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

International audienceMicrobial gene expression was followed for 23 days within a mesocosm (M1) isolating 50m(3) of seawater and in the surrounding waters in the Noumea lagoon, New Caledonia, in the southwest Pacific as part of the VAriability of vertical and tropHIc transfer of diazotroph derived N in the south wEst Pacific (VAHINE) experiment. The aim of VAHINE was to examine the fate of diazotroph-derived nitrogen (DDN) in a low-nutrient, low-chlorophyll ecosystem. On day 4 of the experiment, the mesocosm was fertilized with phosphate. In the lagoon, gene expression was dominated by the cyanobacterium Synechococcus, closely followed by Alphaproteobacteria. In contrast, drastic changes in the microbial community composition and transcriptional activity were triggered within the mesocosm within the first 4 days, with transcription bursts from different heterotrophic bacteria in rapid succession. The microbial composition and activity of the surrounding lagoon ecosystem appeared more stable, although following similar temporal trends as in M1. We detected significant gene expression from Chromerida in M1, as well as the Noumea lagoon, suggesting these photoautotrophic alveolates were present in substantial numbers in the open water. Other groups contributing substantially to the metatranscriptome were affiliated with marine Euryarchaeota Candidatus Thalassoarchaea (inside and outside) and Myoviridae bacteriophages likely infecting Synechococcus, specifically inside M1. High transcript abundances for ammonium transporters and glutamine synthetase in many different taxa (e.g., Pelagibacteraceae, Synechococcus, Prochlorococcus, and Rhodobacteraceae) was consistent with the known preference of most bacteria for this nitrogen source. In contrast, Alteromonadaceae highly expressed urease genes; Rhodobacteraceae and Prochlorococcus showed some urease expression, too. Nitrate reductase transcripts were detected on day 10 very prominently in Synechococcus and in Halomonadaceae. Alkaline phosphatase was expressed prominently only between days 12 and 23 in different organisms, suggesting that the microbial community was not limited by phosphate, even before the fertilization on day 4, whereas the post-fertilization community was. We observed high expression of the Synechococcus sqdB gene, only transiently lowered following phosphate fertilization. SqdB encodes UDP-sulfoquinovose synthase, possibly enabling marine picocyanobacteria to minimize their phosphorus requirements by substitution of phospholipids with sulphur-containing glycerolipids. This result suggests a link between sqdB expression and phosphate availability in situ. Gene expression of diazotrophic cyanobacteria was mainly attributed to Trichodesmium and Richelia intracellularis (diatom-diazotroph association) in the Noumea lagoon and initially in M1. UCYN-A (Candidatus Atelocyanobacterium) transcripts were the third most abundant and declined both inside and outside after day 4, consistent with 16S- and nifH-based analyses. Transcripts related to the Epithemia turgida endosymbiont and Cyanothece ATCC 51142 increased during the second half of the experiment

Combined Effects of CO2 and Light on the N2-Fixing Cyanobacterium Trichodesmium IMS101: A Mechanistic View1

The marine diazotrophic cyanobacterium Trichodesmium responds to elevated atmospheric CO2 partial pressure (pCO2) with higher N2 fixation and growth rates. To unveil the underlying mechanisms, we examined the combined influence of pCO2 (150 and 900 μatm) and light (50 and 200 μmol photons m−2 s−1) on Trichodesmium IMS101. We expand on a complementary study that demonstrated that while elevated pCO2 enhanced N2 fixation and growth, oxygen evolution and carbon fixation increased mainly as a response to high light. Here, we investigated changes in the photosynthetic fluorescence parameters of photosystem II, in ratios of the photosynthetic units (photosystem I:photosystem II), and in the pool sizes of key proteins involved in the fixation of carbon and nitrogen as well as their subsequent assimilation. We show that the combined elevation in pCO2 and light controlled the operation of the CO2-concentrating mechanism and enhanced protein activity without increasing their pool size. Moreover, elevated pCO2 and high light decreased the amounts of several key proteins (NifH, PsbA, and PsaC), while amounts of AtpB and RbcL did not significantly change. Reduced investment in protein biosynthesis, without notably changing photosynthetic fluxes, could free up energy that can be reallocated to increase N2 fixation and growth at elevated pCO2 and light. We suggest that changes in the redox state of the photosynthetic electron transport chain and posttranslational regulation of key proteins mediate the high flexibility in resources and energy allocation in Trichodesmium. This strategy should enable Trichodesmium to flourish in future surface oceans characterized by elevated pCO2, higher temperatures, and high light

