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Batsch M, Guex I, Todorov H, Heiman CM, Vacheron J, Vorholt JA, Keel C, van der Meer JR. Fragmented micro-growth habitats present opportunities for alternative competitive outcomes. Nat Commun 2024; 15:7591. [PMID: 39217178 PMCID: PMC11365936 DOI: 10.1038/s41467-024-51944-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024] Open
Abstract
Bacteria in nature often thrive in fragmented environments, like soil pores, plant roots or plant leaves, leading to smaller isolated habitats, shared with fewer species. This spatial fragmentation can significantly influence bacterial interactions, affecting overall community diversity. To investigate this, we contrast paired bacterial growth in tiny picoliter droplets (1-3 cells per 35 pL up to 3-8 cells per species in 268 pL) with larger, uniform liquid cultures (about 2 million cells per 140 µl). We test four interaction scenarios using different bacterial strains: substrate competition, substrate independence, growth inhibition, and cell killing. In fragmented environments, interaction outcomes are more variable and sometimes even reverse compared to larger uniform cultures. Both experiments and simulations show that these differences stem mostly from variation in initial cell population growth phenotypes and their sizes. These effects are most significant with the smallest starting cell populations and lessen as population size increases. Simulations suggest that slower-growing species might survive competition by increasing growth variability. Our findings reveal how microhabitat fragmentation promotes diverse bacterial interaction outcomes, contributing to greater species diversity under competitive conditions.
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Affiliation(s)
- Maxime Batsch
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Isaline Guex
- Department of Mathematics, University of Fribourg, CH-1700, Fribourg, Switzerland
| | - Helena Todorov
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Clara M Heiman
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Julia A Vorholt
- Institute for Microbiology, Swiss Federal Institute of Technology (ETH Zürich), CH-8049, Zürich, Switzerland
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Jan Roelof van der Meer
- Department of Fundamental Microbiology, University of Lausanne, CH-1015, Lausanne, Switzerland.
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2
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Shabardina V, Dharamshi JE, Ara PS, Antó M, Bascón FJ, Suga H, Marshall W, Scazzocchio C, Casacuberta E, Ruiz-Trillo I. Ichthyosporea: a window into the origin of animals. Commun Biol 2024; 7:915. [PMID: 39075159 PMCID: PMC11286789 DOI: 10.1038/s42003-024-06608-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Accepted: 07/19/2024] [Indexed: 07/31/2024] Open
Abstract
Ichthyosporea is an underexplored group of unicellular eukaryotes closely related to animals. Thanks to their phylogenetic position, genomic content, and development through a multinucleate coenocyte reminiscent of some animal embryos, the members of Ichthyosporea are being increasingly recognized as pivotal to the study of animal origins. We delve into the existing knowledge of Ichthyosporea, identify existing gaps and discuss their life cycles, genomic insights, development, and potential to be model organisms. We also discuss the underestimated diversity of ichthyosporeans, based on new environmental data analyses. This review will be an essential resource for researchers venturing into the study of ichthyosporeans.
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Affiliation(s)
- Victoria Shabardina
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
| | - Jennah E Dharamshi
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden
| | - Patricia S Ara
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Meritxell Antó
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Fernando J Bascón
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Hiroshi Suga
- Faculty of Life and Environmental Sciences, Prefectural University of Hiroshima, Shobara, Japan
| | - Wyth Marshall
- Bluefrontier Biological Services, Campbell River, BC, Canada
| | - Claudio Scazzocchio
- Department of Life Sciences, Imperial College London, London, UK
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Elena Casacuberta
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.
- ICREA, Barcelona, Spain.
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3
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Philippe A, Salaun M, Quemener M, Noël C, Tallec K, Lacroix C, Coton E, Burgaud G. Colonization and Biodegradation Potential of Fungal Communities on Immersed Polystyrene vs. Biodegradable Plastics: A Time Series Study in a Marina Environment. J Fungi (Basel) 2024; 10:428. [PMID: 38921415 PMCID: PMC11204492 DOI: 10.3390/jof10060428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 05/30/2024] [Accepted: 06/13/2024] [Indexed: 06/27/2024] Open
Abstract
Plastic pollution of the ocean is a major environmental threat. In this context, a better understanding of the microorganisms able to colonize and potentially degrade these pollutants is of interest. This study explores the colonization and biodegradation potential of fungal communities on foamed polystyrene and alternatives biodegradable plastics immersed in a marina environment over time, using the Brest marina (France) as a model site. The methodology involved a combination of high-throughput 18S rRNA gene amplicon sequencing to investigate fungal taxa associated with plastics compared to the surrounding seawater, and a culture-dependent approach to isolate environmentally relevant fungi to further assess their capabilities to utilize polymers as carbon sources. Metabarcoding results highlighted the significant diversity of fungal communities associated with both foamed polystyrene and biodegradable plastics, revealing a dynamic colonization process influenced by the type of polymer and immersion time. Notably, the research suggests a potential for certain fungal species to utilize polymers as a carbon source, emphasizing the need for further exploration of fungal biodegradation potential and mechanisms.
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Affiliation(s)
- Aurélie Philippe
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France; (A.P.); (M.S.); (M.Q.); (E.C.)
| | - Marie Salaun
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France; (A.P.); (M.S.); (M.Q.); (E.C.)
| | - Maxence Quemener
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France; (A.P.); (M.S.); (M.Q.); (E.C.)
| | - Cyril Noël
- Ifremer, IRSI, SeBiMER Service de Bioinformatique de l’Ifremer, F-29280 Plouzané, France;
| | - Kévin Tallec
- CEDRE Centre de Documentation, de Recherche et d’Expérimentations sur les Pollutions Accidentelles des Eaux, 715 Rue Alain Colas, CS 41836, CEDEX 2, 29218 Brest, France; (K.T.); (C.L.)
| | - Camille Lacroix
- CEDRE Centre de Documentation, de Recherche et d’Expérimentations sur les Pollutions Accidentelles des Eaux, 715 Rue Alain Colas, CS 41836, CEDEX 2, 29218 Brest, France; (K.T.); (C.L.)
| | - Emmanuel Coton
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France; (A.P.); (M.S.); (M.Q.); (E.C.)
| | - Gaëtan Burgaud
- Univ Brest, INRAE, Laboratoire Universitaire de Biodiversité et Écologie Microbienne, F-29280 Plouzané, France; (A.P.); (M.S.); (M.Q.); (E.C.)
- Institut Universitaire de France, France
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4
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Campello-Nunes PH, da Silva-Neto ID, da S Paiva T, Soares CAG, Fernandes NM. Ciliate diversity in rodrigo de freitas lagoon (Rio de Janeiro, Brazil) from an integrative standpoint. Braz J Microbiol 2024; 55:1489-1505. [PMID: 38401009 PMCID: PMC11153468 DOI: 10.1007/s42770-024-01291-4] [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] [Received: 09/25/2023] [Accepted: 02/18/2024] [Indexed: 02/26/2024] Open
Abstract
The Rodrigo de Freitas Lagoon is a highly eutrophic lacustrine system and has one of the longest histories of exploration and anthropic alteration in Brazil. Despite its relevance, limited studies explored the diversity of micro-eukaryotes in the lagoon. Ciliates (Alveolata, Ciliophora) are overlooked in environmental microbiology, especially in tropical and subtropical ecosystems, resulting in limited knowledge about their diversity and functional relevance in South American habitats, particularly in coastal lagoons. To fill this gap, here we investigated the diversity of ciliates in a brackish coastal lagoon in an urban area of Rio de Janeiro, Brazil, applying and comparing the performance of morphological and metabarcoding approaches. The metabarcoding analysis, based on high-throughput sequencing of the hipervariable region V4 of the 18S rRNA genes detected 37 molecular operational taxonomic units (MOTUs) assigned to Ciliophora, representing only about a half (56.9%) of the diversity detected by microscopy, which counted 65 ciliate morphotypes. The most representative classes in both approaches were Spirotrichea and Oligohymenophorea. The metabarcoding analysis revealed that 35.3% of the ciliate MOTUs had less than 97% similarity to available sequences in the NCBI database, indicating that more than one-third of these MOTUs potentially represents still not represented or undescribed ciliate species in current databases. Our findings indicate that metabarcoding techniques can significantly enhance the comprehension of ciliate diversity in tropical environments, but the scarcity of reference sequences of brackish ciliates in molecular databases represents a challenge to the taxonomic assignment of the MOTUs. This study provides new insights into the diversity of ciliates in a threatened coastal lagoon, revealing a vast array of still unknown and rare ciliate taxonomic units in tropical environments.
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Affiliation(s)
- Pedro H Campello-Nunes
- Laboratório de Protistologia, Departamento de Zoologia, Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Inácio D da Silva-Neto
- Laboratório de Protistologia, Departamento de Zoologia, Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Thiago da S Paiva
- Laboratório de Protistologia, Departamento de Zoologia, Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Carlos A G Soares
- Laboratório de Genética Molecular de Eucariontes E Simbiontes, Departamento de Genética, Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Noemi M Fernandes
- Laboratório de Protistologia, Departamento de Zoologia, Universidade Federal Do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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5
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Korn R, Berg C, Bersier LF, Gray SM, Thallinger GG. Habitat conditions and not moss composition mediate microbial community structure in Swiss peatlands. Environ Microbiol 2024; 26:e16631. [PMID: 38757479 DOI: 10.1111/1462-2920.16631] [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: 09/25/2023] [Accepted: 04/05/2024] [Indexed: 05/18/2024]
Abstract
Peatlands, one of the oldest ecosystems, globally store significant amounts of carbon and freshwater. However, they are under severe threat from human activities, leading to changes in water, nutrient and temperature regimes in these delicate systems. Such shifts can trigger a substantial carbon flux into the atmosphere and diminish the water-holding capacity of peatlands. Microbes associated with moss in peatlands play a crucial role in providing these ecosystem services, which are at risk due to global change. Therefore, understanding the factors influencing microbial composition and function is vital. Our study focused on five peatlands along an altitudinal gradient in Switzerland, where we sampled moss on hummocks containing Sarracenia purpurea. Structural equation modelling revealed that habitat condition was the primary predictor of community structure and directly influenced other environmental variables. Interestingly, the microbial composition was not linked to the local moss species identity. Instead, microbial communities varied significantly between sites due to differences in acidity levels and nitrogen availability. This finding was also mirrored in a co-occurrence network analysis, which displayed a distinct distribution of indicator species for acidity and nitrogen availability. Therefore, peatland conservation should take into account the critical habitat characteristics of moss-associated microbial communities.
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Affiliation(s)
- Rachel Korn
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | | | | | - Sarah M Gray
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Gerhard G Thallinger
- Institute of Biomedical Informatics, Graz University of Technology, Graz, Austria
- OMICS Center Graz, BioTechMed, Graz, Austria
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6
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Thøgersen MS, Zervas A, Stougaard P, Ellegaard-Jensen L. Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland. Front Microbiol 2024; 15:1358787. [PMID: 38655082 PMCID: PMC11035741 DOI: 10.3389/fmicb.2024.1358787] [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: 12/20/2023] [Accepted: 03/08/2024] [Indexed: 04/26/2024] Open
Abstract
The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column. Seven different archaeal phyla were documented in multiple locations inside the columns. The columns also contained a rich eukaryotic diversity with 27 phyla representing microalgae, protists, fungi, and small animals. Based on metagenomic sequencing, 25 high-quality MAGs were assembled and analyzed for the presence of genes involved in cycling of nitrogen, sulfur, and phosphorous as well as genes encoding carbohydrate-active enzymes (CAZymes), showing a potentially very bioactive microbial community.
