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Mukherjee I, Grujčić V, Salcher MM, Znachor P, Seďa J, Devetter M, Rychtecký P, Šimek K, Shabarova T. Integrating depth-dependent protist dynamics and microbial interactions in spring succession of a freshwater reservoir. ENVIRONMENTAL MICROBIOME 2024; 19:31. [PMID: 38720385 PMCID: PMC11080224 DOI: 10.1186/s40793-024-00574-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 04/30/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Protists are essential contributors to eukaryotic diversity and exert profound influence on carbon fluxes and energy transfer in freshwaters. Despite their significance, there is a notable gap in research on protistan dynamics, particularly in the deeper strata of temperate lakes. This study aimed to address this gap by integrating protists into the well-described spring dynamics of Římov reservoir, Czech Republic. Over a 2-month period covering transition from mixing to established stratification, we collected water samples from three reservoir depths (0.5, 10 and 30 m) with a frequency of up to three times per week. Microbial eukaryotic and prokaryotic communities were analysed using SSU rRNA gene amplicon sequencing and dominant protistan groups were enumerated by Catalysed Reporter Deposition-Fluorescence in situ Hybridization (CARD-FISH). Additionally, we collected samples for water chemistry, phyto- and zooplankton composition analyses. RESULTS Following the rapid changes in environmental and biotic parameters during spring, protistan and bacterial communities displayed swift transitions from a homogeneous community to distinct strata-specific communities. A prevalence of auto- and mixotrophic protists dominated by cryptophytes was associated with spring algal bloom-specialized bacteria in the epilimnion. In contrast, the meta- and hypolimnion showcased a development of a protist community dominated by putative parasitic Perkinsozoa, detritus or particle-associated ciliates, cercozoans, telonemids and excavate protists (Kinetoplastida), co-occurring with bacteria associated with lake snow. CONCLUSIONS Our high-resolution sampling matching the typical doubling time of microbes along with the combined microscopic and molecular approach and inclusion of all main components of the microbial food web allowed us to unveil depth-specific populations' successions and interactions in a deep lentic ecosystem.
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Affiliation(s)
- Indranil Mukherjee
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic.
| | - Vesna Grujčić
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden
| | - Michaela M Salcher
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
| | - Petr Znachor
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005, Ceske Budejovice, Czech Republic
| | - Jaromír Seďa
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
| | - Miloslav Devetter
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
- Biology Centre of the Czech Academy of Sciences, Institute of Soil Biology and Biogeochemistry, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
| | - Pavel Rychtecký
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
| | - Karel Šimek
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic
- Faculty of Science, University of South Bohemia, 37005, Ceske Budejovice, Czech Republic
| | - Tanja Shabarova
- Biology Centre of the Czech Academy of Sciences, Institute of Hydrobiology, Na Sádkách 7, 37005, Ceske Budejovice, Czech Republic.
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2
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Bruto M, Oger PM, Got P, Bernard C, Melayah D, Cloarec LA, Duval C, Escalas A, Duperron S, Guigard L, Leboulanger C, Ader M, Sarazin G, Jézéquel D, Agogué H, Troussellier M, Hugoni M. Phytoplanktonic species in the haloalkaline Lake Dziani Dzaha select their archaeal microbiome. Mol Ecol 2023; 32:6824-6838. [PMID: 37901963 DOI: 10.1111/mec.17179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 09/18/2023] [Accepted: 10/09/2023] [Indexed: 10/31/2023]
Abstract
Microorganisms are key contributors of aquatic biogeochemical cycles but their microscale ecology remains largely unexplored, especially interactions occurring between phytoplankton and microorganisms in the phycosphere, that is the region immediately surrounding phytoplankton cells. The current study aimed to provide evidence of the phycosphere taking advantage of a unique hypersaline, hyperalkaline ecosystem, Lake Dziani Dzaha (Mayotte), where two phytoplanktonic species permanently co-dominate: a cyanobacterium, Arthrospira fusiformis, and a green microalga, Picocystis salinarum. To assay phycospheric microbial diversity from in situ sampling, we set up a flow cytometry cell-sorting methodology for both phytoplanktonic populations, coupled with metabarcoding and comparative microbiome diversity. We focused on archaeal communities as they represent a non-negligible part of the phycospheric diversity, however their role is poorly understood. This work is the first which successfully explores in situ archaeal diversity distribution showing contrasted phycospheric compositions, with P. salinarum phycosphere notably enriched in Woesearchaeales OTUs while A. fusiformis phycosphere was enriched in methanogenic lineages affiliated OTUs such as Methanomicrobiales or Methanofastidiosales. Most archaeal OTUs, including Woesearchaeales considered in literature as symbionts, were either ubiquitous or specific of the free-living microbiome (i.e. present in the 3-0.2 μm fraction). Seminally, several archaeal OTUs were enriched from the free-living microbiome to the phytoplankton phycospheres, suggesting (i) either the inhibition or decrease of other OTUs, or (ii) the selection of specific OTUs resulting from the physical influence of phytoplanktonic species on surrounding Archaea.
