High-resolution metagenomic reconstruction of the freshwater spring bloom.

Autor: Kavagutti VS; Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic. viniciuskavagutti@gmail.com.; Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic. viniciuskavagutti@gmail.com., Bulzu PA; Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic., Chiriac CM; Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic., Salcher MM; Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic., Mukherjee I; Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic., Shabarova T; Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic., Grujčić V; Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.; Present address: Department of Ecology, Environment and Plant Sciences, Stockholm University, Stockholm, Sweden., Mehrshad M; Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.; Present address: Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden., Kasalický V; Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic., Andrei AS; Limnological Station, Microbial Evogenomics Lab (MiEL), University of Zurich, Kilchberg, Switzerland., Jezberová J; Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic., Seďa J; Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic., Rychtecký P; Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic., Znachor P; Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic.; Faculty of Science, University of South Bohemia, Branišovská 31, 370 05, České Budějovice, Czech Republic., Šimek K; Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic., Ghai R; Institute of Hydrobiology, Biology Centre CAS, Na Sádkách 7, 370 05, České Budějovice, Czech Republic. ghai.rohit@gmail.com.
Jazyk: angličtina
Zdroj: Microbiome [Microbiome] 2023 Jan 26; Vol. 11 (1), pp. 15. Date of Electronic Publication: 2023 Jan 26.
DOI: 10.1186/s40168-022-01451-4
Abstrakt: Background: The phytoplankton spring bloom in freshwater habitats is a complex, recurring, and dynamic ecological spectacle that unfolds at multiple biological scales. Although enormous taxonomic shifts in microbial assemblages during and after the bloom have been reported, genomic information on the microbial community of the spring bloom remains scarce.
Results: We performed a high-resolution spatio-temporal sampling of the spring bloom in a freshwater reservoir and describe a multitude of previously unknown taxa using metagenome-assembled genomes of eukaryotes, prokaryotes, and viruses in combination with a broad array of methodologies. The recovered genomes reveal multiple distributional dynamics for several bacterial groups with progressively increasing stratification. Analyses of abundances of metagenome-assembled genomes in concert with CARD-FISH revealed remarkably similar in situ doubling time estimates for dominant genome-streamlined microbial lineages. Discordance between quantitations of cryptophytes arising from sequence data and microscopic identification suggested the presence of hidden, yet extremely abundant aplastidic cryptophytes that were confirmed by CARD-FISH analyses. Aplastidic cryptophytes are prevalent throughout the water column but have never been considered in prior models of plankton dynamics. We also recovered the first metagenomic-assembled genomes of freshwater protists (a diatom and a haptophyte) along with thousands of giant viral genomic contigs, some of which appeared similar to viruses infecting haptophytes but owing to lack of known representatives, most remained without any indication of their hosts. The contrasting distribution of giant viruses that are present in the entire water column to that of parasitic perkinsids residing largely in deeper waters allows us to propose giant viruses as the biological agents of top-down control and bloom collapse, likely in combination with bottom-up factors like a nutrient limitation.
Conclusion: We reconstructed thousands of genomes of microbes and viruses from a freshwater spring bloom and show that such large-scale genome recovery allows tracking of planktonic succession in great detail. However, integration of metagenomic information with other methodologies (e.g., microscopy, CARD-FISH) remains critical to reveal diverse phenomena (e.g., distributional patterns, in situ doubling times) and novel participants (e.g., aplastidic cryptophytes) and to further refine existing ecological models (e.g., factors affecting bloom collapse). This work provides a genomic foundation for future approaches towards a fine-scale characterization of the organisms in relation to the rapidly changing environment during the course of the freshwater spring bloom. Video Abstract.
(© 2023. The Author(s).)
Databáze: MEDLINE
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