Proteogenic Dipeptides Are Characterized by Diel Fluctuations and Target of Rapamycin Complex-Signaling Dependency in the Model Plant Arabidopsis thaliana

As autotrophic organisms, plants capture light energy to convert carbon dioxide into ATP, nicotinamide adenine dinucleotide phosphate (NADPH), and sugars, which are essential for the biosynthesis of building blocks, storage, and growth. At night, metabolism and growth can be sustained by mobilizing carbon (C) reserves. In response to changing environmental conditions, such as light-dark cycles, the small-molecule regulation of enzymatic activities is critical for reprogramming cellular metabolism. We have recently demonstrated that proteogenic dipeptides, protein degradation products, act as metabolic switches at the interface of proteostasis and central metabolism in both plants and yeast. Dipeptides accumulate in response to the environmental changes and act via direct binding and regulation of critical enzymatic activities, enabling C flux distribution. Here, we provide evidence pointing to the involvement of dipeptides in the metabolic rewiring characteristics for the day-night cycle in plants. Specifically, we measured the abundance of 13 amino acids and 179 dipeptides over short- (SD) and long-day (LD) diel cycles, each with different light intensities. Of the measured dipeptides, 38 and eight were characterized by day-night oscillation in SD and LD, respectively, reaching maximum accumulation at the end of the day and then gradually falling in the night. Not only the number of dipeptides, but also the amplitude of the oscillation was higher in SD compared with LD conditions. Notably, rhythmic dipeptides were enriched in the glucogenic amino acids that can be converted into glucose. Considering the known role of Target of Rapamycin (TOR) signaling in regulating both autophagy and metabolism, we subsequently investigated whether diurnal fluctuations of dipeptides levels are dependent on the TOR Complex (TORC). The Raptor1b mutant (raptor1b), known for the substantial reduction of TOR kinase activity, was characterized by the augmented accumulation of dipeptides, which is especially pronounced under LD conditions. We were particularly intrigued by the group of 16 dipeptides, which, based on their oscillation under SD conditions and accumulation in raptor1b, can be associated with limited C availability or photoperiod. By mining existing protein-metabolite interaction data, we delineated putative protein interactors for a representative dipeptide Pro-Gln. The obtained list included enzymes of C and amino acid metabolism, which are also linked to the TORC-mediated metabolic network. Based on the obtained results, we speculate that the diurnal accumulation of dipeptides contributes to its metabolic adaptation in response to changes in C availability. We hypothesize that dipeptides would act as alternative respiratory substrates and by directly modulating the activity of the focal enzymes.

Diel investments in metabolite production and consumption in a model microbial system

Organic carbon transfer between surface ocean photosynthetic and heterotrophic microbes is a central but poorly understood process in the global carbon cycle. In a model community in which diatom extracellular release of organic molecules sustained growth of a co-cultured bacterium, we determined quantitative changes in the diatom endometabolome and the bacterial uptake transcriptome over two diel cycles. Of the nuclear magnetic resonance (NMR) peaks in the diatom endometabolites, 38% had diel patterns with noon or mid-afternoon maxima; the remaining either increased (36%) or decreased (26%) through time. Of the genes in the bacterial uptake transcriptome, 94% had a diel pattern with a noon maximum; the remaining decreased over time (6%). Eight diatom endometabolites identified with high confidence were matched to the bacterial genes mediating their utilization. Modeling of these coupled inventories with only diffusion-based phytoplankton extracellular release could not reproduce all the patterns. Addition of active release mechanisms for physiological balance and bacterial recognition significantly improved model performance. Estimates of phytoplankton extracellular release range from only a few percent to nearly half of annual net primary production. Improved understanding of the factors that influence metabolite release and consumption by surface ocean microbes will better constrain this globally significant carbon flux.

Seasonality of the particle number concentration and size distribution: a global analysis retrieved from the network of Global Atmosphere Watch (GAW) near-surface observatories

