Picocyanobacteria Community and Cyanophage Infection Responses to Nutrient Enrichment in a Mesocosms Experiment in Oligotrophic Waters

Abstract

Prochlorococcus and Synechococcus are pico-sized cyanobacteria that play a fundamental role in oceanic primary production, being particularly important in warm, nutrient-poor waters. Their potential response to nutrient enrichment is expected to be contrasting and to differ from larger phytoplankton species. Here, we used a metagenomic approach to characterize the responses to nutrient enrichment in the community of picocyanobacteria and to analyze the cyanophage response during a mesocosms experiment in the oligotrophic Red Sea. Natural picoplankton community was dominated by Synechococcus clade II, with marginal presence of Prochlorococcus (0.3% bacterial reads). Increased nutrient input triggered a fast Synechococcus bloom, with clade II being the dominant, with no response of Prochlorococcus growth. The largest bloom developed in the mesocosms receiving a single initial input of nutrients, instead of daily additions. The relative abundances of cyanophage sequences in cellular metagenomes increased during the experiment from 12.6% of total virus reads up to 40% in the treatment with the largest Synechococcus bloom. The subsequent collapse of the bloom pointed to a cyanophage infection on Synechococcus that reduced its competitive capacity, and was then followed by a diatom bloom. The cyanophage attack appears to have preferentially affected the most abundant Synechococcus clade II, increasing the evenness within the host population. Our results highlight the relevance of host-phage interactions on determining population dynamics and diversity of Synechococcus populations.

Keywords: Synechococcus; bloom; clade; cyanophages; metagenomics.

FIGURE 1

Synechococcus cell abundances (in 10⁶ cells mL^–1, ± range) determined along the duration of the experiment for control and nutrient addition treatments (NP-I, initial nitrate and phosphate addition; NPSi-I, initial nitrate, phosphate and silicate addition; NP-C, continuous initial nitrate and phosphate addition; NPSi-C, continuous nitrate, phosphate and silicate addition).

FIGURE 2

Relationship between the cell abundance measured using flow cytometry and the number of rpsC reads for Synechococcus, determined during our experiment and broken down for each treatment and day.

FIGURE 3

Changes over time in the different clades of Synechococcus found for control and nutrient addition treatments, according to the relative count of gene reads (%). Each color corresponds to a different clade; unidentified reads are represented as “unidentified” and colored gray (see legend).

FIGURE 4

(A) Changes in Synechococcus clade richness with time (in days). Dashed line indicates the average richness at the beginning of the experiment. (B) Changes in Shannon’s equitability for Synechococcus with time (in days). Dashed line indicates the value for this index at the beginning of the experiment. (C) Relationship between Shannon’s equitability and the number of reads (in Log₁₀) for Synechococcus.

FIGURE 5

Changes in the relative proportions of reads assigned to Synechococcus phages and other viruses on days 1 and 6 under each treatment. Viral reads assigned to cyanophages, but with primary host unidentified to genus level are represented as “Other cyanophages.” The black line represents the number of reads of all virus present.

FIGURE 6

Comparison between the timing of Synechococcus cell abundances (cells mL^–1) and number of Synechococcus phage reads along the experiment, estimated as mean values for the duplicate mesocosms (± standard errors), for the control and continuous treatments (A), and for the initial treatments (B).

FIGURE 7

Heatmap showing the number of reads (average values from duplicate mesocosm bags) for the most abundant Synechococcus phages for all treatments, from days 1 to 20.