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7
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Yadav BNS, Sharma P, Maurya S, Yadav RK. Metagenomics and metatranscriptomics as potential driving forces for the exploration of diversity and functions of micro-eukaryotes in soil. 3 Biotech 2023; 13:423. [PMID: 38047037 PMCID: PMC10689336 DOI: 10.1007/s13205-023-03841-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 11/02/2023] [Indexed: 12/05/2023] Open
Abstract
Micro-eukaryotes are ubiquitous and play vital roles in diverse ecological systems, yet their diversity and functions are scarcely known. This may be due to the limitations of formerly used conventional culture-based methods. Metagenomics and metatranscriptomics are enabling to unravel the genomic, metabolic, and phylogenetic diversity of micro-eukaryotes inhabiting in different ecosystems in a more comprehensive manner. The in-depth study of structural and functional characteristics of micro-eukaryote community residing in soil is crucial for the complete understanding of this major ecosystem. This review provides a deep insight into the methodologies employed under these approaches to study soil micro-eukaryotic organisms. Furthermore, the review describes available computational tools, pipelines, and database sources and their manipulation for the analysis of sequence data of micro-eukaryotic origin. The challenges and limitations of these approaches are also discussed in detail. In addition, this review summarizes the key findings of metagenomic and metatranscriptomic studies on soil micro-eukaryotes. It also highlights the exploitation of these methods to study the structural as well as functional profiles of soil micro-eukaryotic community and to screen functional eukaryotic protein coding genes for biotechnological applications along with the future perspectives in the field.
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Affiliation(s)
- Bhupendra Narayan Singh Yadav
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Priyanka Sharma
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Shristy Maurya
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
| | - Rajiv Kumar Yadav
- Molecular Biology and Genetic Engineering Laboratory, Department of Botany, Faculty of Science, University of Allahabad, Prayagraj, Uttar Pradesh 211002 India
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8
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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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Carvalho da Silva V, Fernandes N. Protist taxonomic and functional diversity in aquatic ecosystems of the Brazilian Atlantic Forest. PeerJ 2023; 11:e15762. [PMID: 37547721 PMCID: PMC10402703 DOI: 10.7717/peerj.15762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 06/27/2023] [Indexed: 08/08/2023] Open
Abstract
The Brazilian Atlantic Forest and its associated ecosystems are highly biodiverse but still understudied, especially with respect to eukaryotic microbes. Protists represent the largest proportion of eukaryotic diversity and play important roles in nutrient cycling and maintenance of the ecosystems in which they occur. However, much of protist diversity remains unknown, particularly in the Neotropics. Understanding the taxonomic and functional diversity of these organisms is urgently needed, not only to fill this gap in our knowledge, but also to enable the development of public policies for biological conservation. This is the first study to investigate the taxonomic and trophic diversity of the major protist groups in freshwater systems and brackish coastal lagoons located in fragments of the Brazilian Atlantic Forest by DNA metabarcoding, using high-throughput sequencing of the gene coding for the V4 region of the 18S rRNA gene. We compared α and β diversity for all protist communities and assessed the relative abundance of phototrophic, consumer, and parasitic taxa. We found that the protist communities of coastal lagoons are as diverse as the freshwater systems studied in terms of α diversity, although differed significantly in terms of taxonomic composition. Our results still showed a notable functional homogeneity between the trophic groups in freshwater environments. Beta diversity was higher among freshwater samples, suggesting a greater level of heterogeneity within this group of samples concerning the composition and abundance of OTUs.Ciliophora was the most represented group in freshwater, while Diatomea dominated diversity in coastal lagoons.
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10
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Sen K, Bai M, Li J, Ding X, Sen B, Wang G. Spatial Patterns of Planktonic Fungi Indicate Their Potential Contributions to Biological Carbon Pump and Organic Matter Remineralization in the Water Column of South China Sea. J Fungi (Basel) 2023; 9:640. [PMID: 37367576 DOI: 10.3390/jof9060640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 05/25/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023] Open
Abstract
Fungi have long been known to be dynamic in coastal water columns with multiple trophic modes. However, little is known about their interactions with abiotic and biotic components, contribution to the biological carbon pump (BCP), and organic matter remineralization in the oceanic water column. In this study, we investigated how fungi vary spatially and how their variations relate to that of bacteria in the water column of the South China Sea (SCS). Fungi were about three orders less prevalent than bacteria, and the main factors influencing their distribution were depth, temperature, and distance from the sites of riverine inputs. The decline in the abundance of fungi with depth was less steep than that of bacteria. Correlation tests revealed a strong positive association between the abundance of fungi and bacteria, especially in the twilight (r = 0.62) and aphotic (r = 0.70) zones. However, the co-occurrence network revealed mutual exclusion between certain members of fungi and bacteria. The majority of fungi in the water column were saprotrophs, which indicated that they were generally involved in the degradation of organic matter, particularly in twilight and aphotic zones. Similar to bacteria, the involvement of fungi in the metabolism of carbohydrates, proteins, and lipids was predicted, pointing to their participation in the turnover of organic carbon and the biogeochemical cycling of carbon, nitrogen, and sulfur. These findings suggest that fungi play a role in BCP and support their inclusion in marine microbial ecosystem models.
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Affiliation(s)
- Kalyani Sen
- Centre for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Mohan Bai
- Centre for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Jiaqian Li
- Centre for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Xueyan Ding
- Centre for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Biswarup Sen
- Centre for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
| | - Guangyi Wang
- Centre for Marine Environmental Ecology, School of Environmental Science and Engineering, Tianjin University, Tianjin 300072, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin 300072, China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin 300072, China
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11
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Yang Q, Li D, Chen W, Zhu L, Zou X, Hu L, Yuan Y, He S, Shi F. Dynamics of Bacterioplankton Communities during Wet and Dry Seasons in the Danjiangkou Reservoir in Hubei, China. Life (Basel) 2023; 13:life13051206. [PMID: 37240851 DOI: 10.3390/life13051206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/20/2023] [Accepted: 04/27/2023] [Indexed: 05/28/2023] Open
Abstract
Water quality is directly linked to drinking water safety for millions of people receiving the water. The Danjiangkou Reservoir is the main water source for the Middle Route of the South-to-North Water Diversion Project (MR-SNWDP), located in the vicinity of Henan and Hubei provinces in China. Aquatic microorganisms are key indicators of biologically assessing and monitoring the water quality of the reservoir as they are sensitive to environmental and water quality changes. This study aimed to investigate the spatiotemporal variations in bacterioplankton communities during wet (April) and dry (October) seasons at eight monitoring points in Hanku reservoir and five monitoring points in Danku reservoir. Each time point had three replicates, labeled as wet season Hanku (WH), wet season Danku (WD), dry season Hanku (DH), and dry season Danku (DD) of Danjiangkou Reservoir in 2021. High-throughput sequencing (Illumina PE250) of the 16S rRNA gene was performed, and alpha (ACE and Shannon) and beta (PCoA and NDMS) diversity indices were analyzed. The results showed that the dry season (DH and DD) had more diverse bacterioplankton communities compared to the wet season (WH and WD). Proteobacteria, Actinobacteria, and Firmicutes were the most abundant phyla, and Acinetobacter, Exiguobacterium, and Planomicrobium were abundant in the wet season, while polynucleobacter was abundant in the dry season. The functional prediction of metabolic pathways revealed six major functions including carbohydrate metabolism, membrane transport, amino acid metabolism, signal transduction, and energy metabolism. Redundancy analysis showed that environmental parameters greatly affected bacterioplankton diversity during the dry season compared to the wet season. The findings suggest that seasonality has a significant impact on bacterioplankton communities, and the dry season has more diverse communities influenced by environmental parameters. Further, the relatively high abundance of certain bacteria such as Acinetobacter deteriorated the water quality during the wet season compared to the dry season. Our findings have significant implications for water resource management in China, and other countries facing similar challenges. However, further investigations are required to elucidate the role of environmental parameters in influencing bacterioplankton diversity in order to devise potential strategies for improving water quality management in the reservoir.
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Affiliation(s)
- Qing Yang
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Dewang Li
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Wei Chen
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Liming Zhu
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Xi Zou
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Lian Hu
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Yujie Yuan
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Shan He
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
| | - Fang Shi
- Institute of Hydroecology, Ministry of Water Resources & Chinese Academy of Sciences, Wuhan 430079, China
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12
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Simons AL, Theroux S, Osborne M, Nuzhdin S, Mazor R, Steele J. Zeta diversity patterns in metabarcoded lotic algal assemblages as a tool for bioassessment. ECOLOGICAL APPLICATIONS : A PUBLICATION OF THE ECOLOGICAL SOCIETY OF AMERICA 2023; 33:e2812. [PMID: 36708145 DOI: 10.1002/eap.2812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
Assessments of the ecological health of algal assemblages in streams typically focus on measures of their local diversity and classify individuals by morphotaxonomy. Such assemblages are often connected through various ecological processes, such as dispersal, and may be more accurately assessed as components of regional-, rather than local-scale assemblages. With recent declines in the costs of sequencing and computation, it has also become increasingly feasible to use metabarcoding to more accurately classify algal species and perform regional-scale bioassessments. Recently, zeta diversity has been explored as a novel method of constructing regional bioassessments for groups of streams. Here, we model the use of zeta diversity to investigate whether stream health can be determined by the landscape diversity of algal assemblages. We also compare the use of DNA metabarcoding and morphotaxonomy classifications in these zeta diversity-based bioassessments of regional stream health. From 96 stream samples in California, we used various orders of zeta diversity to construct models of biotic integrity for multiple assemblages of diatoms, as well as hybrid assemblages of diatoms in combination with soft-bodied algae, using taxonomy data generated with both DNA sequencing as well as traditional morphotaxonomic approaches. We compared our ability to evaluate the ecological health of streams with the performance of multiple algal indices of biological condition. Our zeta diversity-based models of regional biotic integrity were more strongly correlated with existing indices for algal assemblages classified using metabarcoding compared to morphotaxonomy. Metabarcoding for diatoms and hybrid algal assemblages involved rbcL and 18S V9 primers, respectively. Importantly, we also found that these algal assemblages, independent of the classification method, are more likely to be assembled under a process of niche differentiation rather than stochastically. Taken together, these results suggest the potential for zeta diversity patterns of algal assemblages classified using metabarcoding to inform stream bioassessments.
