Global analysis of gene expression dynamics within the marine microbial community during the VAHINE mesocosm experiment in the South West Pacific

The dynamics of microbial gene expression was followed for 23 days within a mesocosm (M1) isolating 50 m3 of seawater and in the surrounding waters in the Nouméa lagoon, New Caledonia, in the South West Pacific as part of the VAHINE experiment. The aim of this experiment was to examine the fate of diazotroph-derived nitrogen (DDN) in a Low Nutrient, Low Chlorophyll ecosystem. In the lagoon, gene expression was dominated by the cyanobacterium Synechococcus, closely followed by alphaproteobacteria. In contrast, alphaproteobacteria dominated the gene expression in M1 until day 12, among them Rhodobacteraceae, rapidly gaining a high share in the metatranscriptome and peaking at day 4, followed by a burst in Altermonadaceae-related gene expression on days 8 and 10 and from Idiomarinaceae on day 10 in rapid succession. Thus, drastic dynamical changes in the microbial community composition and activity were triggered within the mesocosm already within the first 4 days, whereas the composition and activity of the lagoon ecosystem appeared more stable, although following similar temporal trends. We detected significant gene expression from Chromerida in M1, as well as the Nouméa lagoon, suggesting these photoautotrophic alveolates were present in substantial numbers in the open water. Other clearly detectable groups contributing to the metatranscriptome were affiliated with marine Euryarchaeota Candidatus Thalassoarchaea (inside and outside) and Myoviridae bacteriophages likely infecting Synechococcus, specifically inside M1. The high expression of genes encoding ammonium transporters and glutamine synthetase in many different taxa (e.g., Pelagibacteraceae, Synechococcus, Prochlorococcus and Rhodobacteraceae) observed in M1 over long periods underscored the preference of most bacteria for this nitrogen source. In contrast, Alteromonadaceae highly expressed urease genes, and also Rhodobacteraceae and Prochlorococcus showed some urease expression. Nitrate reductase expression was detected on day 10 very prominently in Synechococcus and in the Halomonadaceae. The mesocosm was fertilized by the addition of phosphate on day 4, thus genes involved in phosphate assimilation were analysed in more detail. Expression of alkaline phosphatase was prominent between day 12 and 23 in different organisms and not expressed before the fertilization, suggesting that the microbial community was initially adapted to the ambient phosphate levels and not phosphate limited, whereas the post-fertilization community had to actively acquire it. At the same time, most pronounced on day 23, we observed the high expression of the Synechococcus sqdB gene, encoding an enzyme for the synthesis of sulphoquinovosyldiacylglycerols, which might substitute phospholipids. In this way marine picocyanobacteria could minimize their phosphorus requirements, which is further consistent with the idea of phosphorus stress at the end of the experiment. The specific gene expression of diazotrophic cyanobacteria could be mainly attributed to Trichodesmium and Richelia intracellularis strains (diatom-diazotroph associations), both in the Nouméa lagoon and initially in M1. Strikingly, Trichodesmium transcript abundance was an order of magnitude higher in M1 than in the lagoon on days 2 and 4, dropping steeply after that. UCYN-A (Candidatus Atelocyanobacterium) transcripts were the third most abundant and declined both inside and outside after day 4, consistent with both 16S- and nifH-based analyses. Consistent with UCYN-C nifH tags increasing after day 14 in M1, transcripts related to the Epithemia turgida endosymbiont and Cyanothece ATCC 51142 increased from day 14 and maintained a higher share until the end of the experiment at day 23, suggesting these cyanobacteria were causing the observed high N2 fixation rates.