This file set contains supplementary dataset for paper "Hou, S. et al.Benefit from decline: The primary transcriptome of Alteromonas macleodii str. Te101 during Trichodesmium demise. (accepted)." Please refer to this paper for more information. File Description:Supplemental Dataset S1: Genome-wide visualization of predicted TSS and coverage for the genome of Alteromonasmacleodii str. Te101.Supplementary Dataset 2: Genome-wide GO assignments of Alteromonasmacleodii str. Te101 proteins.
How To Cite This Dataset: If you find this dataset useful to your research, please consider to cite the main paper: Hou, S. et al. Benefit from decline: The primary transcriptome of Alteromonas macleodii str. Te101 when Trichodesmium collapses. (accepted)
Recent studies on the diazotrophic cyanobacterium Trichodesmium erythraeum (IMS101) showed that increasing CO2 partial pressure (pCO2) enhances N2 fixation and growth. Significant uncertainties remain as to the degree of the sensitivity to pCO2, its modification by other environmental factors, and underlying processes causing these responses. To address these questions, we examined the responses of Trichodesmium IMS101 grown under a matrix of low and high levels of pCO2 (150 and 900 μatm) and irradiance (50 and 200 μmol photons m−2 s−1). Growth rates as well as cellular carbon and nitrogen contents increased with increasing pCO2 and light levels in the cultures. The pCO2-dependent stimulation in organic carbon and nitrogen production was highest under low light. High pCO2 stimulated rates of N2 fixation and prolonged the duration, while high light affected maximum rates only. Gross photosynthesis increased with light but did not change with pCO2. HCO3− was identified as the predominant carbon source taken up in all treatments. Inorganic carbon uptake increased with light, but only gross CO2 uptake was enhanced under high pCO2. A comparison between carbon fluxes in vivo and those derived from 13C fractionation indicates high internal carbon cycling, especially in the low-pCO2 treatment under high light. Light-dependent oxygen uptake was only detected under low pCO2 combined with high light or when low-light-acclimated cells were exposed to high light, indicating that the Mehler reaction functions also as a photoprotective mechanism in Trichodesmium. Our data confirm the pronounced pCO2 effect on N2 fixation and growth in Trichodesmium and further show a strong modulation of these effects by light intensity. We attribute these responses to changes in the allocation of photosynthetic energy between carbon acquisition and the assimilation of carbon and nitrogen under elevated pCO2. These findings are supported by a complementary study looking at photosynthetic fluorescence parameters of photosystem II, photosynthetic unit stoichiometry (photosystem I:photosystem II), and pool sizes of key proteins in carbon and nitrogen acquisition.
Abstract. 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 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 Nouméa 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 Nouméa 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.
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Summary Photosynthetic oxygen‐evolving microorganisms contend with continuous self‐production of molecular oxygen and reactive oxygen species. The deleterious effects of reactive oxygen species are exacerbated for cyanobacterial nitrogen‐fixers (diazotrophs) due to the innate sensitivity of nitrogenase to oxygen. This renders incompatible the processes of oxygen‐evolving photosynthesis and N‐fixation. We examined total antioxidative potential of various diazotrophic and non‐diazotrophic cyanobacteria. We focused on Trichodesmium spp., a bloom‐forming marine diazotroph that contributes significantly to global nitrogen fixation. Among the species tested, Trichodesmium possessed the highest antioxidant activity. Moreover, while proteins constituted the dominant antioxidative component of all other cyanobacteria tested, Trichodesmium was unique in that small‐molecule natural products provided the majority of antioxidant activity, while proteins constituted only 13% of total antioxidant activity. Bioassay‐guided fractionation followed by high‐performance liquid chromatography profiling of antioxidant purified fractions identified the highly potent antioxidant all‐ trans ‐β‐carotene, and small amounts of 9‐ cis ‐β‐carotene and retinyl palmitate. Search of the Trichodesmium genome identified protein sequences homologous to key enzymes in the β‐carotene to retinyl palmitate biosynthetic pathway, including 33–37% identity to lecithin retinol acyltransferase. The present study demonstrates the importance of carotenoids in Trichodesmium 's arsenal of defensive compounds against oxidative damage and protection of nitrogenase from oxygen and its radicals.
Abstract Phytoplankton produces methane (CH4), a potent greenhouse gas. Little is known about the relationship between their CH4 production and photosynthesis, the predominant biological pathway of CO2 sequestration in the ocean. We show that CH4 released by the widespread, bloom-forming marine microalga Emiliania huxleyi grown under different light levels correlated positively with photosynthetic electron transfer and carbon fixation. We ruled out the possibility of classical methanogenesis in the cultures and showed that under saturating light E. huxleyi produces CH4 at a maximal rate of about 6.6 ×10− 11 µg CH4 cell− 1 d− 1 or 3.9 µg CH4 g− 1 particulate organic carbon d− 1, and cannot generate CH4 in darkness. Accounting for the CH4 released vs CO2 fixed, the stronger global warming potential of CH4, and estimates of CO2 that reaches the ocean interior, we conclude that E. huxleyi’s contribution to the marine biological carbon pump may be attenuated by up to 13% due to its CH4 release.