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Affiliation(s)
- Ariel Levi Simons
- Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, USA
| | - Susanna Theroux
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Melisa Osborne
- Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, USA
| | - Sergey Nuzhdin
- Dornsife College of Letters, Arts and Sciences, University of Southern California, Los Angeles, California, USA
| | - Raphael Mazor
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
| | - Joshua Steele
- Southern California Coastal Water Research Project, Costa Mesa, California, USA
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Galachyants Y, Zakharova Y, Bashenkhaeva M, Petrova D, Kopyrina L, Likhoshway Y. Microeukaryotic Communities of the Long-Term Ice-Covered Freshwater Lakes in the Subarctic Region of Yakutia, Russia. DIVERSITY 2023. [DOI: 10.3390/d15030454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Currently, microeukaryotic communities of the freshwater arctic and subarctic ecosystems are poorly studied. Still, these are of considerable interest due to the species biogeography and autecology as well as global climate change. Here, we used high-throughput 18S rRNA amplicon sequencing to study the microeukaryotic communities of the large subarctic freshwater lakes Labynkyr and Vorota in Yakutia, Russia, during the end of the ice cover period, from April to June. By applying the statistical methods, we coupled the microeukaryotic community structure profiles with available discrete factor variables and hydrophysical, hydrochemical, and environmental parameters. The sub-ice layer and the water column communities were differentiated due to the temporal change in environmental conditions, particularly temperature regime and electric conductivity. Additionally, the community composition of unicellular eukaryotes in lakes Labynkyr and Vorota was changing due to seasonal environmental factors, with these alterations having similar patterns in both sites. We suggest the community developed in the sub-ice layer in April serves as a primer for summer freshwater microeukaryotes. Our results extend the current knowledge on the community composition and seasonal succession of unicellular eukaryotes within subarctic freshwater ecosystems.
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14
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Kalu EI, Reyes-Prieto A, Barbeau MA. Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy. ISME COMMUNICATIONS 2023; 3:21. [PMID: 36918616 PMCID: PMC10014957 DOI: 10.1038/s43705-023-00226-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 02/15/2023] [Accepted: 02/28/2023] [Indexed: 03/16/2023]
Abstract
Protists (microbial eukaryotes) are a critically important but understudied group of microorganisms. They are ubiquitous, represent most of the genetic and functional diversity among eukaryotes, and play essential roles in nutrient and energy cycling. Yet, protists remain a black box in marine sedimentary ecosystems like the intertidal mudflats in the Bay of Fundy. The harsh conditions of the intertidal zone and high energy nature of tides in the Bay of Fundy provide an ideal system for gaining insights into the major food web players, diversity patterns and potential structuring influences of protist communities. Our 18S rDNA metabarcoding study quantified seasonal variations and vertical stratification of protist communities in Bay of Fundy mudflat sediments. Three 'SAR' lineages were consistently dominant (in terms of abundance, richness, and prevalence), drove overall community dynamics and formed the core microbiome in sediments. They are Cercozoa (specifically thecate, benthic gliding forms), Bacillariophyta (mainly cosmopolitan, typically planktonic diatoms), and Dinophyceae (dominated by a toxigenic, bloom-forming species). Consumers were the dominant trophic functional group and were comprised mostly of eukaryvorous and bacterivorous Cercozoa, and omnivorous Ciliophora, while phototrophs were dominated by Bacillariophyta. The codominance of Apicomplexa (invertebrate parasites) and Syndiniales (protist parasites) in parasite assemblages, coupled with broader diversity patterns, highlighted the combined marine and terrestrial influences on microbial communities inhabiting intertidal sediments. Our findings, the most comprehensive in a hypertidal benthic system, suggest that synergistic interactions of both local and regional processes (notably benthic-pelagic coupling) may drive heterogenous microbial distribution in high-energy coastal systems.
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Affiliation(s)
- Eke I Kalu
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada.
| | | | - Myriam A Barbeau
- Department of Biology, University of New Brunswick, Fredericton, NB, Canada
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15
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Yuan LL, Mitchell RM, Pollard AI, Nietch CT, Pilgrim EM, Smucker NJ. Understanding the effects of phosphorus on diatom richness in rivers and streams using taxon-environment relationships. FRESHWATER BIOLOGY 2023; 68:473-486. [PMID: 37538102 PMCID: PMC10395338 DOI: 10.1111/fwb.14040] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/11/2022] [Indexed: 08/05/2023]
Abstract
Changes in phosphorus concentrations affect periphytic diatom composition in streams, yet we rarely observe strong relationships between diatom richness and phosphorus. In contrast, changes in conductivity are strongly associated with differences in both diatom composition and richness. We hypothesised that we could better understand the mechanisms that control the phosphorus-richness relationship by examining relationships between phosphorus and the occurrence of individual diatom taxa, comparing these with relationships between conductivity and taxon occurrence, and documenting how niche breadths of taxa affect richness patterns. We estimated relationships between phosphorus and taxon occurrence using DNA metabarcoding data of diatoms collected from 1,811 sites distributed across the conterminous U.S.A. and contrasted patterns in these relationships with those between conductivity and taxon occurrence. The distribution of taxon optima for phosphorus was bimodal, with most optima located at either the maximum or minimum observed phosphorus concentration. The distribution of taxon optima for conductivity was unimodal. Niche breadths of taxa for phosphorus and for conductivity both generally increased with optimum values. The distribution of conductivity optima gave rise to a prominent hump-shaped relationship between richness and conductivity. The relationship between richness and phosphorus was also slightly hump-shaped, but this relationship would not be expected from the bimodal distribution of optima. Instead, we determined that broad niche breadths caused the hump-shaped relationship between richness and phosphorus. Our results highlight the nuanced effects that increased P loadings exert on diatom assemblages in rivers and streams and identify reasons that weak relationships between taxon richness and increased phosphorus have been observed. These findings allow us to better describe how excess phosphorus and subsets of taxa and their niche breadths contribute to patterns of taxa richness in diatom assemblages, and to improve the tools used to manage phosphorus pollution.
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Affiliation(s)
- Lester L. Yuan
- Office of Water, U. S. Environmental Protection Agency, Washington, District of Columbia, U.S.A
| | - Richard M. Mitchell
- Office of Water, U. S. Environmental Protection Agency, Washington, District of Columbia, U.S.A
| | - Amina I. Pollard
- Office of Water, U. S. Environmental Protection Agency, Washington, District of Columbia, U.S.A
| | - Christopher T. Nietch
- Office of Research and Development, U. S. Environmental Protection Agency, Cincinnati, Ohio, U.S.A
| | - Erik M. Pilgrim
- Office of Research and Development, U. S. Environmental Protection Agency, Cincinnati, Ohio, U.S.A
| | - Nathan J. Smucker
- Office of Research and Development, U. S. Environmental Protection Agency, Cincinnati, Ohio, U.S.A
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16
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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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17
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Linz DM, Sienkiewicz N, Struewing I, Stelzer EA, Graham JL, Lu J. Metagenomic mapping of cyanobacteria and potential cyanotoxin producing taxa in large rivers of the United States. Sci Rep 2023; 13:2806. [PMID: 36797305 PMCID: PMC9935515 DOI: 10.1038/s41598-023-29037-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Cyanobacteria and cyanotoxin producing cyanobacterial blooms are a trending focus of current research. Many studies focus on bloom events in lentic environments such as lakes or ponds. Comparatively few studies have explored lotic environments and fewer still have examined the cyanobacterial communities and potential cyanotoxin producers during ambient, non-bloom conditions. Here we used a metagenomics-based approach to profile non-bloom microbial communities and cyanobacteria in 12 major U.S. rivers at multiple time points during the summer months of 2019. Our data show that U.S. rivers possess microbial communities that are taxonomically rich, yet largely consistent across geographic location and time. Within these communities, cyanobacteria often comprise significant portions and frequently include multiple species with known cyanotoxin producing strains. We further characterized these potential cyanotoxin producing taxa by deep sequencing amplicons of the microcystin E (mcyE) gene. We found that rivers containing the highest levels of potential cyanotoxin producing cyanobacteria consistently possess taxa with the genetic potential for cyanotoxin production and that, among these taxa, the predominant genus of origin for the mcyE gene is Microcystis. Combined, these data provide a unique perspective on cyanobacteria and potential cyanotoxin producing taxa that exist in large rivers across the U.S. and can be used to better understand the ambient conditions that may precede bloom events in lotic freshwater ecosystems.
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Affiliation(s)
- David M. Linz
- grid.418698.a0000 0001 2146 2763Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH USA
| | - Nathan Sienkiewicz
- grid.418698.a0000 0001 2146 2763Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH USA
| | - Ian Struewing
- grid.418698.a0000 0001 2146 2763Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH USA
| | - Erin A. Stelzer
- grid.2865.90000000121546924U.S. Geological Survey, Columbus, OH USA
| | | | - Jingrang Lu
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, USA.
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18
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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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Debroas D, Hochart C, Galand PE. Seasonal microbial dynamics in the ocean inferred from assembled and unassembled data: a view on the unknown biosphere. ISME COMMUNICATIONS 2022; 2:87. [PMID: 37938749 PMCID: PMC9723795 DOI: 10.1038/s43705-022-00167-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 08/23/2022] [Accepted: 09/02/2022] [Indexed: 11/09/2023]
Abstract
In environmental metagenomic experiments, a very high proportion of the microbial sequencing data (> 70%) remains largely unexploited because rare and closely related genomes are missed in short-read assemblies. The identity and the potential metabolisms of a large fraction of natural microbial communities thus remain inaccessible to researchers. The purpose of this study was to explore the genomic content of unassembled metagenomic data and test their level of novelty. We used data from a three-year microbial metagenomic time series of the NW Mediterranean Sea, and conducted reference-free and database-guided analysis. The results revealed a significant genomic difference between the assembled and unassembled reads. The unassembled reads had a lower mean identity against public databases, and fewer metabolic pathways could be reconstructed. In addition, the unassembled fraction presented a clear temporal pattern, unlike the assembled ones, and a specific community composition that was similar to the rare communities defined by metabarcoding using the 16S rRNA gene. The rare gene pool was characterised by keystone bacterial taxa, and the presence of viruses, suggesting that viral lysis could maintain some taxa in a state of rarity. Our study demonstrates that unassembled metagenomic data can provide important information on the structure and functioning of microbial communities.
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Affiliation(s)
- Didier Debroas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, 63000, Clermont-Ferrand, France.
| | - Corentin Hochart
- Sorbonne Universités, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
| | - Pierre E Galand
- Sorbonne Universités, CNRS, Laboratoire d'Ecogéochimie des Environnements Benthiques (LECOB), Observatoire Océanologique de Banyuls, Banyuls sur Mer, France
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20
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Larval gut microbiome of Pelidnota luridipes (Coleoptera: Scarabaeidae): high bacterial diversity, different metabolic profiles on gut chambers and species with probiotic potential. World J Microbiol Biotechnol 2022; 38:210. [PMID: 36050590 DOI: 10.1007/s11274-022-03387-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Accepted: 08/11/2022] [Indexed: 10/14/2022]
Abstract
Pelidnota luridipes Blanchard (1850) is a tropical beetle of the family Scarabaeidae, whose larvae live on wood without parental care. Microbiota of mid- and hindgut of larvae was evaluated by culture-dependent and independent methods, and the results show a diverse microbiota, with most species of bacteria and fungi shared between midgut and hindgut. We isolated 272 bacterial and 29 yeast isolates, identified in 57 and 7 species, respectively, while using metabarcoding, we accessed 1,481 and 267 OTUs of bacteria and fungi, respectively. The composition and abundance of bacteria and fungi differed between mid- and hindgut, with a tendency for higher richness and diversity of yeasts in the midgut, and bacteria on the hindgut. Some taxa are abundant in the intestine of P. luridipes larvae, such as Firmicutes, Bacteroidetes, Proteobacteria, and Actinobacteria; as well as Saccharomycetales and Trichosporonales yeasts. Mid- and hindgut metabolic profiles differ (e.g. biosynthesis of amino acids, cofactors, and lipopolysaccharides) with higher functional diversity in the hindgut. Isolates have different functional traits such as secretion of hydrolytic enzymes and antibiosis against pathogens. Apiotrichum siamense L29A and Bacillus sp. BL17B protected larvae of the moth Galleria mellonella, against infection by the pathogens Listeria monocytogenes ATCC19111 and Pseudomonas aeruginosa ATCC 9027. This is the first work with the larval microbiome of a Rutelini beetle, demonstrating its diversity and potential in prospecting microbial products as probiotics. The functional role of microbiota for the nutrition and adaptability of P. luridipes larvae needs to be evaluated in the future.
