Abstract
BackgroundPlants can suffer ammonium (NH4+) toxicity, particularly when NH4+ is supplied as the sole nitrogen source. However, our knowledge about the underlying mechanisms of NH4+ toxicity is still largely unknown. Lemna minor, a model duckweed species, can grow well in high NH4+ environment but to some extent can also suffer toxic effects. The transcriptomic and physiological analysis of L. minor responding to high NH4+ may provide us some interesting and useful information not only in toxic processes, but also in tolerance mechanisms.ResultsThe L. minor cultured in the Hoagland solution were used as the control (NC), and in two NH4+ concentrations (NH4+ was the sole nitrogen source), 84 mg/L (A84) and 840 mg/L (A840) were used as stress treatments. The NH4+ toxicity could inhibit the growth of L. minor. Reactive oxygen species (ROS) and cell death were studied using stained fronds under toxic levels of NH4+. The malondialdehyde content and the activities of superoxide dismutase and peroxidase increased from NC to A840, rather than catalase and ascorbate peroxidase. A total of 6.62G nucleotides were generated from the three distinct libraries. A total of 14,207 differentially expressed genes (DEGs) among 70,728 unigenes were obtained. All the DEGs could be clustered into 7 profiles. Most DEGs were down-regulated under NH4+ toxicity. The genes required for lignin biosynthesis in phenylpropanoid biosynthesis pathway were up-regulated. ROS oxidative-related genes and programmed cell death (PCD)-related genes were also analyzed and indicated oxidative damage and PCD occurring under NH4+ toxicity.ConclusionsThe first large transcriptome study in L. minor responses to NH4+ toxicity was reported in this work. NH4+ toxicity could induce ROS accumulation that causes oxidative damage and thus induce cell death in L. minor. The antioxidant enzyme system was activated under NH4+ toxicity for ROS scavenging. The phenylpropanoid pathway was stimulated under NH4+ toxicity. The increased lignin biosynthesis might play an important role in NH4+ toxicity resistance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0774-8) contains supplementary material, which is available to authorized users.
Highlights
Plants can suffer ammonium (NH4 +) toxicity, when NH4 + is supplied as the sole nitrogen source
This could indicate that the NH4 + concentrations of 84 mg/L affected the propagation of L. minor, and the much higher concentration of 840 mg/L significantly inhibited the growth and could cause some damage
All the 14,207 differentially expressed gene (DEG) could be clustered into 7 profiles by short time-series expression miner software (STEM) (Additional file 5: Figure S4; Additional file 6), in which 12,959 DEGs were further clustered into 3 profiles (p-value ≤ 0.05), including two down-regulated patterns (Profile 1 and Profile 0) and one up-regulated pattern (Profile 7) (Fig. 2b-d)
Summary
Plants can suffer ammonium (NH4 +) toxicity, when NH4 + is supplied as the sole nitrogen source. Our knowledge about the underlying mechanisms of NH4 + toxicity is still largely unknown. The transcriptomic and physiological analysis of L. minor responding to high NH4 + may provide us some interesting and useful information in toxic processes, and in tolerance mechanisms. The knowledge on NH4 + toxicity has greatly expanded in recent years, but the underlying mechanism are still largely unclear, further researches, especially in the subcellular level, using more advanced -omics approaches to follow up NH4 +-induced global changes in plants are required [8, 18]. Transcriptome analysis is an effective method for global expression profiling of genes involved in stresses and toxicity in living organisms [19, 20]. With the rapid development of high-throughput sequencing, the next-generation transcriptome profiling approach or RNA sequencing (RNA-seq) has been gaining wide attention and use
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