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Affiliation(s)
- Maxime Bruto
- VetAgro Sup, Anses, UMR Mycoplasmoses Animales, Marcy l'Etoile, France
| | - Philippe M Oger
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Patrice Got
- MARBEC, Univ Montpellier, IRD, CNRS, Ifremer, Sète, France
| | - Cécile Bernard
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM) MNHN-CNRS, Muséum National d'Histoire Naturelle, Paris Cedex 05, France
| | - Delphine Melayah
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Lilian A Cloarec
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | - Charlotte Duval
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM) MNHN-CNRS, Muséum National d'Histoire Naturelle, Paris Cedex 05, France
| | - Arthur Escalas
- MARBEC, Univ Montpellier, IRD, CNRS, Ifremer, Sète, France
| | - Sébastien Duperron
- UMR 7245 Molécules de Communication et Adaptations des Microorganismes (MCAM) MNHN-CNRS, Muséum National d'Histoire Naturelle, Paris Cedex 05, France
| | - Ludivine Guigard
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
| | | | - Magali Ader
- Institut de Physique du Globe de Paris, Université Paris Cité, Paris, France
| | - Gerard Sarazin
- Institut de Physique du Globe de Paris, Université Paris Cité, Paris, France
| | - Didier Jézéquel
- Institut de Physique du Globe de Paris, Université Paris Cité, Paris, France
- UMR CARRTEL, INRAE-USMB, Thonon, France
| | - Hélène Agogué
- LIENSs, UMR7266, La Rochelle Université - CNRS, La Rochelle, France
| | | | - Mylène Hugoni
- Universite Claude Bernard Lyon 1, INSA Lyon, CNRS, UMR 5240 Microbiologie, Adaptation et Pathogénie, Villeurbanne, France
- Institut Universitaire de France (IUF), Paris, France
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3
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Marguš M, Ahel M, Čanković M, Ljubešić Z, Terzić S, Hodak Kobasić V, Ciglenečki I. Phytoplankton pigment dynamics in marine lake fluctuating between stratified and holomictic euxinic conditions. MARINE POLLUTION BULLETIN 2023; 191:114931. [PMID: 37075558 DOI: 10.1016/j.marpolbul.2023.114931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 04/05/2023] [Accepted: 04/07/2023] [Indexed: 05/03/2023]
Abstract
Biomass dynamics in the marine lake are strongly dependent on seasonal variability in vertical stratification, indicating rapid adaptation of phytoplankton to short-term changes in the water column. A small marine lake (Rogoznica Lake, Croatia), which fluctuates between stably stratified and holomictic euxinic conditions, was used as a model to study the phytoplankton responses to environmental perturbations, in particular the anoxic stress, caused by periodic holomixia. The epilimnion showed significant temporal and vertical variability with a chlorophyll a subsurface maximum with the highest biomass near the chemocline. Fucoxanthin-containing biomass (diatoms) dominated in the epilimnion in colder seasons and was first to recover after holomictic euxinic events. The shift towards the smaller groups prevailed during highly stratified water column conditions in warmer seasons. Results for the hypolimnion were more enigmatic, with high concentrations of alloxanthin, zeaxanthin, and violaxanthin indicating the presence of a viable small-size mixotrophic community under extreme conditions.
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Affiliation(s)
- Marija Marguš
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Marijan Ahel
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
| | - Milan Čanković
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Zrinka Ljubešić
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000 Zagreb, Croatia
| | - Senka Terzić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Vedranka Hodak Kobasić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
| | - Irena Ciglenečki
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia
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4
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Mitsi K, Richter DJ, Arroyo AS, López-Escardó D, Antó M, Oterino AG, Ruiz-Trillo I. Taxonomic composition, community structure and molecular novelty of microeukaryotes in a temperate oligomesotrophic lake as revealed by metabarcoding. Sci Rep 2023; 13:3119. [PMID: 36813945 PMCID: PMC9947120 DOI: 10.1038/s41598-023-30228-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Accepted: 02/18/2023] [Indexed: 02/24/2023] Open
Abstract
Microbial eukaryotes are diverse and ecologically important organisms, yet sampling constraints have hindered the understanding of their distribution and diversity in freshwater ecosystems. Metabarcoding has provided a powerful complement to traditional limnological studies, revealing an unprecedented diversity of protists in freshwater environments. Here, we aim to expand our knowledge of the ecology and diversity of protists in lacustrine ecosystems by targeting the V4 hypervariable region of the 18S rRNA gene in water column, sediment and biofilm samples collected from Sanabria Lake (Spain) and surrounding freshwater ecosystems. Sanabria is a temperate lake, which are relatively understudied by metabarcoding in comparison to alpine and polar lakes. The phylogenetic diversity of microbial eukaryotes detected in Sanabria spans all currently recognized eukaryotic supergroups, with Stramenopiles being the most abundant and diverse supergroup in all sampling sites. Parasitic microeukaryotes account for 21% of the total protist ASVs identified in our study and were dominated by Chytridiomycota, both in terms of richness and abundance, in all sampling sites. Sediments, biofilms and water column samples harbour distinct microbial communities. Phylogenetic placement of poorly assigned and abundant ASVs indicates molecular novelty inside Rhodophyta, Bigyra, early-branching Nucletmycea and Apusomonadida. In addition, we report the first freshwater incidence of the previously exclusively marine genera Abeoforma and Sphaeroforma. Our results contribute to a deeper understanding of microeukaryotic communities in freshwater ecosystems, and provide the first molecular reference for future biomonitoring surveys in Sanabria Lake.