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Biderre‐Petit C, Charvy J, Bronner G, Chauvet M, Debroas D, Gardon H, Hennequin C, Jouan‐Dufournel I, Moné A, Monjot A, Ravet V, Vellet A, Lepère C. FreshOmics
: a manually curated and standardized –omics database for investigating freshwater microbiomes. Mol Ecol Resour 2022; 23:222-232. [DOI: 10.1111/1755-0998.13692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/22/2022] [Accepted: 07/25/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Corinne Biderre‐Petit
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Jean‐Christophe Charvy
- 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
| | - Marina Chauvet
- 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
| | - Hélène Gardon
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Claire Hennequin
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Isabelle Jouan‐Dufournel
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Anne Moné
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Arthur Monjot
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
| | - Viviane Ravet
- 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
| | - Cécile Lepère
- CNRS, Laboratoire Microorganismes: Génome et Environnement Université Clermont Auvergne Clermont‐Ferrand France
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Abdullah Al M, Xue Y, Xiao P, Xu J, Chen H, Mo Y, Shimeta J, Yang J. Community assembly of microbial habitat generalists and specialists in urban aquatic ecosystems explained more by habitat type than pollution gradient. WATER RESEARCH 2022; 220:118693. [PMID: 35667165 DOI: 10.1016/j.watres.2022.118693] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 04/19/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Urban freshwater ecosystems have important ecosystem functions, provide habitats for diverse microbial communities and are susceptible to multiple interconnected factors such as environmental pollution. Despite the ecological significance of bacteria and microeukaryotes, little is known about how their community assembly responds to various environmental factors across water and sediment habitats and ecological processes shaping them. Here, environmental DNA-based approaches were used to investigate the community assembly processes of bacteria and microeukaryotes (including habitat generalists and specialists) in urban water and sediment across an urban-pollution gradient in Wuhan, central China. The diversity, community composition and potential function of bacteria and microeukaryotes showed significantly stronger variation between water and sediment than across an urban pollution gradient. Although, bacterial and microeukaryotic community assemblies were dominated by strong selection processes in both water and sediment habitats, but a contrasting community assembly mechanism was identified between habitat generalists and specialists. Bacterial and microeukaryotic communities showed a greater response to physicochemical variability in water, while a strong distance-decay relationship was found in sediment. Further, cross-kingdom microbial network analysis revealed strong modular associations of bacteria and microeukaryotes, meanwhile, microeukaryotic habitat specialists might be keystone, but generalists have higher proportion of connections in the networks. This study provides significant insights into the response of bacteria and microeukaryotes to different urban pollutions between water and sediment, and the ecological processes structuring microbial community dynamics across habitat types under anthropogenic disturbances.
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Affiliation(s)
- Mamun Abdullah Al
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanyuan Xue
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Peng Xiao
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Jing Xu
- State Key Laboratory of Water Resources and Hydropower Engineering Science, Wuhan University, Wuhan 430072, China
| | - Huihuang Chen
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuanyuan Mo
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jeff Shimeta
- School of Science, RMIT University, Melbourne, Victoria 3000, Australia
| | - Jun Yang
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinses Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China.
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23
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Fan Y, Fu Q, Zhang S, Zhang M, Chang S, Zhao S, Wang M. Spatiotemporal variation in nitrogen and phosphorus levels and microbial community in the upstream water transport channel to the Douhe Reservoir. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:50471-50487. [PMID: 35233670 DOI: 10.1007/s11356-022-19273-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 02/13/2022] [Indexed: 06/14/2023]
Abstract
The Douhe Reservoir is an important diversion water source and drinking water resource for Tianjin and the Tangshan cities. Panjiakou, Daheiting, Qiuzhuang, and the Douhe Reservoirs located from top to bottom in the LuanHe River region forming a group of cascade reservoirs. After over 30 years of aquaculture, the concentration of nitrogen (N) and phosphorus (P) have exceeded Class III of Environmental Quality Standard for Surface Water in China. We selected the Douhe Reservoir as the study site and choose sampling points in several upstream reservoirs and main reservoir area, and we collected a total of 18 water samples. Moreover, the distribution characteristics of N and P levels in flood season and dry season were studied in the Douhe Reservoir and upstream water channel, respectively. The results indicated that there were significant spatial differences between N and P distribution in the Douhe Reservoir and the upstream sites. We observed that the distribution of N and P had seasonal characteristics, and the contents of nitrate(NO3--N), nitrogen(TN), total phosphorus(TP), and total dissolved phosphorus(TDP) in flood periods were higher than those in dry periods. The microbial community structure illustrated that the dominant phylum displayed seasonal differences between the upstream channel and the reservoir area. Among them, the abundance of some genera changed with the location of the channel, the microbial community structure, and the levels of N and P, especially in flood season. Particularly, NO3--N and TN had the most significant correlation. Hence, this study presented an important theoretical foundation for the risk prevention and the control of nutrient elements in the LuanHe River basin in the future, which would enhance the drinking water safety of Tianjin and Tangshan residents.
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Affiliation(s)
- Yueting Fan
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory of Drinking Water Source Protection, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Qing Fu
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory of Drinking Water Source Protection, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Shusong Zhang
- College of Ocean and Bioengineering, Yancheng Teachers University, Yancheng, 224007, China
| | - Moli Zhang
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory of Drinking Water Source Protection, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Sheng Chang
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory of Drinking Water Source Protection, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China.
| | - Shaoyan Zhao
- National Engineering Laboratory for Lake Pollution Control and Ecological Restoration, State Environmental Protection Key Laboratory of Drinking Water Source Protection, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Minling Wang
- Shandong Yantai Ecological Environmental Monitoring Center, Shandong, 264000, China
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24
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Protist Diversity and Metabolic Strategy in Freshwater Lakes Are Shaped by Trophic State and Watershed Land Use on a Continental Scale. mSystems 2022; 7:e0031622. [PMID: 35730947 PMCID: PMC9426515 DOI: 10.1128/msystems.00316-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Protists play key roles in aquatic food webs as primary producers, predators, nutrient recyclers, and symbionts. However, a comprehensive view of protist diversity in freshwaters has been challenged by the immense environmental heterogeneity among lakes worldwide. We assessed protist diversity in the surface waters of 366 freshwater lakes across a north temperate to subarctic range covering nearly 8.4 million km2 of Canada. Sampled lakes represented broad gradients in size, trophic state, and watershed land use. Hypereutrophic lakes contained the least diverse and most distinct protist communities relative to nutrient-poor lakes. Greater taxonomic variation among eutrophic lakes was mainly a product of heterotroph and mixotroph diversity, whereas phototroph assemblages were more similar under high-nutrient conditions. Overall, local physicochemical factors, particularly ion and nutrient concentrations, elicited the strongest responses in community structure, far outweighing the effects of geographic gradients. Despite their contrasting distribution patterns, obligate phototroph and heterotroph turnover was predicted by an overlapping set of environmental factors, while the metabolic plasticity of mixotrophs may have made them less predictable. Notably, protist diversity was associated with variation in watershed soil pH and agricultural crop coverage, pointing to human impact on the land-water interface that has not been previously identified in studies on smaller scales. Our study exposes the importance of both within-lake and external watershed characteristics in explaining protist diversity and biogeography, critical information for further developing an understanding of how freshwater lakes and their watersheds are impacted by anthropogenic stressors. IMPORTANCE Freshwater lakes are experiencing rapid changes under accelerated anthropogenic stress and a warming climate. Microorganisms underpin aquatic food webs, yet little is known about how freshwater microbial communities are responding to human impact. Here, we assessed the diversity of protists and their myriad ecological roles in lakes varying in size across watersheds experiencing a range of land use pressures by leveraging data from a continental-scale survey of Canadian lakes. We found evidence of human impact on protist assemblages through an association with lake trophic state and extending to agricultural activity and soil characteristics in the surrounding watershed. Furthermore, trophic state appeared to explain the distributions of phototrophic and heterotrophic protists in contrasting ways. Our findings highlight the vulnerability of lake ecosystems to increased land use and the importance of assessing terrestrial interfaces to elucidate freshwater ecosystem dynamics.
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25
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Ren Z, Zhang Y, Li X, Zhang C. Biogeography of Micro-Eukaryotic Communities in Sediment of Thermokarst Lakes Are Jointly Controlled by Spatial, Climatic, and Physicochemical Factors Across the Qinghai-Tibet Plateau. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.901107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Thermokarst lakes are formed following ice-rich permafrost thaw and widely distribute in the cold regions with high latitude and elevation. However, the micro-eukaryotic communities (MECs) in thermokarst lakes are not well studied. Employing 18S rRNA gene sequencing, we assessed the biogeography of MECs and their driving factors in sediments of thermokarst lakes across the Qinghai-Tibet Plateau (QTP). Results showed that Diatom, Gastrotricha, Nematozoa, Ciliophora, and Cercozoa were dominant lineages in relative abundance and OTU richness. MECs varied substantially across the lakes in terms of diversity and composition. Structural equation modeling and mantel test showed that both OTU richness and community structure of MECs had close relationships with spatial factors, climatic factors, and sediment properties, particularly with latitude, mean annual precipitation, pH, as well as nutrient concentrations and stoichiometric ratios. Moreover, different groups of microbial eukaryotes (taxonomic groups and co-occurrence modules) responded differentially to the measured environmental variables. The results suggested that the biogeography of sediment MECs of thermokarst lakes on the QTP were jointly controlled by spatial and climatic factors as well as sediment properties. This study provides the first view of the composition, diversity, and underlying drivers of MECs dynamic in surface sediments of thermokarst lakes across the QTP.
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26
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Bock C, Olefeld JL, Vogt JC, Albach DC, Boenigk J. Phylogenetic and functional diversity of Chrysophyceae in inland waters. ORG DIVERS EVOL 2022. [DOI: 10.1007/s13127-022-00554-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
AbstractChrysophyceae are a diverse group of planktonic protists widely distributed in freshwater. They encompass a variety of orders, whereby heterotrophy has evolved independently in several phylogenetic lineages. Therefore, closely related taxa evolved that developed different feeding strategies (photo-, mixo-, heterotrophy). In high-throughput sequencing studies, the Chrysophyceae were usually addressed as a group rather than split in individual phylogenetic orders. Also because of the close relationship of the distinct nutritional strategies, no functional statements were made about nutritional patterns. Based on an extensive phylogenetic tree and phylogenetic placement, we link OTU diversity of Chrysophyceae from 218 freshwater lakes with phylogenetic affiliations. This provides information on the relative importance of lineages affiliated with different nutrition modes. Our study demonstrates that Chrysophyceae are one of the most common groups in freshwaters. We found Chrysophyceae in 213 out of 218 sample sites across Europe and in several sites they belong to the most commonly retrieved taxa. Ochromonadales and a Chrysosacca-Apoikiida clade (including Apoikiida, Chrysosaccales, Chrysastrella) are the most widespread Chrysophyceae groups and show a high degree of OTU diversity. Most detected and assignable OTUs were affiliated with mixotrophic Chrysophyceae. Niche width differs only slightly between members of different clades and between the different trophic modes. We found several OTUs within the Ochromonadales, Synurales, and Chrysosacca-Apoikiida clade, that show a wide distribution and large tolerance ranges concerning ecophysiological factors.
