineages were more diverse. We detected members of up to 21 bacterial phyla or candidate divisions, including lineages possibly involved in microbialite formation, such as sulfate-reducing Deltaproteobacteria but also Firmicutes and very diverse taxa likely able to degrade complex polymeric substances, such as Planctomycetales, Bacteroidetes and Verrucomicrobia. Heterotrophic eukaryotes were dominated by Fungi (including members of the basal Rozellida or Cryptomycota), Choanoflagellida, Nucleariida, Amoebozoa, Alveolata and Stramenopiles. The diversity and relative abundance of many eukaryotic lineages suggest an unforeseen role for protists in microbialite ecology. Many lineages from lake microbialites were successfully maintained in aquaria. Interestingly, the diversity detected in aquarium microbialites was higher than in field samples, possibly due to more stable and favorable laboratory conditions. The maintenance of highly diverse natural microbialites in laboratory aquaria holds promise to study the role of different metabolisms in the formation of these structures under controlled conditions.
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Affiliation(s)
- Estelle Couradeau
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France
- Institut de Minéralogie et de Physique des Milieux Condensés, CNRS UMR 7590, Université Pierre et Marie Curie, Paris, France
- Institut de Physique du Globe de Paris, CNRS UMR 7154, Université Paris Diderot, Paris, France
| | - Karim Benzerara
- Institut de Minéralogie et de Physique des Milieux Condensés, CNRS UMR 7590, Université Pierre et Marie Curie, Paris, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France
| | - Emmanuelle Gérard
- Institut de Physique du Globe de Paris, CNRS UMR 7154, Université Paris Diderot, Paris, France
| | - Józef Kaźmierczak
- Institute of Paleobiology, Polish Academy of Sciences, Warszawa, Poland
| | - Rosaluz Tavera
- Departamento de Ecología y Recursos Naturales, Facultad de Ciencias, Universidad Nacional Autónoma de México, Distrito Federal, Mexico
| | - Purificación López-García
- Unité d'Ecologie, Systématique et Evolution, CNRS UMR 8079, Université Paris-Sud, Orsay, France
- * E-mail:
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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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Composition and variability of biofouling organisms in seawater reverse osmosis desalination plants. Appl Environ Microbiol 2011; 77:4390-8. [PMID: 21551282 DOI: 10.1128/aem.00122-11] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Seawater reverse osmosis (SWRO) membrane biofouling remains a common challenge in the desalination industry, but the marine bacterial community that causes membrane fouling is poorly understood. Microbial communities at different stages of treatment processes (intake, cartridge filtration, and SWRO) of a desalination pilot plant were examined by both culture-based and culture-independent approaches. Bacterial isolates were identified to match the genera Shewanella, Alteromonas, Vibrio, and Cellulophaga based on 16S rRNA gene sequencing analysis. The 16S rRNA gene clone library of the SWRO membrane biofilm showed that a filamentous bacterium, Leucothrix mucor, which belongs to the gammaproteobacteria, accounted for nearly 30% of the clone library, while the rest of the microorganisms (61.2% of the total clones) were related to the alphaproteobacteria. 16S rRNA gene terminal restriction fragment length polymorphism (T-RFLP) analysis indicated that bacteria colonizing the SWRO membrane represented a subportion of microbes in the source seawater; however, they were quite different from those colonizing the cartridge filter. The examination of five SWRO membranes from desalination plants located in different parts of the world showed that although the bacterial communities from the membranes were not identical to each other, some dominant bacteria were commonly observed. In contrast, bacterial communities in source seawater were significantly different based on location and season. Microbial profiles from 14 cartridge filters collected from different plants also revealed spatial trends.
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Zhao B, Chen M, Sun Y, Yang J, Chen F. Genetic diversity of picoeukaryotes in eight lakes differing in trophic status. Can J Microbiol 2011; 57:115-26. [PMID: 21326353 DOI: 10.1139/w10-107] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genetic diversity of picoeukaryotes (0.2-5.0 µm) was investigated in 8 lakes differing in trophic status in Nanjing, China. Denaturing gradient gel electrophoresis (DGGE) and cloning and sequencing of 18S rRNA genes were applied to analyze the picoeukaryotic communities. DGGE analysis showed that among the 8 lakes, the diversity of picoeukaryotes was greatest in the mesotrophic Lake Nan (24 bands) and least in the oligotrophic Lake Qian (12 bands). Cluster analysis of DGGE profiles revealed that the 8 lakes were grouped into 2 distinct clusters. Cluster 1 contained lakes Mochou, Zixia, Huashen, Nan, Pipa, and Qian, while cluster 2 contained lakes Xuanwu and Baijia. Clone libraries were constructed from the mesotrophic Lake Xuanwu and the oligotrophic Lake Zixia, and the 2 libraries were compared using the program LIBSHUFF. This analysis indicated that the picoeukaryotic community composition differed significantly between the 2 lakes (p = 0.001). A total of 25 operational taxonomic units were detected; 18 (62 clones) were related to known eukaryotic groups, while 7 (30 clones) were not affiliated with any known eukaryotic group. Alveolates and stramenopiles were the dominant groups in Lake Xuanwu, while alveolates and chlorophyta predominated in Lake Zixia. Multivariate statistical analysis indicated that the differences in the picoeukaryotic community composition of the 8 lakes might be related to trophic status and top-down regulation by metazooplankton.
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Affiliation(s)
- Biying Zhao
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Science, Nanjing 210008, China
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