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Affiliation(s)
- Konstantina Mitsi
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de La Barceloneta, 37-49, 08033, Barcelona, Spain.
| | - Daniel J. Richter
- grid.507636.10000 0004 0424 5398Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de La Barceloneta, 37-49, 08033 Barcelona, Spain
| | - Alicia S. Arroyo
- grid.507636.10000 0004 0424 5398Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de La Barceloneta, 37-49, 08033 Barcelona, Spain
| | - David López-Escardó
- grid.418218.60000 0004 1793 765XInstitut de Ciències del Mar (CSIC), Passeig Marítim de La Barceloneta, 37-49, 08033 Barcelona, Spain
| | - Meritxell Antó
- grid.507636.10000 0004 0424 5398Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de La Barceloneta, 37-49, 08033 Barcelona, Spain
| | | | - Iñaki Ruiz-Trillo
- grid.507636.10000 0004 0424 5398Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Passeig Marítim de La Barceloneta, 37-49, 08033 Barcelona, Spain ,grid.425902.80000 0000 9601 989XInstitució Catalana de Recerca I Estudis Avançats (ICREA), Passeig Lluís Companys, 23, 08010 Barcelona, Spain
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5
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Melayah D, Bontemps Z, Bruto M, Nguyen A, Oger P, Hugoni M. Metabarcoding of the Three Domains of Life in Aquatic Saline Ecosystems. Methods Mol Biol 2022; 2605:17-35. [PMID: 36520387 DOI: 10.1007/978-1-0716-2871-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
High-throughput amplicon sequencing, known as metabarcoding, is a powerful technique to decipher exhaustive microbial diversity considering specific gene markers. While most of the studies investigating ecosystem functioning through microbial diversity targeted only one domain of life, either bacteria, or archaea or microeukaryotes, the remaining challenge in microbial ecology is to uncover the integrated view of microbial diversity occurring in ecosystems. Indeed, interactions occurring between the different microbial counterparts are now recognized having a great impact on stability and resilience of ecosystems. Here, we summarize protocols describing sampling, molecular, and simultaneous metabarcoding of bacteria, archaea, and microeukaryotes, as well as a bioinformatic pipeline allowing the study of exhaustive microbial diversity in natural aquatic saline samples.
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Affiliation(s)
- Delphine Melayah
- Université de Lyon, INSA Lyon, CNRS, UMR5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France
| | - Zélia Bontemps
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Maxime Bruto
- Université de Lyon, VetAgro Sup, Anses, UMR Mycoplasmoses Animales, Marcy l'Etoile, France
| | | | - Philippe Oger
- Université de Lyon, INSA Lyon, CNRS, UMR5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France
| | - Mylène Hugoni
- Université de Lyon, INSA Lyon, CNRS, UMR5240 Microbiologie Adaptation et Pathogénie, Villeurbanne, France.
- Institut Universitaire de France (IUF), Paris, France.
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6
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Swanner ED, Wüstner M, Leung T, Pust J, Fatka M, Lambrecht N, Chmiel HE, Strauss H. Seasonal phytoplankton and geochemical shifts in the subsurface chlorophyll maximum layer of a dimictic ferruginous lake. Microbiologyopen 2022; 11:e1287. [PMID: 35765183 PMCID: PMC9108440 DOI: 10.1002/mbo3.1287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/27/2022] [Indexed: 11/10/2022] Open
Abstract
Subsurface chlorophyll maxima layers (SCML) are ubiquitous features of stratified aquatic systems. Availability of the micronutrient iron is known to influence marine SCML, but iron has not been explored in detail as a factor in the development of freshwater SCML. This study investigates the relationship between dissolved iron and the SCML within the dimictic, ferruginous lake Grosses Heiliges Meer in northern Germany. The occurrence of the SCML under nonferruginous conditions in the spring and ferruginous conditions in the fall are context to explore temporal changes in the phytoplankton community and indicators of primary productivity. Results indicate that despite more abundant chlorophyll in the spring, the SCML sits below a likely primary productivity maximum within the epilimnion, inferred based on colocated dissolved oxygen, δ13 CDIC , and pH maxima. The peak amount of chlorophyll in the SCML is lower in the fall than in the spring, but in the fall the SCML is colocated with elevated dissolved iron concentrations and a local δ13 CDIC maximum. Cyanobacteria and Chlorophyta have elevated abundances within the SCML in the fall. Further investigation of the relationship of iron to primary productivity within ferruginous SCML may help to understand the environmental controls on primary productivity in past ferruginous oceans.