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27
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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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28
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Selak L, Osterholz H, Stanković I, Hanžek N, Udovič MG, Dittmar T, Orlić S. Adaptations of microbial communities and dissolved organics to seasonal pressures in a mesotrophic coastal Mediterranean lake. Environ Microbiol 2022; 24:2282-2298. [PMID: 35106913 DOI: 10.1111/1462-2920.15924] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 01/21/2022] [Accepted: 01/25/2022] [Indexed: 11/29/2022]
Abstract
In lake ecosystems, changes in eukaryotic and prokaryotic microbes and the concentration and availability of dissolved organic matter (DOM) produced within or supplied to the system by allochthonous sources are components that characterize complex processes in the microbial loop. We address seasonal changes of microbial communities and DOM in the largest Croatian lake, Vrana. This shallow lake is connected to the Adriatic Sea and is impacted by agricultural activity. Microbial community and DOM structure were driven by several environmental stressors, including drought, seawater intrusion, and heavy precipitation events. Bacterial composition of different lifestyles (free-living and particle-associated) differed and only a part of the particle-associated bacteria correlated with microbial eukaryotes. Oscillations of cyanobacterial relative abundance along with chlorophyll a revealed a high primary production season characterized by increased levels of autochthonous DOM that promoted bacterial processes of organic matter degradation. From our results, we infer that in coastal freshwater lakes dependent on precipitation-evaporation balance, prolonged dry season coupled with heavy irrigation impact microbial communities at different trophic levels even if salinity increases only slightly and allochthonous DOM inputs decrease. These pressures, if applied more frequently or at higher concentrations, could have the potential to overturn the trophic state of the lake. This article is protected by copyright. All rights reserved.
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Affiliation(s)
| | - Helena Osterholz
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany.,Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Igor Stanković
- Hrvatske vode, Central Water Management Laboratory, Zagreb, Croatia
| | - Nikola Hanžek
- Hrvatske vode, Central Water Management Laboratory, Zagreb, Croatia
| | - Marija Gligora Udovič
- University of Zagreb, Faculty of Science, Department of Biology, Rooseveltov trg 6, Zagreb, Croatia
| | - Thorsten Dittmar
- Institute for Chemistry and Biology of the Marine Environment, Carl von Ossietzky University, Oldenburg, Germany.,Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
| | - Sandi Orlić
- Ruđer Bošković Institute, Zagreb, Croatia.,Center of Excellence for Science and Technology-Integration of Mediterranean Region (STIM), Split, Croatia
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29
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Itoïz S, Metz S, Derelle E, Reñé A, Garcés E, Bass D, Soudant P, Chambouvet A. Emerging Parasitic Protists: The Case of Perkinsea. Front Microbiol 2022; 12:735815. [PMID: 35095782 PMCID: PMC8792838 DOI: 10.3389/fmicb.2021.735815] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 11/25/2021] [Indexed: 11/13/2022] Open
Abstract
The last century has witnessed an increasing rate of new disease emergence across the world leading to permanent loss of biodiversity. Perkinsea is a microeukaryotic parasitic phylum composed of four main lineages of parasitic protists with broad host ranges. Some of them represent major ecological and economical threats because of their geographically invasive ability and pathogenicity (leading to mortality events). In marine environments, three lineages are currently described, the Parviluciferaceae, the Perkinsidae, and the Xcellidae, infecting, respectively, dinoflagellates, mollusks, and fish. In contrast, only one lineage is officially described in freshwater environments: the severe Perkinsea infectious agent infecting frog tadpoles. The advent of high-throughput sequencing methods, mainly based on 18S rRNA assays, showed that Perkinsea is far more diverse than the previously four described lineages especially in freshwater environments. Indeed, some lineages could be parasites of green microalgae, but a formal nature of the interaction needs to be explored. Hence, to date, most of the newly described aquatic clusters are only defined by their environmental sequences and are still not (yet) associated with any host. The unveiling of this microbial black box presents a multitude of research challenges to understand their ecological roles and ultimately to prevent their most negative impacts. This review summarizes the biological and ecological traits of Perkinsea-their diversity, life cycle, host preferences, pathogenicity, and highlights their diversity and ubiquity in association with a wide range of hosts.
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Affiliation(s)
- Sarah Itoïz
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, Plouzané, France
| | | | | | - Albert Reñé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta, Barcelona, Spain
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar, CSIC, Pg. Marítim de la Barceloneta, Barcelona, Spain
| | - David Bass
- Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, United Kingdom
- Department of Life Sciences, The Natural History Museum, London, United Kingdom
- Biosciences, University of Exeter, Exeter, United Kingdom
| | | | - Aurélie Chambouvet
- Univ Brest, CNRS, IRD, Ifremer, LEMAR, Plouzané, France
- Sorbonne Université, CNRS, UMR 7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, Roscoff, France
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30
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Patchy Distributions and Distinct Niche Partitioning of Mycoplankton Populations across a Nearshore to Open Ocean Gradient. Microbiol Spectr 2021; 9:e0147021. [PMID: 34908435 PMCID: PMC8672894 DOI: 10.1128/spectrum.01470-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Evidence increasingly suggests planktonic fungi (or mycoplankton) play an important role in marine food webs and biogeochemical cycles. In order to better understand their ecological role and how oceanographic gradients from the coastal to open ocean shape the mycoplankton community, molecular approaches were used to study fungal dynamics along a repeatedly sampled, five-station transect beginning at the mouth of an estuary and continuing 87 km across the continental shelf to the oligotrophic waters at the boundary of the Sargasso Sea. Similar to patterns in chlorophyll a, fungal 18S rRNA gene abundance showed a sharp decrease from nearshore to offshore stations. While Shannon's diversity was not statistically different across the transect, nonmetric multidimensional scaling (NMDS) ordination revealed that fungal communities at the nearshore station were significantly different from those at other stations. Even though spatial gradients were consistently strong, the shelf mycoplankton were more similar to those of the offshore communities when temperature was high (>20°C) and while they shifted toward the nearshore communities when temperature was low (<19°C), suggesting a role for additional seasonal factors (such as temperature) in shaping mycoplankton distributions. However, overall phylotype distributions were patchy with few taxa observed at all stations and the majority observed at a single station with the nearshore station exhibiting the largest number of exclusive phylotypes. Overall, our findings revealed the patchy spatial distributions and distinct niche partitioning of mycoplankton populations across a nearshore to open ocean gradient, which improved our understanding of fungal ecology in coastal waters. IMPORTANCE Fungi are an important, but understudied, group of heterotrophic microbes in marine environments. Traditionally, fungi in the coastal ocean were largely assumed to be derived from terrestrial inputs. Yet here we find many fungal taxa are endemic to the open ocean environment but are rare or absent in nearshore waters, suggesting they are not washed into the ocean from the land. As observed for the bacterioplankton, coastal oceanographic gradients can function as habitat barriers to partition fungal communities. Compared to the bacterioplankton, however, the mycoplankton exhibit a much patchier distribution pattern, suggesting differential drivers and the potential for spatially/temporally limited habitats or strong density-dependent selection. Therefore, our results show that mycoplankton in the coastal ocean may play a significant but complementary role to that of the bacterioplankton.
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31
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Paramecium bursaria—A Complex of Five Cryptic Species: Mitochondrial DNA COI Haplotype Variation and Biogeographic Distribution. DIVERSITY 2021. [DOI: 10.3390/d13110589] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Ciliates are a diverse protistan group and many consist of cryptic species complexes whose members may be restricted to particular biogeographic locations. Mitochondrial genes, characterized by a high resolution for closely related species, were applied to identify new species and to distinguish closely related morphospecies. In the current study, we analyzed 132 sequences of COI mtDNA fragments obtained from P. bursaria species collected worldwide. The results allowed, for the first time, to generate a network of COI haplotypes and demonstrate the relationships between P. bursaria strains, as well as to confirm the existence of five reproductively isolated haplogroups. The P. bursaria haplogroups identified in the present study correspond to previously reported syngens (R1, R2, R3, R4, and R5), thus we decided to propose the following binominal names for each of them: P. primabursaria, P. bibursaria, P. tribursaria, P. tetrabursaria, and P. pentabursaria, respectively. The phylogeographic distribution of P. bursaria species showed that P. primabursaria and P. bibursaria were strictly Eurasian, except for two South Australian P. bibursaria strains. P. tribursaria was found mainly in Eastern Asia, in two stands in Europe and in North America. In turn, P. tetrabursaria was restricted to the USA territory, whereas P. pentabursaria was found in two European localities.
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32
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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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33
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Abdullah Al M, Xue Y, Xiao P, Chen H, Zhang C, Duan M, Yang J. DNA metabarcoding reveals the significant influence of anthropogenic effects on microeukaryotic communities in urban waterbodies. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2021; 285:117336. [PMID: 34052609 DOI: 10.1016/j.envpol.2021.117336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 04/02/2021] [Accepted: 05/06/2021] [Indexed: 06/12/2023]
Abstract
Biological monitoring and assessment are the first and most fundamental steps towards diagnosing ecological or environmental quality. Increasing anthropogenic impact on urban ecosystems has prompted the development of less expensive and more efficient bioassessment approaches. Generally, a morphospecies based approach is effective for plants and large organisms but challenging for the microbial biosphere. To overcome this challenge, we used high-throughput DNA sequencing for predicting anthropogenic effects on microeukaryotic communities in urban waterbodies along a pollution gradient in Wuhan City, central China in summer 2019. Our results indicated that microeukaryotic community structure was distinct between non-urban polluted reservoir and urban polluted waterbodies. The heterogeneity of environmental condition significantly affected the microeukaryotic diversity, community structure, and species interactions. Integrated co-occurring network analysis revealed that the pollution gradient has a significant adverse impact on network complexity and network dissimilarity. These results revealed that the significant variation in anthropogenically-driven environmental condition shaped microeukaryotic communities in urban freshwater ecosystems. Furthermore, we observed that the relative abundance of indicative OTUs were significantly and negatively correlated with pollution level and these indicative OTUs could be used to predict the water quality status with up to 77% success. Thus, our multiple approaches combining 18S rDNA amplicon sequencing, co-occurring network and indicator species analyses suggest that this study gives a novel approach based on microeukaryotic communities to assess and predict the water quality status of urban aquatic environments.
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Affiliation(s)
- Mamun Abdullah Al
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China; University of Chinese Academy of Sciences, Beijing, 100049, PR China; Institute of Marine Sciences, University of Chittagong, Chittagong, 4331, Bangladesh
| | - Yuanyuan Xue
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China
| | - Peng Xiao
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China
| | - Huihuang Chen
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China
| | - Chaoshuo Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China
| | - Ming Duan
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, PR China.
| | - Jun Yang
- Aquatic Eco-Health Group, Fujian Key Laboratory of Watershed Ecology, Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen, 361021, PR China.