Dynamics of transparent exopolymer particles (TEP) during the VAHINE mesocosm experiment in the New Caledonian lagoon

In the marine environment, transparent exopolymeric particles (TEP) produced from abiotic and biotic sources link the particulate and dissolved carbon pools and are essential vectors enhancing vertical carbon flux. We characterized spatial and temporal dynamics of TEP during the VAHINE experiment that investigated the fate of diazotroph-derived nitrogen and carbon in three replicate dissolved inorganic phosphorus (DIP)-fertilized 50 m3 enclosures in the oligotrophic New Caledonian lagoon. During the 23 days of the experiment, we did not observe any depth-dependent changes in TEP concentrations in the three sampled depths (1, 6, 12 m). TEP carbon (TEP-C) content averaged 28.9 ±  9.3 and 27.0 ±  7.2 % of total organic carbon (TOC) in the mesocosms and surrounding lagoon respectively and was strongly and positively coupled with TOC during P2 (i.e., days 15–23). TEP concentrations in the mesocosms declined for the first 9 days after DIP fertilization (P1  =  days 5–14) and then gradually increased during the second phase. Temporal changes in TEP concentrations paralleled the growth and mortality rates of the diatom–diazotroph association of Rhizosolenia and Richelia that predominated the diazotroph community during P1. By P2, increasing total primary and heterotrophic bacterial production consumed the supplemented P and reduced availability of DIP. For this period, TEP concentrations were negatively correlated with DIP availability and turnover time of DIP (TDIP), while positively associated with enhanced alkaline phosphatase activity (APA) that occurs when the microbial populations are P stressed. During P2, increasing bacterial production (BP) was positively correlated with higher TEP concentrations, which were also coupled with the increased growth rates and aggregation of the unicellular cyanobacterial Group C (UCYN-C) diazotrophs that bloomed during this period. We conclude that the composite processes responsible for the formation and breakdown of TEP yielded a relatively stable TEP pool available as both a carbon source and facilitating aggregation and flux throughout the experiment. TEP were probably mostly influenced by abiotic physical processes during P1, while biological activity (BP, diazotrophic growth and aggregation, export production) mainly impacted TEP concentrations during P2 when DIP availability was limited

Diazotrophs are overlooked contributors to carbon and nitrogen export to the deep ocean

Diazotrophs are widespread microorganisms that alleviate nitrogen limitation in 60% of our oceans, thereby regulating marine productivity. Yet, the group-specific contribution of diazotrophs to organic matter export has not been quantified, which so far has impeded an accurate assessment of their impact on the biological carbon pump. Here, we examine the fate of five groups of globally-distributed diazotrophs by using an original combination of mesopelagic particle sampling devices across the subtropical South Pacific Ocean. We demonstrate that cyanobacterial and non-cyanobacterial diazotrophs are exported down to 1000 m depth. Surprisingly, group-specific export turnover rates point to a more efficient export of small unicellular cyanobacterial diazotrophs (UCYN) relative to the larger and filamentous Trichodesmium. Phycoerythrin-containing UCYN-B and UCYN-C-like cells were recurrently found embedded in large (>50 µm) organic aggregates or organized into clusters of tens to hundreds of cells linked by an extracellular matrix, presumably facilitating their export. Beyond the South Pacific, our data are supported by analysis of the Tara Oceans metagenomes collected in other ocean basins, extending the scope of our results globally. We show that, when diazotrophs are found in the euphotic zone, they are also systematically present in mesopelagic waters, suggesting their transport to the deep ocean. We thus conclude that diazotrophs are a significant part of the carbon sequestered in the deep ocean and, therefore, they need to be accounted in regional and global estimates of export