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Affiliation(s)
| | - Marina Wüstner
- Center for Applied GeoscienceUniversity of TübingenTübingenGermany
| | - Tania Leung
- Department of Geological & Atmospheric SciencesIowa State UniversityAmesIowaUSA
| | - Jürgen Pust
- Naturschutzgebietes Heiliges MeerLandschaftsverband Westfalen‐Lippe (LWL) Museum für NaturkundeReckeGermany
| | - Micah Fatka
- Department of Geological & Atmospheric SciencesIowa State UniversityAmesIowaUSA
| | - Nick Lambrecht
- Department of Geological & Atmospheric SciencesIowa State UniversityAmesIowaUSA
| | - Hannah E. Chmiel
- Environmental Engineering InstituteÉcole Polytechnique Fédérale de LausanneLausanneSwitzerland
| | - Harald Strauss
- Institute for Geology and PaleontologyUniversity of MünsterMünsterGermany
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7
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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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8
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Mazière C, Agogué H, Cravo-Laureau C, Cagnon C, Lanneluc I, Sablé S, Fruitier-Arnaudin I, Dupuy C, Duran R. New insights in bacterial and eukaryotic diversity of microbial mats inhabiting exploited and abandoned salterns at the Ré Island (France). Microbiol Res 2021; 252:126854. [PMID: 34454310 DOI: 10.1016/j.micres.2021.126854] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/09/2021] [Accepted: 08/21/2021] [Indexed: 01/04/2023]
Abstract
In order to understand the effect of human practices on microbial mats organisation, the study aimed to investigate the biodiversity within microbial mats from exploited and abandoned salterns. Despite several attempts, archaeal 16S rRNA gene fragment sequences were not obtained, indicating that microbial mats were probably dominated by Bacteria with very low abundance of Archaea (< 1%). Thus, the study compared the bacterial and meiofaunal diversity of microbial mats from abandoned and exploited salterns. The higher salinity (101 ± 3.7 psu vs. 51.1 ± 0.7 psu; Welch t-test p < 0.05) of the exploited site maintained lower bacterial diversity in comparison to the abandoned site where the salinity gradient was no longer maintained. However, the microbial mats exhibited similar bacterial class composition while the eukaryotic diversity was significantly higher in the exploited saltern. The abandoned saltern was dominated by sulfate-reducing bacteria and Nematoda, while the exploited saltern was characterized by the presence of halophilic bacteria belonging to Marinobacter, Salinivibrio and Rhodohalobacter genera, and the larger abundance of Hypotrichia (ciliates). Such bacterial and eukaryotic diversity difference might be explained by human actions for salt recovery in exploited salterns such as scraping the surface of microbial mat and increasing salinity renewing the microbial mat each year. Such action decreases the bacterial diversity changing the food web structure that favour the presence of a larger diversity of eukaryotic organisms. Our study provides new insights on microbial mat communities inhabiting salterns, especially the consequences of abandoning saltern exploitation.
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Affiliation(s)
- Camille Mazière
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France; UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | - Hélène Agogué
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | | | - Christine Cagnon
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France
| | - Isabelle Lanneluc
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | - Sophie Sablé
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | - Ingrid Fruitier-Arnaudin
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | - Christine Dupuy
- UMR 7266 LIENSs (Littoral Environnement et Sociétés), CNRS - La Rochelle Université - 2, Rue Olympe de Gouges, 17000, LA ROCHELLE, France
| | - Robert Duran
- Universite de Pau et des Pays de l'Adour, E2S UPPA, CNRS, IPREM, Pau, France.
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9
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Fermani P, Metz S, Balagué V, Descy JP, Morana C, Logares R, Massana R, Sarmento H. Microbial eukaryotes assemblages and potential novel diversity in four tropical East-African Great Lakes. FEMS Microbiol Ecol 2021; 97:6335480. [PMID: 34338764 DOI: 10.1093/femsec/fiab114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 07/30/2021] [Indexed: 01/21/2023] Open
Abstract
East-African Great Lakes are old and unique natural resources heavily utilized by their bordering countries. In those lakes, ecosystem functioning is dominated by pelagic processes, where microorganisms are key components, however protistan diversity is barely known. We investigated the community composition of small eukaryotes (< 10 µm) in surface waters of four African Lakes (Kivu, Edward, Albert and Victoria) by sequencing the 18S rRNA gene. Moreover, in the meromictic Lake Kivu, two stations were vertically studied. We found high protistan diversity distributed in 779 operational taxonomic units (OTUs), spanning in eleven high-rank lineages, being Alveolata (31%), Opisthokonta (20%) and Stramenopiles (17%) the most represented supergroups. Surface protistan assemblage were associated to conductivity and productivity gradients; whereas depth, had a strong effect on protistan community in Kivu, with higher contribution of heterotrophic organisms. Approximately 40% of OTUs had low similarity (< 90%) with reported sequences in public databases, these were mostly coming from deep anoxic waters of Kivu, suggesting a high extent of novel diversity. We also detected several taxa so far considered exclusive of marine ecosystems. Our results unveiled a complex and largely undescribed protistan community, in which several lineages have adapted to different niches after crossing the salinity boundary.