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Endophytic and rhizospheric bacterial communities are affected differently by the host plant species and environmental contamination. Symbiosis 2021. [DOI: 10.1007/s13199-021-00804-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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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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36
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Wilden B, Traunspurger W, Geisen S. Inventory of the benthic eukaryotic diversity in the oldest European lake. Ecol Evol 2021; 11:11207-11215. [PMID: 34429912 PMCID: PMC8366835 DOI: 10.1002/ece3.7907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/19/2021] [Accepted: 06/22/2021] [Indexed: 11/22/2022] Open
Abstract
We have profound knowledge on biodiversity on Earth including plants and animals. In the recent decade, we have also increased our understanding on microorganisms in different hosts and the environment. However, biodiversity is not equally well studied among different biodiversity groups and Earth's systems with eukaryotes in freshwater sediments being among the least known. In this study, we used high-throughput sequencing of the 18S rRNA gene to investigate the entire diversity of benthic eukaryotes in three distinct habitats (littoral sediment and hard substrate, profundal sediment) of Lake Ohrid, the oldest European lake. Eukaryotic sequences were dominated by annelid and arthropod animals (54% of all eukaryotic reads) and protists (Ochrophyta and Ciliophora; together 40% of all reads). Eukaryotic diversity was 15% higher in the deep profundal than on either near-surface hard substrates or littoral sediments. The three habitats differed in their taxonomic and functional community composition. Specifically, heterotrophic organisms accounted for 92% of the reads in the profundal, whereas phototrophs accounted for 43% on the littoral hard substrate. The profundal community was the most homogeneous, and its network was the most complex, suggesting its highest stability among the sampled habitats.
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Affiliation(s)
- Benjamin Wilden
- Department of Animal EcologyBielefeld UniversityBielefeldGermany
| | | | - Stefan Geisen
- Laboratory of NematologyWageningen UniversityWageningenThe Netherlands
- Netherlands Department of Terrestrial EcologyNetherlands Institute for Ecology (NIOO‐KNAW)WageningenThe Netherlands
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Dubuffet A, Chauvet M, Moné A, Debroas D, Lepère C. A phylogenetic framework to investigate the microsporidian communities through metabarcoding and its application to lake ecosystems. Environ Microbiol 2021; 23:4344-4359. [PMID: 34081807 DOI: 10.1111/1462-2920.15618] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/27/2021] [Accepted: 05/29/2021] [Indexed: 11/29/2022]
Abstract
Microsporidia are obligate intracellular eukaryotic parasites known to parasitize many species of the animal kingdom as well as some protists. However, their diversity is underestimated, in part as a consequence of the failure of 'universal' primers to detect them in metabarcoding studies. Besides, due to the inconsistency between taxonomy and phylogenetic data, available databases may assign incorrectly sequences obtained with high-throughput sequencing. In this work, we developed a comprehensive reference database which positions microsporidian SSU rRNA gene sequences within a coherent ranked phylogenetic framework. We used this phylogenetic framework to study the microsporidian diversity in lacustrine ecosystems, focusing on < 150 μm planktonic size fractions. Our analysis shows a high diversity of Microsporidia, with the identification of 1531 OTUs distributed within seven clades, of which 76% were affiliated to clade IV2 and 20% to clade I (nomenclature presented hereby). About a quarter of the obtained sequences shared less than 85% identity to the closest known species, which might represent undescribed genera or families infecting small hosts. Variations in the abundance of Microsporidia were recorded between the two lakes sampled and across the sampling period, which might be explained by spatio-temporal variations of their potential hosts such as microeukaryotes and metazooplankton.
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Affiliation(s)
- Aurore Dubuffet
- CNRS, Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, Clermont-Ferrand, F-63000, France
| | - Marina Chauvet
- 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
| | - Didier Debroas
- 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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Lalla C, Calvaruso R, Dick S, Reyes-Prieto A. Winogradsky columns as a strategy to study typically rare microbial eukaryotes. Eur J Protistol 2021; 80:125807. [PMID: 34091379 DOI: 10.1016/j.ejop.2021.125807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Revised: 05/05/2021] [Accepted: 05/11/2021] [Indexed: 11/28/2022]
Abstract
Winogradsky columns have been widely used to study soil microbial communities, but the vast majority of those investigations have focused on the ecology and diversity of bacteria. In contrast, microbial eukaryotes (ME) have been regularly overlooked in studies based on experimental soil columns. Despite the recognized ecological relevance of ME in soil communities, investigations focused on ME diversity and the abundance of certain groups of interest are still scarce. In the present study, we used DNA metabarcoding (high-throughput sequencing of the V4 region of the 18S rRNA locus) to survey the ME diversity and abundance in an experimental Winogradsky soil column. Consistent with previous surveys in natural soils, our survey identified members of Cercozoa (Rhizaria; 31.2%), Apicomplexa and Ciliophora (Alveolata; 12.5%) as the predominant ME groups, but at particular depths we also detected the abundant presence of ME lineages that are typically rare in natural environments, such as members of the Vampyrellida (Rhizaria) and Breviatea (Amorphea). Our survey demonstrates that experimental soil columns are an efficient enrichment-culture approach that can enhance investigations about the diversity and ecology of ME in soils.
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Affiliation(s)
- Clarissa Lalla
- Department of Biology, University of New Brunswick, Fredericton. 10 Bailey Drive, Fredericton, New Brunswick E3B 5A3, Canada
| | - Rossella Calvaruso
- Department of Biology, University of New Brunswick, Fredericton. 10 Bailey Drive, Fredericton, New Brunswick E3B 5A3, Canada
| | - Sophia Dick
- Department of Biology, University of New Brunswick, Fredericton. 10 Bailey Drive, Fredericton, New Brunswick E3B 5A3, Canada
| | - Adrian Reyes-Prieto
- Department of Biology, University of New Brunswick, Fredericton. 10 Bailey Drive, Fredericton, New Brunswick E3B 5A3, Canada.
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40
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David GM, López-García P, Moreira D, Alric B, Deschamps P, Bertolino P, Restoux G, Rochelle-Newall E, Thébault E, Simon M, Jardillier L. Small freshwater ecosystems with dissimilar microbial communities exhibit similar temporal patterns. Mol Ecol 2021; 30:2162-2177. [PMID: 33639035 DOI: 10.1111/mec.15864] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/27/2022]
Abstract
Despite small freshwater ecosystems being biodiversity reservoirs and contributing significantly to greenhouse fluxes, their microbial communities remain largely understudied. Yet, microorganisms intervene in biogeochemical cycling and impact water quality. Because of their small size, these ecosystems are in principle more sensitive to disturbances, seasonal variation and pluri-annual climate change. However, how microbial community composition varies over space and time, and whether archaeal, bacterial and microbial eukaryote communities behave similarly remain unanswered. Here, we aim to unravel the composition and intra/interannual temporal dynamic patterns for archaea, bacteria and microbial eukaryotes in a set of small freshwater ecosystems. We monitored archaeal and bacterial community composition during 24 consecutive months in four ponds and one brook from northwestern France by 16S rRNA gene amplicon sequencing (microbial eukaryotes were previously investigated for the same systems). Unexpectedly for oxic environments, bacterial Candidate Phyla Radiation (CPR) were highly diverse and locally abundant. Our results suggest that microbial community structure is mainly driven by environmental conditions acting over space (ecosystems) and time (seasons). A low proportion of operational taxonomic units (OTUs) (<1%) was shared by the five ecosystems despite their geographical proximity (2-9 km away), making microbial communities almost unique in each ecosystem and highlighting the strong selective influence of local environmental conditions. Marked and similar seasonality patterns were observed for archaea, bacteria and microbial eukaryotes in all ecosystems despite strong turnovers of rare OTUs. Over the 2-year survey, microbial community composition varied despite relatively stable environmental parameters. This suggests that biotic associations play an important role in interannual community assembly.
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Affiliation(s)
- Gwendoline M David
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | | | - David Moreira
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Benjamin Alric
- Irstea, UR RiverLy, Laboratoire d'écotoxicologie, centre de Lyon-Villeurbanne, Villeurbanne, France
| | - Philippe Deschamps
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Paola Bertolino
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Gwendal Restoux
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Emma Rochelle-Newall
- Sorbonne Université, UPEC, CNRS, IRD, INRAE, Institute d'Ecologie de des Sciences de l'Environnement de Paris, iEES-Paris, Paris, France
| | - Elisa Thébault
- Sorbonne Université, UPEC, CNRS, IRD, INRAE, Institute d'Ecologie de des Sciences de l'Environnement de Paris, iEES-Paris, Paris, France
| | - Marianne Simon
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
| | - Ludwig Jardillier
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution, Orsay, France
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Sagova-Mareckova M, Boenigk J, Bouchez A, Cermakova K, Chonova T, Cordier T, Eisendle U, Elersek T, Fazi S, Fleituch T, Frühe L, Gajdosova M, Graupner N, Haegerbaeumer A, Kelly AM, Kopecky J, Leese F, Nõges P, Orlic S, Panksep K, Pawlowski J, Petrusek A, Piggott JJ, Rusch JC, Salis R, Schenk J, Simek K, Stovicek A, Strand DA, Vasquez MI, Vrålstad T, Zlatkovic S, Zupancic M, Stoeck T. Expanding ecological assessment by integrating microorganisms into routine freshwater biomonitoring. WATER RESEARCH 2021; 191:116767. [PMID: 33418487 DOI: 10.1016/j.watres.2020.116767] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 12/14/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
Bioindication has become an indispensable part of water quality monitoring in most countries of the world, with the presence and abundance of bioindicator taxa, mostly multicellular eukaryotes, used for biotic indices. In contrast, microbes (bacteria, archaea and protists) are seldom used as bioindicators in routine assessments, although they have been recognized for their importance in environmental processes. Recently, the use of molecular methods has revealed unexpected diversity within known functional groups and novel metabolic pathways that are particularly important in energy and nutrient cycling. In various habitats, microbial communities respond to eutrophication, metals, and natural or anthropogenic organic pollutants through changes in diversity and function. In this review, we evaluated the common trends in these changes, documenting that they have value as bioindicators and can be used not only for monitoring but also for improving our understanding of the major processes in lotic and lentic environments. Current knowledge provides a solid foundation for exploiting microbial taxa, community structures and diversity, as well as functional genes, in novel monitoring programs. These microbial community measures can also be combined into biotic indices, improving the resolution of individual bioindicators. Here, we assess particular molecular approaches complemented by advanced bioinformatic analysis, as these are the most promising with respect to detailed bioindication value. We conclude that microbial community dynamics are a missing link important for our understanding of rapid changes in the structure and function of aquatic ecosystems, and should be addressed in the future environmental monitoring of freshwater ecosystems.
