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Bruhn CS, Lundholm N, Hansen PJ, Wohlrab S, John U. Transition from a mixotrophic/heterotrophic protist community during the dark winter to a photoautotrophic spring community in surface waters of Disko Bay, Greenland. Front Microbiol 2024; 15:1407888. [PMID: 38887716 PMCID: PMC11180815 DOI: 10.3389/fmicb.2024.1407888] [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: 04/08/2024] [Accepted: 05/17/2024] [Indexed: 06/20/2024] Open
Abstract
Unicellular eukaryotic plankton communities (protists) are the major basis of the marine food web. The spring bloom is especially important, because of its high biomass. However, it is poorly described how the protist community composition in Arctic surface waters develops from winter to spring. We show that mixotrophic and parasitic organisms are prominent in the dark winter period. The transition period toward the spring bloom event was characterized by a high relative abundance of mixotrophic dinoflagellates, while centric diatoms and the haptophyte Phaeocystis pouchetii dominated the successive phototrophic spring bloom event during the study. The data shows a continuous community shift from winter to spring, and not just a dormant spring community waiting for the right environmental conditions. The spring bloom initiation commenced while sea ice was still scattering and absorbing the sunlight, inhibiting its penetration into the water column. The initial increase in fluorescence was detected relatively deep in the water column at ~55 m depth at the halocline, at which the photosynthetic cells accumulated, while a thick layer of snow and sea ice was still obstructing sunlight penetration of the surface water. This suggests that water column stratification and a complex interplay of abiotic factors eventually promote the spring bloom initiation.
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Affiliation(s)
- Claudia Sabine Bruhn
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz-Centre Potsdam, German Research Centre for Geosciences GFZ, Potsdam, Germany
| | - Nina Lundholm
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Per Juel Hansen
- Department of Biology, Marine Biological Station, University of Copenhagen, Helsingør, Denmark
| | - Sylke Wohlrab
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany
| | - Uwe John
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Oldenburg, Germany
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Ahme A, Happe A, Striebel M, Cabrerizo MJ, Olsson M, Giesler J, Schulte-Hillen R, Sentimenti A, Kühne N, John U. Warming increases the compositional and functional variability of a temperate protist community. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 926:171971. [PMID: 38547992 DOI: 10.1016/j.scitotenv.2024.171971] [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: 02/02/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/06/2024]
Abstract
Phototrophic protists are a fundamental component of the world's oceans by serving as the primary source of energy, oxygen, and organic nutrients for the entire ecosystem. Due to the high thermal seasonality of their habitat, temperate protists could harbour many well-adapted species that tolerate ocean warming. However, these species may not sustain ecosystem functions equally well. To address these uncertainties, we conducted a 30-day mesocosm experiment to investigate how moderate (12 °C) and substantial (18 °C) warming compared to ambient conditions (6 °C) affect the composition (18S rRNA metabarcoding) and ecosystem functions (biomass, gross oxygen productivity, nutritional quality - C:N and C:P ratio) of a North Sea spring bloom community. Our results revealed warming-driven shifts in dominant protist groups, with haptophytes thriving at 12 °C and diatoms at 18 °C. Species responses primarily depended on the species' thermal traits, with indirect temperature effects on grazing being less relevant and phosphorus acting as a critical modulator. The species Phaeocystis globosa showed highest biomass on low phosphate concentrations and relatively increased in some replicates of both warming treatments. In line with this, the C:P ratio varied more with the presence of P. globosa than with temperature. Examining further ecosystem responses under warming, our study revealed lowered gross oxygen productivity but increased biomass accumulation whereas the C:N ratio remained unaltered. Although North Sea species exhibited resilience to elevated temperatures, a diminished functional similarity and heightened compositional variability indicate potential ecosystem repercussions for higher trophic levels. In conclusion, our research stresses the multifaceted nature of temperature effects on protist communities, emphasising the need for a holistic understanding that encompasses trait-based responses, indirect effects, and functional dynamics in the face of exacerbating temperature changes.