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Affiliation(s)
- Paulina Fermani
- Laboratorio de Ecología Acuática. Instituto Tecnológico de Chascomús (UNSAM-CONICET) Chascomús, Buenos Aires, Argentina
| | - Sebastián Metz
- University of Brest, CNRS, IRD, Ifremer, LEMAR, F-29280, Plouzané, France
| | - Vanessa Balagué
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain
| | | | - Cédric Morana
- Unit of Chemical Oceanography, University of Liège, Liège, Belgium
| | - Ramiro Logares
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - Ramon Massana
- Institut de Ciències del Mar (CSIC), Passeig Marítim de la Barceloneta, 37-49, ES-08003, Barcelona, Catalonia, Spain
| | - Hugo Sarmento
- Departamento de Hidrobiologia (DHb), Universidade Federal de São Carlos, São Carlos - SP, Brazil
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10
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Quillaguamán J, Guzmán D, Campero M, Hoepfner C, Relos L, Mendieta D, Higdon SM, Eid D, Fernández CE. The microbiome of a polluted urban lake harbors pathogens with diverse antimicrobial resistance and virulence genes. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 273:116488. [PMID: 33485000 DOI: 10.1016/j.envpol.2021.116488] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Revised: 12/28/2020] [Accepted: 01/07/2021] [Indexed: 06/12/2023]
Abstract
Bacterial resistance to antibiotics is one of the greatest threats to the modern human population. Paradoxically, urban settlements are often culpable in generating such resistance by influencing the adaptation of bacterial communities via pollution of natural ecosystems. Urban lakes are well-known examples of this problem, as they often receive discharges of both domestic and industrial wastewater. In this study, we used shotgun metagenome sequencing to examine the microbial diversity of water and sediment samples of Lake Alalay, a polluted urban lake near Cochabamba, Bolivia. We found that Proteobacteria dominated the relative abundance of both water and sediment samples at levels over 25% and that a significant proportion of the microbial diversity could not be classified (about 9% in water and 22% in sediment). Further metagenomic investigation of antimicrobial resistance (AR) genes identified 277 and 150 AR genes in water and sediment samples, respectively. These included genes with functional annotations for resistance to fluoroquinolones, tetracyclines, phenicols, macrolides, beta-lactams, and rifamycin. A high number of genes involved in bacterial virulence also occurred in both water and sediment samples (169 and 283, respectively), where the virulence gene pscP normally found in the Pseudomonas aeruginosa type III secretion system had the highest relative abundance. Isolated and identified bacteria from water samples also revealed the presence of pathogenic bacteria among the microbiota of Lake Alalay. Seeing as most AR and virulence genes detected in this study are commonly described in nosocomial infections, we provide evidence suggesting that the microbial ecosystem of Lake Alalay presents a severe health risk to the surrounding population.
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Affiliation(s)
- Jorge Quillaguamán
- Center of Biotechnology, Faculty of Science and Technology, Universidad Mayor de San Simón, Cochabamba, Bolivia.
| | - Daniel Guzmán
- Center of Biotechnology, Faculty of Science and Technology, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Melina Campero
- Center of Limnology and Aquatic Resources, Faculty of Science and Technology, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Claudia Hoepfner
- Center of Biotechnology, Faculty of Science and Technology, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Laura Relos
- Center of Biotechnology, Faculty of Science and Technology, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Daniela Mendieta
- Center of Biotechnology, Faculty of Science and Technology, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Shawn M Higdon
- Department of Plant Sciences, University of California, Davis, CA, 95616, United States
| | - Daniel Eid
- Institute of Biomedical Research and Social Research, Faculty of Medicine, Universidad Mayor de San Simón, Cochabamba, Bolivia
| | - Carla E Fernández
- Center of Limnology and Aquatic Resources, Faculty of Science and Technology, Universidad Mayor de San Simón, Cochabamba, Bolivia
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11
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Hirakata Y, Hatamoto M, Oshiki M, Watari T, Kuroda K, Araki N, Yamaguchi T. Temporal variation of eukaryotic community structures in UASB reactor treating domestic sewage as revealed by 18S rRNA gene sequencing. Sci Rep 2019; 9:12783. [PMID: 31484981 PMCID: PMC6726610 DOI: 10.1038/s41598-019-49290-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 08/22/2019] [Indexed: 11/09/2022] Open
Abstract
Eukaryotes are important components of ecosystems in wastewater treatment processes. However, little is known about eukaryotic community in anaerobic wastewater treatment systems. In this study, eukaryotic communities in an up flow anaerobic sludge blanket (UASB) reactor treating domestic sewage during two years of operation were investigated using V4 and V9 regions of 18S rRNA gene for amplicon sequencing. In addition, activated sludge and influent sewage samples were also analyzed and used as the references for aerobic eukaryotic community to characterize anaerobic eukaryotes. The amplicon sequence V4 and V9 libraries detected different taxonomic groups, especially from the UASB samples, suggesting that commonly used V4 and V9 primer pairs could produce a bias for eukaryotic communities analysis. Eukaryotic community structures in the UASB reactor were influenced by the immigration of eukaryotes via influent sewage but were clearly different from the influent sewage and activated sludge. Multivariate statistics indicated that protist genera Cyclidium, Platyophrya and Subulatomonas correlated with chemical oxygen demand and suspended solid concentration, and could be used as bioindicators of treatment performance. Uncultured eukaryotes groups were dominant in the UASB reactor, and their physiological roles need to be examined to understand their contributions to anaerobic processes in future studies.