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Affiliation(s)
- M Sagova-Mareckova
- Dept. of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, Prague 6, 16500, Czechia.
| | - J Boenigk
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany
| | - A Bouchez
- UMR CARRTEL, INRAE, UMR Carrtel, 75 av. de Corzent, FR-74203 Thonon les Bains cedex, France; University Savoie Mont-Blanc, UMR CARRTEL, FR-73370 Le Bourget du Lac, France
| | - K Cermakova
- ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, 15, av. Sécheron, 1202 Geneva, Switzerland
| | - T Chonova
- UMR CARRTEL, INRAE, UMR Carrtel, 75 av. de Corzent, FR-74203 Thonon les Bains cedex, France; University Savoie Mont-Blanc, UMR CARRTEL, FR-73370 Le Bourget du Lac, France
| | - T Cordier
- Department of Genetics and Evolution, University of Geneva, Science III, 4 Boulevard d'Yvoy, 1205 Geneva, Switzerland
| | - U Eisendle
- University of Salzburg, Hellbrunnerstraße 34, 5020 Salzburg, Austria
| | - T Elersek
- National Institute of Biology, Vecna pot 111, SI-1000 Ljubljana, Slovenia
| | - S Fazi
- Water Research Institute, National Research Council of Italy (IRSA-CNR), Via Salaria km 29,300 - C.P. 10, 00015 Monterotondo St., Rome, Italy
| | - T Fleituch
- Institute of Nature Conservation, Polish Academy of Sciences, ul. Adama Mickiewicza 33, 31-120 Krakow, Poland
| | - L Frühe
- Ecology Group, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - M Gajdosova
- Dept. of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czechia
| | - N Graupner
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany
| | - A Haegerbaeumer
- Dept. of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany
| | - A-M Kelly
- School of Natural Sciences, Trinity College Dublin, University of Dublin, College Green, Dublin 2, D02 PN40, Ireland
| | - J Kopecky
- Epidemiology and Ecology of Microoganisms, Crop Research Institute, Drnovská 507, 16106 Prague 6, Czechia
| | - F Leese
- Biodiversity, University of Duisburg-Essen, Universitaetsstraße 5, 45141 Essen, Germany; Aquatic Ecosystem Resarch, University of Duisburg-Essen, Universitaetsstrasse 5 D-45141 Essen, Germany
| | - P Nõges
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, Tartu 51006, Estonia
| | - S Orlic
- Institute Ruđer Bošković, Bijenička 54, 10000 Zagreb, Croatia; Center of Excellence for Science and Technology Integrating Mediterranean, Bijenička 54,10 000 Zagreb, Croatia
| | - K Panksep
- Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 5, Tartu 51006, Estonia
| | - J Pawlowski
- ID-Gene Ecodiagnostics, Campus Biotech Innovation Park, 15, av. Sécheron, 1202 Geneva, Switzerland; Department of Genetics and Evolution, University of Geneva, Science III, 4 Boulevard d'Yvoy, 1205 Geneva, Switzerland; Institute of Oceanology, Polish Academy of Sciences, Powstańców Warszawy 55, 81-712 Sopot, Poland
| | - A Petrusek
- Dept. of Ecology, Faculty of Science, Charles University, Viničná 7, 12844 Prague, Czechia
| | - J J Piggott
- School of Natural Sciences, Trinity College Dublin, University of Dublin, College Green, Dublin 2, D02 PN40, Ireland
| | - J C Rusch
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway; Department of Biosciences, University of Oslo, P.O. Box 1066, Blindern, NO-0316 Oslo, Norway
| | - R Salis
- Department of Biology, Faculty of Science, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
| | - J Schenk
- Dept. of Animal Ecology, Bielefeld University, Konsequenz 45, 33615 Bielefeld, Germany
| | - K Simek
- Institute of Hydrobiology, Biology Centre CAS, Branišovská 31, 370 05 České Budějovice, Czechia
| | - A Stovicek
- Dept. of Microbiology, Nutrition and Dietetics, Czech University of Life Sciences, Kamýcká 129, Prague 6, 16500, Czechia
| | - D A Strand
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway
| | - M I Vasquez
- Department of Chemical Engineering, Cyprus University of Technology, 30 Arch. Kyprianos Str., 3036 Limassol, Cyprus
| | - T Vrålstad
- Norwegian Veterinary Institute, P.O. Box 750, Sentrum, NO-0106 Oslo, Norway
| | - S Zlatkovic
- Ministry of Environmental Protection, Omladinskih brigada 1, 11070 Belgrade, Serbia; Agency "Akvatorija", 11. krajiške divizije 49, 11090 Belgrade, Serbia
| | - M Zupancic
- National Institute of Biology, Vecna pot 111, SI-1000 Ljubljana, Slovenia
| | - T Stoeck
- Ecology Group, Technische Universität Kaiserslautern, D-67663 Kaiserslautern, Germany
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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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Singer D, Seppey CVW, Lentendu G, Dunthorn M, Bass D, Belbahri L, Blandenier Q, Debroas D, de Groot GA, de Vargas C, Domaizon I, Duckert C, Izaguirre I, Koenig I, Mataloni G, Schiaffino MR, Mitchell EAD, Geisen S, Lara E. Protist taxonomic and functional diversity in soil, freshwater and marine ecosystems. ENVIRONMENT INTERNATIONAL 2021; 146:106262. [PMID: 33221595 DOI: 10.1016/j.envint.2020.106262] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 10/31/2020] [Accepted: 11/02/2020] [Indexed: 06/11/2023]
Abstract
Protists dominate eukaryotic diversity and play key functional roles in all ecosystems, particularly by catalyzing carbon and nutrient cycling. To date, however, a comparative analysis of their taxonomic and functional diversity that compares the major ecosystems on Earth (soil, freshwater and marine systems) is missing. Here, we present a comparison of protist diversity based on standardized high throughput 18S rRNA gene sequencing of soil, freshwater and marine environmental DNA. Soil and freshwater protist communities were more similar to each other than to marine protist communities, with virtually no overlap of Operational Taxonomic Units (OTUs) between terrestrial and marine habitats. Soil protists showed higher γ diversity than aquatic samples. Differences in taxonomic composition of the communities led to changes in a functional diversity among ecosystems, as expressed in relative abundance of consumers, phototrophs and parasites. Phototrophs (eukaryotic algae) dominated freshwater systems (49% of the sequences) and consumers soil and marine ecosystems (59% and 48%, respectively). The individual functional groups were composed of ecosystem- specific taxonomic groups. Parasites were equally common in all ecosystems, yet, terrestrial systems hosted more OTUs assigned to parasites of macro-organisms while aquatic systems contained mostly microbial parasitoids. Together, we show biogeographic patterns of protist diversity across major ecosystems on Earth, preparing the way for more focused studies that will help understanding the multiple roles of protists in the biosphere.
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Affiliation(s)
- David Singer
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland; Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, Brazil; UMR CNRS 6112 LPG-BIAF, Université d'Angers, Angers Cedex 1, France.
| | - Christophe V W Seppey
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland; Department of Arctic and Marine Biology, University of Tromsø, Framstredet 39, 9019 Tromsø, Norway.
| | - Guillaume Lentendu
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Micah Dunthorn
- Department of Eukaryotic Microbiology, University of Duisburg-Essen, D-45141 Essen, Germany; Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, D-45141 Essen, Germany
| | - David Bass
- Department of Life Sciences, The Natural History Museum, London, UK
| | - Lassâad Belbahri
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Quentin Blandenier
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland; Real Jardín Botánico de Madrid, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
| | - Didier Debroas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Genome et Environnement, F-63000 Clermont-Ferrand, France
| | - G Arjen de Groot
- Wageningen Environmental Research, Wageningen UR, P.O. Box 47, 6700 AA Wageningen, the Netherlands
| | - Colomban de Vargas
- Sorbonne Université, CNRS, Station Biologique de Roscoff, UMR 7144, ECOMAP, 29680 Roscoff, France; Research Federation for the study of Global Ocean Systems Ecology and Evolution, FR2022/GOSEE, 3 rue Michel-Ange, 75016 Paris, France
| | - Isabelle Domaizon
- Université Savoie Mont Blanc, INRAE, CARRTEL, 74200 Thonon-les-Bains, France
| | - Clément Duckert
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Irina Izaguirre
- Departamento de Ecología, Genética y Evolución, IEGEBA (UBA-CONICET), Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Isabelle Koenig
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland
| | - Gabriela Mataloni
- Instituto de Investigación e Ingeniería Ambiental (IIIA), CONICET, Universidad Nacional de San Martín, Provincia de Buenos Aires 1650, Argentina
| | - M Romina Schiaffino
- Universidad Nacional del Noroeste de la Provincia de Buenos Aires, Centro de Investigaciones y transferencia del Noroeste de la Provincia de Buenos Aires (CITNOBA) - UNNOBA-UNSAdA-CONICET, Junín 6000, Argentina
| | - Edward A D Mitchell
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland; Jardin Botanique de Neuchâtel, Chemin du Perthuis-du-Sault 58, CH-2000 Neuchâtel, Switzerland
| | - Stefan Geisen
- Laboratory of Nematology, Wageningen University and Research, Droevendaalsesteeg 1, 6708PB Wageningen, the Netherlands.
| | - Enrique Lara
- Laboratory of Soil Biodiversity, Institute of Biology, University of Neuchâtel, Rue Emile-Argand 11, CH-2000 Neuchâtel, Switzerland; Real Jardín Botánico de Madrid, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain.
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Qu Z, Forster D, Bruni EP, Frantal D, Kammerlander B, Nachbaur L, Pitsch G, Posch T, Pröschold T, Teubner K, Sonntag B, Stoeck T. Aquatic food webs in deep temperate lakes: Key species establish through their autecological versatility. Mol Ecol 2020; 30:1053-1071. [PMID: 33306859 DOI: 10.1111/mec.15776] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 11/27/2020] [Accepted: 12/04/2020] [Indexed: 11/29/2022]
Abstract
Microbial planktonic communities are the basis of food webs in aquatic ecosystems since they contribute substantially to primary production and nutrient recycling. Network analyses of DNA metabarcoding data sets emerged as a powerful tool to untangle the complex ecological relationships among the key players in food webs. In this study, we evaluated co-occurrence networks constructed from time-series metabarcoding data sets (12 months, biweekly sampling) of protistan plankton communities in surface layers (epilimnion) and bottom waters (hypolimnion) of two temperate deep lakes, Lake Mondsee (Austria) and Lake Zurich (Switzerland). Lake Zurich plankton communities were less tightly connected, more fragmented and had a higher susceptibility to a species extinction scenario compared to Lake Mondsee communities. We interpret these results as a lower robustness of Lake Zurich protistan plankton to environmental stressors, especially stressors resulting from climate change. In all networks, the phylum Ciliophora contributed the highest number of nodes, among them several in key positions of the networks. Associations in ciliate-specific subnetworks resembled autecological species-specific traits that indicate adaptions to specific environmental conditions. We demonstrate the strength of co-occurrence network analyses to deepen our understanding of plankton community dynamics in lakes and indicate biotic relationships, which resulted in new hypotheses that may guide future research in climate-stressed ecosystems.
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Affiliation(s)
- Zhishuai Qu
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Dominik Forster
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
| | - Estelle P Bruni
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland.,Laboratory of Soil Biodiversity, University of Neuchâtel, Neuchâtel, Switzerland
| | - Daniela Frantal
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Barbara Kammerlander
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Laura Nachbaur
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Gianna Pitsch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Thomas Posch
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Kilchberg, Switzerland
| | - Thomas Pröschold
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Katrin Teubner
- Department of Functional and Evolutionary Ecology, University of Vienna, Vienna, Austria
| | - Bettina Sonntag
- Research Department for Limnology, Mondsee, University of Innsbruck, Mondsee, Austria
| | - Thorsten Stoeck
- Ecology Group, Technische Universität Kaiserslautern, Kaiserslautern, Germany
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45
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Mu X, Zhang S, Han B, Hua Z, Fu D, Li P. Impacts of water flow on epiphytic microbes and nutrients removal in constructed wetlands dominated by Vallisneria natans with decreasing temperature. BIORESOURCE TECHNOLOGY 2020; 318:124058. [PMID: 32905946 DOI: 10.1016/j.biortech.2020.124058] [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: 07/11/2020] [Revised: 08/23/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
The mechanisms behind water flow on contaminant removal by a submerged macrophyte-biofilm complex in surface flow wetlands remain to be fully elucidated. In this study, water flow (2.02 ~ 2.12 or 4.06 ~ 4.5 L s-1; hydraulic retention time, 7d) significantly enhanced NH4+-N and COD but inhibited TN and TP removal compared to the static ones. No more than 30% of TN and TP were assimilated by V. natans-biofilm complex in wetland system. Water flow remarkably affected alpha-diversity of microbial community in epiphytic biofilm. As revealed by beta-diversity analysis, turnover played greater contribution to the total dissimilarity than nestedness. Network analyses revealed that the microbial interactions including predation, symbiosis and competition in epiphytic biofilms were much more intensive in the Sept.- Oct. than the Nov.-Dec group. Redundancy and Mantel correlation analyses revealed that temperature played a key role in determining microbial community structure, especially for bacteria.