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Affiliation(s)
- Antonia Ahme
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany.
| | - Anika Happe
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Schleusenstraße 1, 26382 Wilhelmshaven, Germany
| | - Maren Striebel
- Institute for Chemistry and Biology of the Marine Environment (ICBM), University of Oldenburg, Schleusenstraße 1, 26382 Wilhelmshaven, Germany
| | - Marco J Cabrerizo
- Department of Ecology, University of Granada, Campus Fuentenueva s/n 1, 18071 Granada, Spain; Department of Ecology and Animal Biology, University of Vigo, Campus Lagoas Marcosende s/n, 36310 Vigo, Spain
| | - Markus Olsson
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, 106 91 Stockholm, Sweden
| | - Jakob Giesler
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Ruben Schulte-Hillen
- Albert-Ludwigs-Universität Freiburg, Fahnenbergplatz, 79104 Freiburg i.Br., Germany
| | - Alexander Sentimenti
- Albert-Ludwigs-Universität Freiburg, Fahnenbergplatz, 79104 Freiburg i.Br., Germany
| | - Nancy Kühne
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany
| | - Uwe John
- Alfred-Wegener-Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, 27570 Bremerhaven, Germany; Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg, Ammerländer Heersstraße 231, 26129 Oldenburg, Germany
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Müller A, Stark M, Schottenhammel S, John U, Chacón J, Klingl A, Holzer VJC, Schöffer M, Gottschling M. The second most abundant dinophyte in the ponds of a botanical garden is a species new to science. J Eukaryot Microbiol 2024; 71:e13015. [PMID: 38078515 DOI: 10.1111/jeu.13015] [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: 08/17/2023] [Revised: 10/20/2023] [Accepted: 11/14/2023] [Indexed: 03/10/2024]
Abstract
In the microscopy realm, a large body of dark biodiversity still awaits to be uncovered. Unarmoured dinophytes are particularly neglected here, as they only present inconspicuous traits. In a remote German locality, we collected cells, from which a monoclonal strain was established, to study morphology using light and electron microscopy and to gain DNA sequences from the rRNA operon. In parallel, we detected unicellular eukaryotes in ponds of the Botanical Garden Munich-Nymphenburg by DNA-metabarcoding (V4 region of the 18S rRNA gene), weekly sampled over the course of a year. Strain GeoK*077 turned out to be a new species of Borghiella with a distinct position in molecular phylogenetics and characteristic coccoid cells of ovoid shape as the most important diagnostic trait. Borghiella ovum, sp. nov., was also present in artificial ponds of the Botanical Garden and was the second most abundant dinophyte detected in the samples. More specifically, Borghiella ovum, sp. nov., shows a clear seasonality, with high frequency during winter months and complete absence during summer months. The study underlines the necessity to assess the biodiversity, particularly of the microscopy realm more ambitiously, if even common species such as formerly Borghiella ovum are yet unknown to science.
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Affiliation(s)
- Anna Müller
- Faculty of Biology-Systematics, Biodiversity and Evolution of Plants, GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marina Stark
- Faculty of Biology-Systematics, Biodiversity and Evolution of Plants, GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Sophia Schottenhammel
- Faculty of Biology-Systematics, Biodiversity and Evolution of Plants, GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Uwe John
- Helmholtz Centre for Polar and Marine Research, Alfred Wegener Institute, Bremerhaven, Germany
- Helmholtz Institute for Functional Marine Biodiversity at the University of Oldenburg (HIFMB), Oldenburg, Germany
| | - Juliana Chacón
- Faculty of Biology-Systematics, Biodiversity and Evolution of Plants, GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andreas Klingl
- Faculty of Biology-Plant Development and Electron Microscopy, Ludwig-Maximilians-Universität München, Planegg-Martinsried, Germany
| | - Victoria Julia Christine Holzer
- Faculty of Biology-Systematics, Biodiversity and Evolution of Plants, GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marika Schöffer
- Faculty of Biology-Systematics, Biodiversity and Evolution of Plants, GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Marc Gottschling
- Faculty of Biology-Systematics, Biodiversity and Evolution of Plants, GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