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Affiliation(s)
- Yuga Hirakata
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Masashi Hatamoto
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan.
| | - Mamoru Oshiki
- Department of Civil Engineering, National institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-0834, Japan
| | - Takahiro Watari
- Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
| | - Kyohei Kuroda
- Department of Chemical Science and Engineering, National Institute of Technology, Miyakonojo College, 473-1 Yoshio-cho, Miyakonojo, Miyazaki, 885-8567, Japan
| | - Nobuo Araki
- Department of Civil Engineering, National institute of Technology, Nagaoka College, 888 Nishikatakaimachi, Nagaoka, Niigata, 940-0834, Japan
| | - Takashi Yamaguchi
- Department of Science of Technology Innovation, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan.,Department of Civil and Environmental Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata, 940-2188, Japan
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12
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Li W, Morgan-Kiss RM. Influence of Environmental Drivers and Potential Interactions on the Distribution of Microbial Communities From Three Permanently Stratified Antarctic Lakes. Front Microbiol 2019; 10:1067. [PMID: 31156585 PMCID: PMC6530420 DOI: 10.3389/fmicb.2019.01067] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 04/29/2019] [Indexed: 12/14/2022] Open
Abstract
The McMurdo Dry Valley (MDV) lakes represent unique habitats in the microbial world. Perennial ice covers protect liquid water columns from either significant allochthonous inputs or seasonal mixing, resulting in centuries of stable biogeochemistry. Extreme environmental conditions including low seasonal photosynthetically active radiation (PAR), near freezing temperatures, and oligotrophy have precluded higher trophic levels from the food webs. Despite these limitations, diverse microbial life flourishes in the stratified water columns, including Archaea, bacteria, fungi, protists, and viruses. While a few recent studies have applied next generation sequencing, a thorough understanding of the MDV lake microbial diversity and community structure is currently lacking. Here we used Illumina MiSeq sequencing of the 16S and 18S rRNA genes combined with a microscopic survey of key eukaryotes to compare the community structure and potential interactions among the bacterial and eukaryal communities within the water columns of Lakes Bonney (east and west lobes, ELB, and WLB, respectively) and Fryxell (FRX). Communities were distinct between the upper, oxic layers and the dark, anoxic waters, particularly among the bacterial communities residing in WLB and FRX. Both eukaryal and bacterial community structure was influenced by different biogeochemical parameters in the oxic and anoxic zones. Bacteria formed complex interaction networks which were lake-specific. Several eukaryotes exhibit potential interactions with bacteria in ELB and WLB, while interactions between these groups in the more productive FRX were relatively rare.
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Affiliation(s)
- Wei Li
- Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, United States
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13
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Lepère C, Domaizon I, Humbert JF, Jardillier L, Hugoni M, Debroas D. Diversity, spatial distribution and activity of fungi in freshwater ecosystems. PeerJ 2019; 7:e6247. [PMID: 30809429 PMCID: PMC6387782 DOI: 10.7717/peerj.6247] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 11/30/2018] [Indexed: 12/31/2022] Open
Abstract
High-throughput sequencing has given new insights into aquatic fungal community ecology over the last 10 years. Based on 18S ribosomal RNA gene sequences publicly available, we investigated fungal richness and taxonomic composition among 25 lakes and four rivers. We used a single pipeline to process the reads from raw data to the taxonomic affiliation. In addition, we studied, for a subset of lakes, the active fraction of fungi through the 18S rRNA transcripts level. These results revealed a high diversity of fungi that can be captured by 18S rRNA primers. The most OTU-rich groups were Dikarya (47%), represented by putative filamentous fungi more diverse and abundant in freshwater habitats than previous studies have suggested, followed by Cryptomycota (17.6%) and Chytridiomycota (15.4%). The active fraction of the community showed the same dominant groups as those observed at the 18S rRNA genes level. On average 13.25% of the fungal OTUs were active. The small number of OTUs shared among aquatic ecosystems may result from the low abundances of those microorganisms and/or they constitute allochthonous fungi coming from other habitats (e.g., sediment or catchment areas). The richness estimates suggest that fungi have been overlooked and undersampled in freshwater ecosystems, especially rivers, though they play key roles in ecosystem functioning as saprophytes and parasites.