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Affiliation(s)
- Xiaoying Mu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Songhe Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China.
| | - Bing Han
- Yellow River Institute of Hydraulic Research, Zhengzhou 450003, China
| | - Zulin Hua
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Dongwang Fu
- Nanjing Water Planning and Designing Institute. Corp. Ltd, China
| | - Ping Li
- Nanjing Water Planning and Designing Institute. Corp. Ltd, China
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46
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Biological invasions alter environmental microbiomes: A meta-analysis. PLoS One 2020; 15:e0240996. [PMID: 33091062 PMCID: PMC7580985 DOI: 10.1371/journal.pone.0240996] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 10/06/2020] [Indexed: 02/07/2023] Open
Abstract
Biological invasions impact both agricultural and natural systems. The damage can be quantified in terms of both economic loss and reduction of biodiversity. Although the literature is quite rich about the impact of invasive species on plant and animal communities, their impact on environmental microbiomes is underexplored. Here, we re-analyze publicly available data using a common framework to create a global synthesis of the effects of biological invasions on environmental microbial communities. Our findings suggest that non-native species are responsible for the loss of microbial diversity and shifts in the structure of microbial populations. Therefore, the impact of biological invasions on native ecosystems might be more pervasive than previously thought, influencing both macro- and micro-biomes. We also identified gaps in the literature which encourage research on a wider variety of environments and invaders, and the influence of invaders across seasons and geographical ranges.
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47
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Gilbert KJ, Bittleston LS, Naive MAK, Kiszewski AE, Buenavente PAC, Lohman DJ, Pierce NE. Investigation of an Elevational Gradient Reveals Strong Differences Between Bacterial and Eukaryotic Communities Coinhabiting Nepenthes Phytotelmata. MICROBIAL ECOLOGY 2020; 80:334-349. [PMID: 32291478 PMCID: PMC7371667 DOI: 10.1007/s00248-020-01503-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 02/25/2020] [Indexed: 05/24/2023]
Abstract
Elevation is an important determinant of ecological community composition. It integrates several abiotic features and leads to strong, repeatable patterns of community structure, including changes in the abundance and richness of numerous taxa. However, the influence of elevational gradients on microbes is understudied relative to plants and animals. To compare the influence of elevation on multiple taxa simultaneously, we sampled phytotelm communities within a tropical pitcher plant (Nepenthes mindanaoensis) along a gradient from 400 to 1200 m a.s.l. We use a combination of metabarcoding and physical counts to assess diversity and richness of bacteria, micro-eukaryotes, and arthropods, and compare the effect of elevation on community structure to that of regulation by a number of plant factors. Patterns of community structure differed between bacteria and eukaryotes, despite their living together in the same aquatic microhabitats. Elevation influences community composition of eukaryotes to a significantly greater degree than it does bacteria. When examining pitcher characteristics, pitcher dimorphism has an effect on eukaryotes but not bacteria, while variation in pH levels strongly influences both taxa. Consistent with previous ecological studies, arthropod abundance in phytotelmata decreases with elevation, but some patterns of abundance differ between living inquilines and prey.
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Affiliation(s)
- Kadeem J Gilbert
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA.
- Department of Entomology, The Pennsylvania State University, 501 Agricultural Sciences and Industries Building, University Park, PA, 16802, USA.
| | - Leonora S Bittleston
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Room 1-290, Cambridge, MA, 02139, USA
- Department of Biological Sciences, Boise State University, 1910 W University Dr, Boise, ID, 83725, USA
| | - Mark Arcebal K Naive
- Department of Biological Sciences, College of Science and Mathematics, Mindanao State University-Iligan Institute of Technology, Andres Bonifacio Ave, 9200, Iligan, Lanao del Norte, Philippines
| | - Anthony E Kiszewski
- Department of Natural and Applied Sciences, Bentley University, 175 Forest Street, Waltham, MA, 02452, USA
| | | | - David J Lohman
- Entomology Section, National Museum of Natural History, Manila, Philippines
- Biology Department, City College of New York, City University of New York, New York, NY, USA
- Ph.D. Program in Biology, Graduate Center, City University of New York, New York, NY, USA
| | - Naomi E Pierce
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St., Cambridge, MA, 02138, USA
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48
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Santoferrara L, Burki F, Filker S, Logares R, Dunthorn M, McManus GB. Perspectives from Ten Years of Protist Studies by High-Throughput Metabarcoding. J Eukaryot Microbiol 2020; 67:612-622. [PMID: 32498124 DOI: 10.1111/jeu.12813] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 05/29/2020] [Accepted: 05/29/2020] [Indexed: 01/07/2023]
Abstract
During the last decade, high-throughput metabarcoding became routine for analyzing protistan diversity and distributions in nature. Amid a multitude of exciting findings, scientists have also identified and addressed technical and biological limitations, although problems still exist for inference of meaningful taxonomic and ecological knowledge based on short DNA sequences. Given the extensive use of this approach, it is critical to settle our understanding on its strengths and weaknesses and to synthesize up-to-date methodological and conceptual trends. This article summarizes key scientific and technical findings, and identifies current and future directions in protist research that uses metabarcoding.
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Affiliation(s)
- Luciana Santoferrara
- Department of Ecology and Evolutionary Biology, University of Connecticut, Storrs, CT, USA.,Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Fabien Burki
- Department of Organismal Biology, Program in Systematic Biology, and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Sabine Filker
- Department of Molecular Ecology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Ramiro Logares
- Institute of Marine Sciences (ICM), CSIC, Barcelona, Spain
| | - Micah Dunthorn
- Department of Eukaryotic Microbiology, University of Duisburg-Essen, Essen, Germany
| | - George B McManus
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
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49
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Juottonen H, Fontaine L, Wurzbacher C, Drakare S, Peura S, Eiler A. Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly. Environ Microbiol 2020; 22:3158-3171. [PMID: 32372550 DOI: 10.1111/1462-2920.15058] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 04/22/2020] [Accepted: 05/02/2020] [Indexed: 01/04/2023]
Abstract
Despite their key role in biogeochemical processes, particularly the methane cycle, archaea are widely underrepresented in molecular surveys because of their lower abundance compared with bacteria and eukaryotes. Here, we use parallel high-resolution small subunit rRNA gene sequencing to explore archaeal diversity in 109 Swedish lakes and correlate archaeal community assembly mechanisms to large-scale latitudinal, climatic (nemoral to arctic) and nutrient (oligotrophic to eutrophic) gradients. Sequencing with universal primers showed the contribution of archaea was on average 0.8% but increased up to 1.5% of the three domains in forest lakes. Archaea-specific sequencing revealed that freshwater archaeal diversity could be partly explained by lake variables associated with nutrient status. Combined with deterministic co-occurrence patterns this finding suggests that ecological drift is overridden by environmental sorting, as well as other deterministic processes such as biogeographic and evolutionary history, leading to lake-specific archaeal biodiversity. Acetoclastic, hydrogenotrophic and methylotrophic methanogens as well as ammonia-oxidizing archaea were frequently detected across the lakes. Archaea-specific sequencing also revealed representatives of Woesearchaeota and other phyla of the DPANN superphylum. This study adds to our understanding of the ecological range of key archaea in freshwaters and links these taxa to hypotheses about processes governing biogeochemical cycles in lakes.
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Affiliation(s)
- Heli Juottonen
- Limnology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, 75234, Sweden.,Department of Biological and Environmental Science, University of Jyväskylä, P.O. Box 35, Jyväskylä, 40014, Finland
| | - Laurent Fontaine
- Section for Aquatic Biology and Toxicology, Centre for Biogeochemistry in the Anthropocene, Department of Biosciences, University of Oslo, Blindernv. 31, Oslo, 0371, Norway
| | - Christian Wurzbacher
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 463, Göteborg, 405 30, Sweden.,Chair of Urban Water Systems Engineering, Technical University of Munich, Am Coulombwall 3, Garching, 85748, Germany
| | - Stina Drakare
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, SLU, Box 7050, Uppsala, 750 07, Sweden
| | - Sari Peura
- Limnology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, 75234, Sweden.,Department of Forest Mycology and Plant Pathology, Science for Life Laboratory, Swedish University of Agricultural Sciences, Almas allé 5, Uppsala, 75007, Sweden
| | - Alexander Eiler
- Limnology, Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, Uppsala, 75234, Sweden.,Section for Aquatic Biology and Toxicology, Centre for Biogeochemistry in the Anthropocene, Department of Biosciences, University of Oslo, Blindernv. 31, Oslo, 0371, Norway.,eDNA solutions AB, Björkåsgatan 16, Mölndal, 43131, Sweden
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50
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Liu Y, Gong L, Mu X, Zhang Z, Zhou T, Zhang S. Characterization and co-occurrence of microbial community in epiphytic biofilms and surface sediments of wetlands with submersed macrophytes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 715:136950. [PMID: 32007899 DOI: 10.1016/j.scitotenv.2020.136950] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 06/10/2023]
Abstract
Microbes in epiphytic biofilms and surface sediments play crucial roles in the biogeochemical cycles in wetlands. However, little is known about the compositions of microbial community in wetlands dominated with submersed macrophytes. In this study, bacterial and eukaryotic community in epiphytic biofilms and surface sediments were investigated in wetlands with artificial plants and Myriophyllum verticillatum from September (~27 °C) to January (~9 °C). A total of 30 (including 13 bacterial and 17 eukaryotic) and 34 (including 14 bacterial and 20 eukaryotic) phyla were detected in epiphytic biofilms and sediments, respectively. Microbial community in epiphytic biofilms shifted with decreasing temperature, and biofilms on M. verticillatum were generally similar to those on artificial plants. Though the OTUs and Shannon values were significantly higher in sediments than epiphytic biofilms (p < 0.05), numbers of strongly correlated edges detected in biofilms (64 nodes with 182 edges) were at least three times of those in sediments (40 nodes with 57 edges) as revealed by co-occurrence networks analysis (|r| > 0.7, p < 0.05). These data suggest that there were complex interactions among microbes in epiphytic biofilms than sediments. Positive relationships among microbes revealed the predation, symbiosis, parasitism relationships and the collective degradation of organic matter, while negative ones may be ascribed to their different lifestyles. These results highlight that artificial plants play a similar role as submersed macrophytes as microbial carriers and can be potentially used an alternative substitutes to submersed macrophytes in wetlands.
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Affiliation(s)
- Yuansi Liu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Lixue Gong
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Xiaoying Mu
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Ziqiu Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Tiantian Zhou
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China
| | - Songhe Zhang
- Ministry of Education Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, College of Environment, Hohai University, Nanjing 210098, China.
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