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A freshwater radiation of diplonemids

View ORCID ProfileIndranil Mukherjee, View ORCID ProfileMichaela M Salcher, View ORCID ProfileAdrian-Ştefan Andrei, View ORCID ProfileVinicius Silva Kavagutti, View ORCID ProfileTanja Shabarova, View ORCID ProfileVesna Grujčić, View ORCID ProfileMarkus Haber, View ORCID ProfilePaul Layoun, Yoshikuni Hodoki, Shin-ichi Nakano, View ORCID ProfileKarel Šimek, View ORCID ProfileRohit Ghai
doi: https://doi.org/10.1101/2020.05.14.095992
Indranil Mukherjee
1Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, , Na Sadkach 7, 37005, České Budějovice, Czech Republic
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  • For correspondence: indranilmukherjee04@yahoo.com ghai.rohit@gmail.com
Michaela M Salcher
1Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, , Na Sadkach 7, 37005, České Budějovice, Czech Republic
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Adrian-Ştefan Andrei
1Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, , Na Sadkach 7, 37005, České Budějovice, Czech Republic
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Vinicius Silva Kavagutti
1Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, , Na Sadkach 7, 37005, České Budějovice, Czech Republic
2Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, České Budějovice, Czech Republic
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Tanja Shabarova
1Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, , Na Sadkach 7, 37005, České Budějovice, Czech Republic
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Vesna Grujčić
3KTH Royal Institute of Technology, Science for Life Laboratory, Department of Gene Technology, School of Engineering Sciences in Chemistry, Biotechnology and Health, Stockholm, Sweden
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Markus Haber
1Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, , Na Sadkach 7, 37005, České Budějovice, Czech Republic
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Paul Layoun
1Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, , Na Sadkach 7, 37005, České Budějovice, Czech Republic
2Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, České Budějovice, Czech Republic
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Yoshikuni Hodoki
4Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
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Shin-ichi Nakano
4Center for Ecological Research, Kyoto University, Otsu, Shiga, Japan
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Karel Šimek
1Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, , Na Sadkach 7, 37005, České Budějovice, Czech Republic
2Department of Ecosystem Biology, Faculty of Science, University of South Bohemia, Branišovská 1760, 37005, České Budějovice, Czech Republic
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Rohit Ghai
1Department of Aquatic Microbial Ecology, Institute of Hydrobiology, Biology Centre of the Czech Academy of Sciences, , Na Sadkach 7, 37005, České Budějovice, Czech Republic
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  • For correspondence: indranilmukherjee04@yahoo.com ghai.rohit@gmail.com
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Abstract

Diplonemids are considered marine protists and have been reported among the most abundant and diverse eukaryotes in the world oceans. Recently we detected the presence of freshwater diplonemids in Lake Biwa, Japan. However, their distribution and abundances in freshwater ecosystems remain unknown. We assessed abundance and diversity of diplonemids from several geographically distant deep freshwater lakes of the world by amplicon-sequencing, shotgun metagenomics and CARD-FISH. We found diplonemids in all the studied lakes, albeit with low abundances and diversity. We assembled long 18S rRNA sequences from freshwater diplonemids and showed that they form a new lineage distinct from the diverse marine clades. Freshwater diplonemids are a sister-group to marine isolates from coastal and bay areas, suggesting a recent habitat transition from marine to freshwater habitats. Images of CARD-FISH targeted freshwater diplonemids suggest they feed on bacteria. Our analyses of 18S rRNA sequences retrieved from single cell genomes of marine diplonemids shows they encode multiple rRNA copies that may be very divergent from each other, suggesting that marine diplonemid abundance and diversity both have been overestimated. These results have wider implications on assessing eukaryotic abundances in natural habitats by using amplicon-sequencing alone.

Competing Interest Statement

The authors have declared no competing interest.

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Posted May 15, 2020.
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A freshwater radiation of diplonemids
Indranil Mukherjee, Michaela M Salcher, Adrian-Ştefan Andrei, Vinicius Silva Kavagutti, Tanja Shabarova, Vesna Grujčić, Markus Haber, Paul Layoun, Yoshikuni Hodoki, Shin-ichi Nakano, Karel Šimek, Rohit Ghai
bioRxiv 2020.05.14.095992; doi: https://doi.org/10.1101/2020.05.14.095992
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A freshwater radiation of diplonemids
Indranil Mukherjee, Michaela M Salcher, Adrian-Ştefan Andrei, Vinicius Silva Kavagutti, Tanja Shabarova, Vesna Grujčić, Markus Haber, Paul Layoun, Yoshikuni Hodoki, Shin-ichi Nakano, Karel Šimek, Rohit Ghai
bioRxiv 2020.05.14.095992; doi: https://doi.org/10.1101/2020.05.14.095992

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