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Karlicki M, Bednarska A, Hałakuc P, Maciszewski K, Karnkowska A. Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: insights from metabarcoding and machine learning. FEMS Microbiol Ecol 2024; 100:fiae104. [PMID: 39039016 DOI: 10.1093/femsec/fiae104] [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: 03/04/2024] [Revised: 06/21/2024] [Accepted: 07/19/2024] [Indexed: 07/24/2024] Open
Abstract
Microbial communities, which include prokaryotes and protists, play an important role in aquatic ecosystems and influence ecological processes. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and track spatio-temporal dynamics in both marine and freshwater environments. While marine ecosystems have been extensively studied, there is a notable research gap in understanding eukaryotic microbial communities in temperate lakes. Our study addresses this gap by investigating the free-living bacteria and small protist communities in Lake Roś (Poland), a dimictic temperate lake. Metabarcoding analysis revealed that both the bacterial and protist communities exhibit distinct seasonal patterns that are not necessarily shaped by dominant taxa. Furthermore, machine learning and statistical methods identified crucial amplicon sequence variants (ASVs) specific to each season. In addition, we identified a distinct community in the anoxic hypolimnion. We have also shown that the key factors shaping the composition of analysed community are temperature, oxygen, and silicon concentration. Understanding these community structures and the underlying factors is important in the context of climate change potentially impacting mixing patterns and leading to prolonged stratification.
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Affiliation(s)
- Michał Karlicki
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Anna Bednarska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Department of Hydrobiology, Institute of Functional Biology and Ecology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Paweł Hałakuc
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
| | - Kacper Maciszewski
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 1160/31, 370 05 České Budějovice, Czech Republic
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, ul. Żwirki i Wigury 101, 02-089 Warsaw, Poland
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Barbosa M, Lefler FW, Berthold DE, Briggs-Gonzalez VS, Mazzotti FJ, Laughinghouse HD. Trophic State Drives the Diversity of Protists in a Tropical River (New River, Belize). Microorganisms 2022; 10:microorganisms10122425. [PMID: 36557678 PMCID: PMC9782246 DOI: 10.3390/microorganisms10122425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 12/01/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022] Open
Abstract
Land use disrupts the ecosystem functioning of freshwater systems and significantly affects trophic state. Consequently, biodiversity is severely affected by changes to the ecosystem. Microbial eukaryotes (i.e., protists) play an essential role in ecosystem functioning, contributing to biogeochemical processes, nutrient cycling, and food webs. Protist composition is a useful biological quality parameter for monitoring aquatic ecosystems and determining aquatic system health. In this study, we investigated the effects of land usage and trophic state on the communities of microbial eukaryotes in the New River (Belize, C.A.). Land use and trophic state both significantly affected protist community compositions, with impacted and mesotrophic sampled sites having higher biodiversity when compared to other sites. Autotrophic organisms dominated indirectly impacted and eutrophic sites, while impacted and mesotrophic sites had proportional ratios of autotrophic and heterotrophic organisms. Our study highlights the significant effects of trophic gradients on protistan community composition, even at the local scales.
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Affiliation(s)
- Maximiliano Barbosa
- Agronomy Department, Ft. Lauderdale Research and Education Center, University of Florida/IFAS, 3205 College Avenue, Davie, FL 33314, USA
| | - Forrest W. Lefler
- Agronomy Department, Ft. Lauderdale Research and Education Center, University of Florida/IFAS, 3205 College Avenue, Davie, FL 33314, USA
| | - David E. Berthold
- Agronomy Department, Ft. Lauderdale Research and Education Center, University of Florida/IFAS, 3205 College Avenue, Davie, FL 33314, USA
| | - Venetia S. Briggs-Gonzalez
- Wildlife Ecology and Conservation Department, Ft. Lauderdale Research and Education Center, University of Florida/IFAS, 3205 College Avenue, Davie, FL 33314, USA
| | - Frank J. Mazzotti
- Wildlife Ecology and Conservation Department, Ft. Lauderdale Research and Education Center, University of Florida/IFAS, 3205 College Avenue, Davie, FL 33314, USA
| | - H. Dail Laughinghouse
- Agronomy Department, Ft. Lauderdale Research and Education Center, University of Florida/IFAS, 3205 College Avenue, Davie, FL 33314, USA
- Correspondence:
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Metz S, Huber P, Accattatis V, Lopes Dos Santos A, Bigeard E, Unrein F, Chambouvet A, Not F, Lara E, Devercelli M. Freshwater protists: unveiling the unexplored in a large floodplain system. Environ Microbiol 2021; 24:1731-1745. [PMID: 34783136 DOI: 10.1111/1462-2920.15838] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/23/2021] [Accepted: 10/31/2021] [Indexed: 12/25/2022]
Abstract
Protists play a fundamental role in all ecosystems, but we are still far from estimating the total diversity of many lineages, in particular in highly diverse environments, such as freshwater. Here, we survey the protist diversity of the Paraná River using metabarcoding, and we applied an approach that includes sequence similarity and phylogeny to evaluate the degree of genetic novelty of the protists' communities against the sequences described in the reference database PR2 . We observed that ~28% of the amplicon sequence variants were classified as novel according to their similarity with sequences from the reference database; most of them were related to heterotrophic groups traditionally overlooked in freshwater systems. This lack of knowledge extended to those groups within the green algae (Archaeplastida) that are well documented such as Mamiellophyceae, and also to the less studied Pedinophyceae, for which we found sequences representing novel deep-branching clusters. Among the groups with potential novel protists, Bicosoecida (Stramenopiles) were the best represented, followed by Codosiga (Opisthokonta), and the Perkinsea (Alveolata). This illustrates the lack of knowledge on freshwater planktonic protists and also the need for isolation and/or cultivation of new organisms to better understand their role in ecosystem functioning.
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Affiliation(s)
- Sebastian Metz
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, Plouzané, F-29280, France.,Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Buenos Aires, Argentina
| | - Paula Huber
- Departamento de Hidrobiologia, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, São Paulo, 13565-905, Brazil.,Instituto Nacional de Limnología (INALI), Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional del Litoral, Ciudad Universitaria, Santa Fe, Argentina
| | - Victoria Accattatis
- Departamento de Hidrobiologia, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, São Paulo, 13565-905, Brazil
| | | | - Estelle Bigeard
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin UMR7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Fernando Unrein
- Instituto Tecnológico de Chascomús (INTECH), UNSAM-CONICET, Chascomús, Buenos Aires, Argentina
| | | | - Fabrice Not
- Sorbonne Université, CNRS, Laboratoire Adaptation et Diversité en Milieu Marin UMR7144, Station Biologique de Roscoff, Roscoff, 29680, France
| | - Enrique Lara
- Real Jardín Botánico de Madrid, CSIC, Madrid, 28014, Spain
| | - Melina Devercelli
- Departamento de Hidrobiologia, Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luiz, São Carlos, São Paulo, 13565-905, Brazil
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