High-resolution metagenomic reconstruction of the freshwater spring bloom

Abstract

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.

Depth-dependent dynamics of protist communities as an integral part of spring succession in a freshwater reservoir

“…We performed a network analysis to examine the connections between and within the eukaryotic and bacterial communities (Figure 6 were excessively linked to members of Bacteroidota, namely Flavobacteriales, Chitinophagales and Sphingobacteriales, which contributed the highest proportion of nodes in this cluster. These bacterial groups and Sphingomonas (present in module one) were reported as efficient decomposers of phytoplankton derived polymers during spring blooms [28,33,34]. In modules two and three, which represent the later phase of the study, the potential consumers of small molecular substances such as Polynucleobacter sp., Actinobacteriota and copiotrophic Comamonadaceae were present.…”

“…In modules two and three, which represent the later phase of the study, the potential consumers of small molecular substances such as Polynucleobacter sp., Actinobacteriota and copiotrophic Comamonadaceae were present. These bacteria are well known members of spring bloom and disturbance succession [27][28][29]35]. Ciliates present in the epilimnetic network cluster are known for their substratum-attached lifestyle, e.g., fine-filter feeding Vorticella sp.…”

“…Algal blooms are the major factors shaping the spring microbial community not only in the epilimnion [89,90] but also in the deeper strata, due to the enhanced particle flux from the surface waters [80,91]. The bloom of chrysophytes, diatoms and large cryptophytes in the reservoir at the beginning of the sampling campaign was likely decimated by zooplankton or viral lysis [28]. However, ciliates dominated by raptorial prostomes such as Urotricha spp.…”

Assessing the biogeography of marine giant viruses in four oceanic transects

“…Giant viruses have been reported to infect many prevalent marine eukaryotic lineages, including chlorophytes, haptophytes, and choanoflagellates [15,18,33,34], and they are therefore an important factor shaping marine ecological dynamics. Moreover, several studies have shown that giant viruses associated with algal blooms play key roles in carbon export to deeper waters [35][36][37], indicating they are critical components of global carbon cycles. Despite the ecological importance of giant viruses, our understanding of their diversity lags behind that of smaller viruses owing to the widespread use of filtration steps in viral diversity surveys, which often exclude larger viruses [38].…”

Assessing the biogeography of marine giant viruses in four oceanic transects

“…Giant viruses have been reported to infect many prevalent marine eukaryotic lineages, including chlorophytes, haptophytes, and choanoflagellates [ 15 , 18 , 33 , 34 ], and they are therefore an important factor shaping marine ecological dynamics. Moreover, several studies have shown that giant viruses associated with algal blooms play key roles in carbon export to deeper waters [ 35 – 37 ], indicating they are critical components of global carbon cycles. Despite the ecological importance of giant viruses, our understanding of their diversity lags behind that of smaller viruses owing to the widespread use of filtration steps in viral diversity surveys, which often exclude larger viruses [ 38 ].…”