Daily transcriptome changes reveal the role of nitrogen in controlling microcystin synthesis and nutrient transport in the toxic cyanobacterium, Microcystis aeruginosa

Abstract

Background: While transcriptomics have become a valuable tool for linking physiology and ecology in aquatic microbes, the temporal dynamics of global transcriptomic patterns in Microcystis have rarely been assessed. Furthermore, while many microbial studies have explored expression of nutrient transporter genes, few studies have concurrently measured nutrient assimilation rates. Here, we considered how the global transcriptomic patterns and physiology of the cyanobacterium, Microcystis aeruginosa, changed daily as cells were grown from replete to deficient nitrogen (N) conditions and then back to replete conditions.

Results: During N deprivation, Microcystis downregulated genes involved in photosynthesis and respiration, carbon acquisition, lipid metabolism, and amino acid biosynthesis while upregulating genes involved in N acquisition and transport. With increasing N stress, both the strength of expression and number of genes being differentially expressed increased, until N was restored at which point these patterns reversed. Uptake of (15)N-labeled nitrate, ammonium and urea reflected differential expression of genes encoding transporters for these nutrients, with Microcystis appearing to preferentially increase transcription of ammonium and urea transporters and uptake of these compounds during N deprivation. Nitrate uptake and nitrate transporter expression were correlated for one set of transporters but not another, indicating these were high and low affinity nitrate transporters, respectively. Concentrations of microcystin per cell decreased during N deprivation and increased upon N restoration. However, the transcript abundance of genes involved in the synthesis of this compound was complex, as microcystin synthetase genes involved in peptide synthesis were downregulated under N deprivation while genes involved in tailoring and transport were upregulated, suggesting modification of the microcystin molecule under N stress as well as potential alternative functions for these genes and/or this toxin.

Conclusions: Collectively, this study highlights the complex choreography of gene expression, cell physiology, and toxin synthesis that dynamic N levels can elicit in this ecologically important cyanobacterium. Differing expression patterns of genes within the microcystin synthetase operon in response to changing N levels revealed the potential limitations drawing conclusions based on only one gene in this operon.

Fig. 1

Photosynthetic efficiency, chlorophyll, and microcystin trends during the experiment. Photosynthetic efficiency (a), total chlorophyll a (b) and microcystin (MC-LR equivalents) concentrations per cell (c) during the experiment. Nitrogen refeed occurred on day 5. Error bars represent the standard deviation between biological replicates (n = 3). Stars indicate significant differences between treatments (p <0.001, two-way ANOVAR)

Fig. 2

Nitrogen transport and metabolism expression patterns. Heat map of gene expression of genes involved in nitrogen metabolism and transport. Blue colors correspond to a decrease in transcript abundance while red colors correspond to an increase in transcript abundance. White denotes no difference from the control condition

Fig. 3

Microcystin synthetase gene expression patterns. Heat map of gene expression of genes responsible for microcystin synthetase. Blue colors correspond to a decrease in transcript abundance while red colors correspond to an increase in transcript abundance. White denotes no difference from the control condition

Fig. 4

Photosynthesis and respiration gene expression patterns. Heat map of gene expression of genes involved in photosynthesis and respiration. Blue colors correspond to a decrease in transcript abundance while red colors correspond to an increase in transcript abundance. White denotes no difference from the control condition

Fig. 5

Carbon concentration and transport gene expression patterns. Heat map of gene expression of genes involved in carbon concentration and transport. Blue colors correspond to a decrease in transcript abundance while red colors correspond to an increase in transcript abundance. White denotes no difference from the control condition

Fig. 6

Nitrate specific uptake rates and nitrate transporter gene expression patterns. Nitrate specific uptake rates (a) and gene expression of nitrate/nitrite transporters (b & c) during the experiment. Error bars are the standard deviation between biological replicates (n = 3)

Fig. 7

Ammonium specific uptake rates and ammonium transporter gene expression patterns. Ammonium specific uptake rates (a) and gene expression of ammonium transporters (b) during the experiment. Error bars are the standard deviation between biological replicates (n = 3)

Fig. 8

Urea specific uptake rates and urea transporter gene expression patterns. Urea specific uptake rates (a) and gene expression of urea transporters (b) during the experiment. Error bars are the standard deviation between biological replicates (n = 3)

Fig. 9

Bicarbonate specific uptake rates and bicarbonate transporter gene expression patterns. Bicarbonate specific uptake rates (a) and gene expression of the bicarbonate transport system (b) during the experiment. Error bars are the standard deviation between biological replicates (n = 3)