Diversity of nitrogen assimilation pathways among microbial photosynthetic eukaryotes

Abstract

In an effort to better understand the diversity of genes coding for nitrogen (N) uptake and assimilation pathways among microalgae, we analyzed the transcriptomes of five phylogenetically diverse single celled algae originally isolated from the same high arctic marine region. The five photosynthetic flagellates (a pelagophyte, dictyochophyte, chrysoph-yte, cryptophyte and haptophyte) were grown on standard media and media with only urea or nitrate as a nitrogen source; cells were harvested during late exponential growth. Based on homolog protein sequences, transcriptomes of each alga were interrogated to retrieve genes potentially associated with nitrogen uptake and utilization pathways. We further investigated the phylogeny of poorly characterized genes and gene families that were identified. While the phylogeny of the active urea transporter (DUR3) was taxonomically coherent, those for the urea transporter superfamily, putative nitrilases and amidases indicated complex evolutionary histories, and preliminary evidence for horizontal gene transfers. All five algae expressed genes for ammonium assimilation and all but the chrysophyte expressed genes involved in nitrate utilization and the urea cycle. Among the four algae with nitrate transporter transcripts, we detected lower expression levels in three of these (the dictyochophyte, pelagophyte, and cryptophyte) grown in the urea only medium compared with cultures from the nitrate only media. The diversity of N pathway genes in the five algae, and their ability to grow using urea as a nitrogen source, suggest that these flagellates are able to use a variety of organic nitrogen sources, which would be an advantage in an inorganic nitrogen - limited environment, such as the Arctic Ocean.

Conserved Transcriptional Responses to Nutrient Stress in Bloom-Forming Algae

“…Transcription of this family of transporters has been found to increase under P stress in the haptophyte, P. parvum (Beszteri et al, 2012), decrease when grown on urea vs. nitrate in cells of an unidentified cryptophyte (Terrado et al, 2015), and increase under N limitation for the pelagophyte, Aureococcus anophagefferens (Berg et al, 2008). This variable response across taxa is likely reflective of available nitrite levels within the cell rather than external concentrations (Galván, 2002; Maeda et al, 2014).…”

“…A comparison of four prymnesiophytes found a set of core genes shared among all species mapping to essential metabolic pathways such as the biosynthesis of amino acids, carbon metabolism, fatty acid metabolism, and purine and pyrimidine metabolism (Koid et al, 2014). In another example, co-occurring flagellates were found to have similar urea transporters but diverse urease genes and N uptake and assimilation pathways, suggesting varying strategies of survival in the N-limited Arctic Ocean (Terrado et al, 2015). However, few studies have investigated the response similarities and differences of more divergent taxa grown under the same laboratory conditions and sequenced in a similar manner.…”

Comprehensive transcriptome analysis provides new insights into nutritional strategies and phylogenetic relationships of chrysophytes

“…Nevertheless, they have not yet been investigated in detail at a molecular level, and no genomic and only little transcriptomic information of related organisms (Terrado et al, 2015; Keeling et al, 2014; Liu et al, 2016) is available.…”

Host-derived viral transporter protein for nitrogen uptake in infected marine phytoplankton

“…Given the evidence of HGT for genes involved in both N and P metabolisms (7,9,32), the presence of host-derived phosphate transporters in phytoplankton viral genomes (29), and the importance of nutrient availability for phytoplankton and viral replication (33), we hypothesize that functional N transporters would also be found in genomes of phytoplankton viruses. Indeed, a recent analysis of marine viral metagenomes extended the catalog of functions encoded by AMGs and reported the presence of genes putatively encoding NH + 4 transporters in metagenomic assemblies which harbored phage genes (21).…”

“…In oligotrophic environments, and transiently nutrient-depleted environments, phytoplankton species have evolved a range of strategies to optimize nutrient acquisition (4). The genetic repertoire of N and P transporters shows evidence of gene duplication, differential loss, and horizontal gene transfer (HGT) in phytoplankton genomes as well as contrasting gene expression levels (5)(6)(7)(8)(9), suggesting that the evolution of these genes has been driven by adaptation to environmental limitation. Ammonium (NH + 4 ) and nitrate (NO − 3 ) are commonly available N sources for marine phytoplankton (10,11) and, as such, the gene repertoires of cyanobacterial and eukaryotic phytoplankton are configured toward utilization of these two forms of inorganic N sources (12).…”