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Affiliation(s)
- Cécile Lepère
- Laboratoire: Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Isabelle Domaizon
- CARRTEL, Université Savoie Mont Blanc, INRA, Thonon Les Bains, France
| | | | - Ludwig Jardillier
- Unité d'Ecologie, Systématique et Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, Orsay, France
| | - Mylène Hugoni
- CNRS, UMR5557, Ecologie Microbienne, INRA, UMR1418, Université Lyon 1, Villeurbanne Cedex, France
| | - Didier Debroas
- Laboratoire: Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, France
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14
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Hugoni M, Escalas A, Bernard C, Nicolas S, Jézéquel D, Vazzoler F, Sarazin G, Leboulanger C, Bouvy M, Got P, Ader M, Troussellier M, Agogué H. Spatiotemporal variations in microbial diversity across the three domains of life in a tropical thalassohaline lake (Dziani Dzaha, Mayotte Island). Mol Ecol 2018; 27:4775-4786. [DOI: 10.1111/mec.14901] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 11/28/2022]
Affiliation(s)
- Mylène Hugoni
- Université Lyon 1; CNRS; UMR5557; Ecologie Microbienne; INRA; UMR1418; Villeurbanne France
| | - Arthur Escalas
- UMR 7245 MCAM; Muséum National d'Histoire Naturelle - CNRS; CP 39; Paris France
| | - Cécile Bernard
- UMR 7245 MCAM; Muséum National d'Histoire Naturelle - CNRS; CP 39; Paris France
| | - Sébastien Nicolas
- Université Lyon 1; CNRS; UMR5557; Ecologie Microbienne; INRA; UMR1418; Villeurbanne France
| | - Didier Jézéquel
- Institut de Physique du Globe de Paris - Sorbonne Paris Cité; Univ. Paris Diderot; UMR 7154 CNRS; Paris France
| | - Fanny Vazzoler
- UMR 7266 LIENSs CNRS; Univ. La Rochelle; La Rochelle France
| | - Gerard Sarazin
- Institut de Physique du Globe de Paris - Sorbonne Paris Cité; Univ. Paris Diderot; UMR 7154 CNRS; Paris France
| | | | - Marc Bouvy
- UMR 9190; MARBEC; CNRS; Univ. Montpellier; IRD; Ifremer; Montpellier France
| | - Patrice Got
- UMR 9190; MARBEC; CNRS; Univ. Montpellier; IRD; Ifremer; Montpellier France
| | - Magali Ader
- Institut de Physique du Globe de Paris - Sorbonne Paris Cité; Univ. Paris Diderot; UMR 7154 CNRS; Paris France
| | - Marc Troussellier
- UMR 9190; MARBEC; CNRS; Univ. Montpellier; IRD; Ifremer; Montpellier France
| | - Hélène Agogué
- UMR 7266 LIENSs CNRS; Univ. La Rochelle; La Rochelle France
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15
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Grum-Grzhimaylo OA, Debets AJM, Bilanenko EN. Mosaic structure of the fungal community in the Kislo-Sladkoe Lake that is detaching from the White Sea. Polar Biol 2018. [DOI: 10.1007/s00300-018-2347-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Arroyo AS, López-Escardó D, Kim E, Ruiz-Trillo I, Najle SR. Novel Diversity of Deeply Branching Holomycota and Unicellular Holozoans Revealed by Metabarcoding in Middle Paraná River, Argentina. Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00099] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
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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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Banerji A, Bagley M, Elk M, Pilgrim E, Marinson J, Santo Domingo J. Spatial and temporal dynamics of a freshwater eukaryotic plankton community revealed via 18S rRNA gene metabarcoding. HYDROBIOLOGIA 2018; 818:71-86. [PMID: 31595089 PMCID: PMC6781235 DOI: 10.1007/s10750-018-3593-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
DNA metabarcoding is a sophisticated molecular tool that can enhance biological surveys of freshwater plankton communities by providing broader taxonomic coverage and, for certain groups, higher taxonomic resolution compared to morphological methods. We conducted 18S rRNA gene metabarcoding analyses on 214 water samples collected over a four-month period from multiple sites within a freshwater reservoir. We detected 1,314 unique operational taxonomic units that included various metazoans, protists, chlorophytes, and fungi. Alpha diversity differed among sites, suggesting local habitat variation linked to differing species responses. Strong temporal variation was detected at both daily and monthly scales. Diversity and relative abundance patterns for several protist groups (including dinoflagellates, ciliates, and cryptophytes) differed from arthropods (e.g., cladocerans and copepods), a traditional focus of plankton surveys. This suggests that the protists respond to different environmental dimensions and may therefore provide additional information regarding ecosystem status. Comparison of the sequence-based population survey data to conventional-based data revealed similar trends for taxa that were ranked among the most abundant in both approaches, although some groups were missing in each data set. These results highlight the potential benefit of supplementing conventional biological survey approaches with metabarcoding to obtain a more comprehensive understanding of freshwater plankton community structure and dynamics.
