Availability of vitamin B12 and its lower ligand intermediate α-ribazole impact prokaryotic and protist communities in oceanic systems

Genome analyses predict that the cofactor cobalamin (vitamin B12, called B12 herein) is produced by only one-third of all prokaryotes but almost all encode at least one B12-dependent enzyme, in most cases methionine synthase. This implies that the majority of prokaryotes relies on exogenous B12 supply and interacts with producers. B12 consists of a corrin ring centred around a cobalt ion and the lower ligand 5’6-dimethylbenzimidazole (DMB). It has never been tested whether availability of this pivotal cofactor, DMB or its intermediate α-ribazole affect growth and composition of prokaryotic microbial communities. Here we show that in the subtropical, equatorial and polar frontal Pacific Ocean supply of B12 and α-ribazole enhances heterotrophic prokaryotic production and alters the composition of prokaryotic and heterotrophic protist communities. In the polar frontal Pacific, the SAR11 clade and Oceanospirillales increased their relative abundances upon B12 supply. In the subtropical Pacific, Oceanospirillales increased their relative abundance upon B12 supply as well but also downregulated the transcription of the btuB gene, encoding the outer membrane permease for B12. Surprisingly, Prochlorococcus, known to produce pseudo-B12 and not B12, exhibited significant upregulation of genes encoding key proteins of photosystem I + II, carbon fixation and nitrate reduction upon B12 supply in the subtropical Pacific. These findings show that availability of B12 and α-ribazole affect growth and composition of prokaryotic and protist communities in oceanic systems thus revealing far-reaching consequences of methionine biosynthesis and other B12-dependent enzymatic reactions on a community level

Biodegradability of hydrothermally altered deep-sea dissolved organic matter

Deep-sea dissolved organic matter (DOM) constitutes a huge carbon reservoir in the worlds' oceans that – despite its abundance – is virtually unused as a substrate by marine heterotrophs. Heating within hydrothermal systems induces major molecular modifications of deep-sea DOM. Here, we tested the hypothesis that hydrothermal heating of deep-sea DOM enhances bioavailability. Aliquots of DOM extracted from the deep North Pacific (North Equatorial Pacific Intermediate Water; NEqPIW) were re-dissolved in artificial seawater and subjected to temperatures of 100 and 200 °C (40 MPa) using Dickson-type reactors. In agreement with earlier findings we observed a temperature-related drop in dissolved organic carbon (DOC) concentration (−6.1% at 100 °C, −21.0% at 200 °C) that predominantly affected the solid-phase extractable (SPE-DOC) fraction (−18.2% at 100 °C, −51.4% at 200 °C). Fourier-transform ion cyclotron resonance mass spectrometric (FT-ICR-MS) analysis confirmed a temperature-related reduction of average molecular mass, O/C ratios, double bond equivalents (DBE) and a relative increase in aromaticity (AImod). This thermally altered DOM was added (25 μmol L−1 DOC) to deep-water samples from the South West Pacific (Kermadec Arc, RV Sonne / SO253, 32° 37.706′ S | 179° 38.728′ W) and incubated with the prevailing natural microbial community. After 16 days at 4 °C in the dark, prokaryotic cell counts in incubations containing the full spectrum of thermally-degraded DOM (extractable and non-extractable compounds) had increased considerably (on average 21× for DOM100°C and 27× for DOM200°C). In contrast, prokaryotic growth in incubations to which only solid-phase extractable thermally-altered DOM was added was not enhanced compared to control incubations. The experiments demonstrate that temperature-driven degradation of deep-sea recalcitrant DOM within hydrothermal systems turns fractions of it accessible to microbes. The thermally-produced DOM compounds that stimulate microbial growth are not retained on reversed-phase resins (SPE-DOM) and are likely low-molecular mass organic acids. Despite the comprehensive compositional modifications of the solid-phase extractable (SPE-DOM) fraction through heating, it remains inaccessible to microbes at the investigated concentration levels. The microbial incubation resulted in only minor and mostly insignificant overall changes in SPE-DOM molecular composition and concentration

Lipidomic analysis of roseobacters of the pelagic RCA cluster and their response to phosphorus limitation

The marine roseobacter-clade affiliated cluster (RCA) represents one of the most abundant groups of bacterioplankton in the global oceans, particularly in temperate and sub-polar regions. They play a key role in the biogeochemical cycling of various elements and are important players in oceanic climate-active trace gas metabolism. In contrast to copiotrophic roseobacter counterparts such as Ruegeria pomeroyi DSS-3 and Phaeobacter sp. MED193, RCA bacteria are truly pelagic and have smaller genomes. We have previously shown that RCA bacteria do not appear to encode the PlcP-mediated lipid remodeling pathway, whereby marine heterotrophic bacteria remodel their membrane lipid composition in response to phosphorus (P) stress by substituting membrane glycerophospholipids with alternative glycolipids or betaine lipids. In this study, we report lipidomic analysis of six RCA isolates. In addition to the commonly found glycerophospholipids such as phosphatidylglycerol (PG) and phosphatidylethanolamine (PE), RCA bacteria synthesize a relatively uncommon phospholipid, acylphosphatidylglycerol, which is not found in copiotrophic roseobacters. Instead, like the abundant SAR11 clade, RCA bacteria upregulate ornithine lipid biosynthesis in response to P stress, suggesting a key role of this aminolipid in the adaptation of marine heterotrophs to oceanic nutrient limitation

HEPScore: A new CPU benchmark for the WLCG

HEPScore is a new CPU benchmark created to replace the HEPSPEC06 benchmark that is currently used by the WLCG for procurement, computing resource pledges and performance studies. The development of the new benchmark, based on HEP applications or workloads, has involved many contributions from software developers, data analysts, experts of the experiments, representatives of several WLCG computing centres, as well as the WLCG HEPScore Deployment Task Force. In this contribution, we review the selection of workloads and the validation of the new HEPScore benchmark.Comment: Paper submitted to the proceedings of the Computing in HEP Conference 2023, Norfol

A Roadmap for HEP Software and Computing R&D for the 2020s

Particle physics has an ambitious and broad experimental programme for the coming decades. This programme requires large investments in detector hardware, either to build new facilities and experiments, or to upgrade existing ones. Similarly, it requires commensurate investment in the R&D of software to acquire, manage, process, and analyse the shear amounts of data to be recorded. In planning for the HL-LHC in particular, it is critical that all of the collaborating stakeholders agree on the software goals and priorities, and that the efforts complement each other. In this spirit, this white paper describes the R&D activities required to prepare for this software upgrade.Peer reviewe

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