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Martin JL, Santi I, Pitta P, John U, Gypens N. Towards quantitative metabarcoding of eukaryotic plankton: an approach to improve 18S rRNA gene copy number bias. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.85794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Plankton metabarcoding is increasingly implemented in marine ecosystem assessments and is more cost-efficient and less time-consuming than monitoring based on microscopy (morphological). 18S rRNA gene is the most widely used marker for groups’ and species’ detection and classification within marine eukaryotic microorganisms. These datasets have commonly relied on the acquisition of organismal abundances directly from the number of DNA sequences (i.e. reads). Besides the inherent technical biases in metabarcoding, the largely varying 18S rRNA gene copy numbers (GCN) among marine protists (ranging from tens to thousands) is one of the most important biological biases for species quantification. In this work, we present a gene copy number correction factor (CF) for four marine planktonic groups: Bacillariophyta, Dinoflagellata, Ciliophora miscellaneous and flagellated cells. On the basis of the theoretical assumption that ‘1 read’ is equivalent to ‘1 GCN’, we used the GCN median values per plankton group to calculate the corrected cell number and biomass relative abundances. The species-specific absolute GCN per cell were obtained from various studies published in the literature. We contributed to the development of a species-specific 18S rRNA GCN database proposed by previous authors. To assess the efficiency of the correction factor we compared the metabarcoding, morphological and corrected relative abundances (in cell number and biomass) of 15 surface water samples collected in the Belgian Coastal Zone. Results showed that the application of the correction factor over metabarcoding results enables us to significantly improve the estimates of cell abundances for Dinoflagellata, Ciliophora and flagellated cells, but not for Bacillariophyta. This is likely to due to large biovolume plasticity in diatoms not corresponding to genome size and gene copy numbers. C-biomass relative abundance estimations directly from amplicon reads were only improved for Dinoflagellata and Ciliophora. The method is still facing biases related to the low number of species GCN assessed. Nevertheless, the increase of species in the GCN database may lead to the refinement of the proposed correction factor.
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Latz MAC, Grujcic V, Brugel S, Lycken J, John U, Karlson B, Andersson A, Andersson AF. Short- and long-read metabarcoding of the eukaryotic rRNA operon: evaluation of primers and comparison to shotgun metagenomics sequencing. Mol Ecol Resour 2022; 22:2304-2318. [PMID: 35437888 DOI: 10.1111/1755-0998.13623] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 03/17/2022] [Accepted: 04/11/2022] [Indexed: 11/30/2022]
Abstract
High-throughput sequencing for analysis of microbial diversity has evolved vastly over the last decade. Currently the go-to method for studying microbial eukaryotes is short-read metabarcoding of variable regions of the 18S rRNA gene with <500 bp amplicons. However, there is a growing interest in applying long-read sequencing of amplicons covering the rRNA operon for improving taxonomic resolution. For both methods, the choice of primers is crucial. It determines if community members are covered, if they can be identified at a satisfactory taxonomic level, and if the obtained community profile is representative. Here, we designed new primers targeting 18S and 28S rRNA based on 177,934 and 21,072 database sequences, respectively. The primers were evaluated in silico along with published primers on reference sequence databases and marine metagenomics datasets. We further evaluated a subset of the primers for short- and long-read sequencing on environmental samples in vitro and compared the obtained community profile with primer-unbiased metagenomic sequencing. Of the short-read pairs, a new V6-V8 pair and the V4_Balzano pair used with a simplified PCR protocol provided good results in silico and in vitro. Fewer differences were observed between the long-read primer pairs. The long-read amplicons and ITS1 alone provided higher taxonomic resolution than V4. Together, our results represent a reference and guide for selection of robust primers for research on and environmental monitoring of microbial eukaryotes.
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Affiliation(s)
- Meike A C Latz
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden.,University of Copenhagen, Department of Plant and Environmental Sciences, Frederiksberg C, Denmark
| | - Vesna Grujcic
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden
| | - Sonia Brugel
- Umeå University, Department of Ecology and Environmental Sciences, Umeå, Sweden
| | - Jenny Lycken
- Swedish Meteorological and Hydrological Institute, Oceanographic Research, Gothenburg, Sweden
| | - Uwe John
- Alfred Wegener Institute Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Bengt Karlson
- Swedish Meteorological and Hydrological Institute, Oceanographic Research, Gothenburg, Sweden
| | - Agneta Andersson
- Umeå University, Department of Ecology and Environmental Sciences, Umeå, Sweden
| | - Anders F Andersson
- KTH Royal Institute of Technology, Department of Gene Technology, Science for Life Laboratory, Stockholm, Sweden
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