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Affiliation(s)
- A Banerji
- US Environmental Protection Agency, Cincinnati, USA
| | - M Bagley
- US Environmental Protection Agency, Cincinnati, USA
| | - M Elk
- US Environmental Protection Agency, Cincinnati, USA
| | - E Pilgrim
- US Environmental Protection Agency, Cincinnati, USA
| | - J Marinson
- US Environmental Protection Agency, Cincinnati, USA
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19
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Fu R, Gong J. Single Cell Analysis Linking Ribosomal (r)DNA and rRNA Copy Numbers to Cell Size and Growth Rate Provides Insights into Molecular Protistan Ecology. J Eukaryot Microbiol 2017; 64:885-896. [PMID: 28499076 PMCID: PMC5697653 DOI: 10.1111/jeu.12425] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 04/03/2017] [Accepted: 05/02/2017] [Indexed: 11/30/2022]
Abstract
Ribosomal (r)RNA and rDNA have been golden molecular markers in microbial ecology. However, it remains poorly understood how ribotype copy number (CN)‐based characteristics are linked with diversity, abundance, and activity of protist populations and communities observed at organismal levels. Here, we applied a single‐cell approach to quantify ribotype CNs in two ciliate species reared at different temperatures. We found that in actively growing cells, the per‐cell rDNA and rRNA CNs scaled with cell volume (CV) to 0.44 and 0.58 powers, respectively. The modeled rDNA and rRNA concentrations thus appear to be much higher in smaller than in larger cells. The observed rRNA:rDNA ratio scaled with CV0.14. The maximum growth rate could be well predicted by a combination of per‐cell ribotype CN and temperature. Our empirical data and modeling on single‐cell ribotype scaling are in agreement with both the metabolic theory of ecology and the growth rate hypothesis, providing a quantitative framework for linking cellular rDNA and rRNA CNs with body size, growth (activity), and biomass stoichiometry. This study also demonstrates that the expression rate of rRNA genes is constrained by cell size, and favors biomass rather than abundance‐based interpretation of quantitative ribotype data in population and community ecology of protists.
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Affiliation(s)
- Rao Fu
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Gong
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, 264003, China.,University of Chinese Academy of Sciences, Beijing, 100049, China.,Laboratory of Microbial Ecology and Matter Cycles, School of Marine Sciences, Sun Yat-Sen University, Zhuhai, 519082, China
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20
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Camacho A, Walter XA, Picazo A, Zopfi J. Photoferrotrophy: Remains of an Ancient Photosynthesis in Modern Environments. Front Microbiol 2017; 8:323. [PMID: 28377745 PMCID: PMC5359306 DOI: 10.3389/fmicb.2017.00323] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 02/15/2017] [Indexed: 11/13/2022] Open
Abstract
Photoferrotrophy, the process by which inorganic carbon is fixed into organic matter using light as an energy source and reduced iron [Fe(II)] as an electron donor, has been proposed as one of the oldest photoautotrophic metabolisms on Earth. Under the iron-rich (ferruginous) but sulfide poor conditions dominating the Archean ocean, this type of metabolism could have accounted for most of the primary production in the photic zone. Here we review the current knowledge of biogeochemical, microbial and phylogenetic aspects of photoferrotrophy, and evaluate the ecological significance of this process in ancient and modern environments. From the ferruginous conditions that prevailed during most of the Archean, the ancient ocean evolved toward euxinic (anoxic and sulfide rich) conditions and, finally, much after the advent of oxygenic photosynthesis, to a predominantly oxic environment. Under these new conditions photoferrotrophs lost importance as primary producers, and now photoferrotrophy remains as a vestige of a formerly relevant photosynthetic process. Apart from the geological record and other biogeochemical markers, modern environments resembling the redox conditions of these ancient oceans can offer insights into the past significance of photoferrotrophy and help to explain how this metabolism operated as an important source of organic carbon for the early biosphere. Iron-rich meromictic (permanently stratified) lakes can be considered as modern analogs of the ancient Archean ocean, as they present anoxic ferruginous water columns where light can still be available at the chemocline, thus offering suitable niches for photoferrotrophs. A few bacterial strains of purple bacteria as well as of green sulfur bacteria have been shown to possess photoferrotrophic capacities, and hence, could thrive in these modern Archean ocean analogs. Studies addressing the occurrence and the biogeochemical significance of photoferrotrophy in ferruginous environments have been conducted so far in lakes Matano, Pavin, La Cruz, and the Kabuno Bay of Lake Kivu. To date, only in the latter two lakes a biogeochemical role of photoferrotrophs has been confirmed. In this review we critically summarize the current knowledge on iron-driven photosynthesis, as a remains of ancient Earth biogeochemistry.
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Affiliation(s)
- Antonio Camacho
- Cavanilles Institute for Biodiversity and Evolutionary Biology, University of ValenciaBurjassot, Spain
| | - Xavier A. Walter
- Bristol BioEnergy Centre, Bristol Robotics Laboratory, University of the West of EnglandBristol, UK
| | - Antonio Picazo
- Cavanilles Institute for Biodiversity and Evolutionary Biology, University of ValenciaBurjassot, Spain
| | - Jakob Zopfi
- Aquatic and Stable Isotope Biogeochemistry, Department of Environmental Sciences, University of BaselBasel, Switzerland
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21
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Novák L, Zubáčová Z, Karnkowska A, Kolisko M, Hroudová M, Stairs CW, Simpson AGB, Keeling PJ, Roger AJ, Čepička I, Hampl V. Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes. BMC Evol Biol 2016; 16:197. [PMID: 27716026 PMCID: PMC5052871 DOI: 10.1186/s12862-016-0771-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 09/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies. RESULTS We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades. CONCLUSIONS Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.
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Affiliation(s)
- Lukáš Novák
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
| | - Zuzana Zubáčová
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
| | - Anna Karnkowska
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Martin Kolisko
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Miluše Hroudová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Courtney W. Stairs
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | | | | | - Andrew J. Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Ivan Čepička
- Department of Zoology, Charles University, Faculty of Science, Prague, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
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