Aerosol particles are a complex component of the atmospheric system which influence climate directly by interacting with solar radiation, and indirectly by contributing to cloud formation. The variety of their sources, as well as the multiple transformations they may undergo during their transport (including wet and dry deposition), result in significant spatial and temporal variability of their properties. Documenting this variability is essential to provide a proper representation of aerosols and cloud condensation nuclei (CCN) in climate models. Using measurements conducted in 2016 or 2017 at 62 ground-based stations around the world, this study provides the most up-to-date picture of the spatial distribution of particle number concentration (Ntot) and number size distribution (PNSD, from 39 sites). A sensitivity study was first performed to assess the impact of data availability on Ntot's annual and seasonal statistics, as well as on the analysis of its diel cycle. Thresholds of 50 % and 60 % were set at the seasonal and annual scale, respectively, for the study of the corresponding statistics, and a slightly higher coverage (75 %) was required to document the diel cycle. Although some observations are common to a majority of sites, the variety of environments characterizing these stations made it possible to highlight contrasting findings, which, among other factors, seem to be significantly related to the level of anthropogenic influence. The concentrations measured at polar sites are the lowest (∼ 102 cm−3) and show a clear seasonality, which is also visible in the shape of the PNSD, while diel cycles are in general less evident, due notably to the absence of a regular day–night cycle in some seasons. In contrast, the concentrations characteristic of urban environments are the highest (∼ 103–104 cm−3) and do not show pronounced seasonal variations, whereas diel cycles tend to be very regular over the year at these stations. The remaining sites, including mountain and non-urban continental and coastal stations, do not exhibit as obvious common behaviour as polar and urban sites and display, on average, intermediate Ntot (∼ 102–103 cm−3). Particle concentrations measured at mountain sites, however, are generally lower compared to nearby lowland sites, and tend to exhibit somewhat more pronounced seasonal variations as a likely result of the strong impact of the atmospheric boundary layer (ABL) influence in connection with the topography of the sites. ABL dynamics also likely contribute to the diel cycle of Ntot observed at these stations. Based on available PNSD measurements, CCN-sized particles (considered here as either >50 nm or >100 nm) can represent from a few percent to almost all of Ntot, corresponding to seasonal medians on the order of ∼ 10 to 1000 cm−3, with seasonal patterns and a hierarchy of the site types broadly similar to those observed for Ntot. Overall, this work illustrates the importance of in situ measurements, in particular for the study of aerosol physical properties, and thus strongly supports the development of a broad global network of near surface observatories to increase and homogenize the spatial coverage of the measurements, and guarantee as well data availability and quality. The results of this study also provide a valuable, freely available and easy to use support for model comparison and validation, with the ultimate goal of contributing to improvement of the representation of aerosol–cloud interactions in models, and, therefore, of the evaluation of the impact of aerosol particles on climate.

Methane in the Danube Delta: the importance of spatial patterns and diel cycles for atmospheric emission estimates

Methane (CH4) is one of the substantial greenhouse gases in our atmosphere, and its concentration has increased by ∼ 4 % over the last decade. Although sources driving these increases are not well constrained, one potential contribution comes from wetlands, which are usually intertwined with rivers, channels and lakes, creating a considerable need to acquire higher-resolution data to facilitate modelling and predictions. Here we took a fully contained sensor set-up to obtain measurements of CH4, O2 and auxiliary parameters, installed on a houseboat for accessibility, to assess and analyse surface water concentrations within the Danube Delta, Romania. During three expeditions in different seasons, we transected a ∼ 400 km route with concentration mapping and two additional stations for monitoring diel cycles. Overall, the delta was a source for CH4 throughout all seasons, with concentrations ranging between 0.113–15.6 µmol L−1. Calculated diffusive CH4 fluxes for the overall delta yielded an average of 49 ± 61 µmol m−2 h−1, corresponding to an extrapolated annual flux of 0.43 ± 0.53 mol m−2 yr−1. The dataset was split into three different subsystems – lakes, rivers and channels – with channels showing the highest variability. We found overlapping CH4 concentrations throughout each subsystem, with large inflows coming from reed beds and channels into the lakes. Seasonal variability and water flow direction also influenced the overall dynamics in each region. We found large to extreme diel cycles in both the lakes and channels, with concentrations varying by an order of magnitude between these two systems. The lake diel cycle showed a clear linear trend with an O2:CH4 molar ratio of -50:1 during the phase of nocturnal convection, with the two water stratified bodies mixing during the night, suggesting daily vertical stratification allowing for macrophytes to create a temporal oxycline due to a lack of light and movement between the stems as previously suggested, and potentially incurring an uncertainty range of a factor of 4.5. Our data illustrate the importance of high-resolution spatio-temporal data collection throughout the entire delta and the increased need for diel cycles in different habitats to improve the concentration and emission estimates from wetland systems.

Diel light cycles affect phytoplankton competition in the global ocean

Light, essential for photosynthesis, is present in two periodic cycles in nature: seasonal and diel. Although seasonality of light is typically resolved in ocean ecosystem and biogeochemistry models because of its significance for seasonal succession and biogeography of phytoplankton, the diel light cycle is generally not resolved. Here we use a three-dimensional global ocean model and compare high temporal resolution simulations with and without diel light cycles. The model simulates 15 phytoplankton types of different cell size, encompassing two broad ecological strategies: small cells with high nutrient affinity (gleaners) and larger cells with high maximal growth rate (opportunists). Both are grazed by zooplankton and limited by nitrogen, phosphorus and iron. Simulations show that diel cycles of light induce diel cycles in phytoplankton populations and limiting nutrients in the global ocean. Diel nutrient cycles are associated with higher concentration of limiting nutrients by up to 200% at low latitudes (-40 to 40), a process that increases opportunists biomass by up to 50%. Size classes with the highest maximal growth rates from both gleaner and opportunist groups are favored the most by diel light cycles. This mechanism weakens as latitude increases because the effects of the seasonal cycle dominate over those of the diel cycle. The present work shows that resource competition under diel light cycles has a significant impact on phytoplankton biogeography, indicating the necessity of resolving diel processes in global ocean models.

Syntrophy between fermentative and purple phototrophic bacteria for carbohydrate-based wastewater treatment

Fermentative chemoorganoheterotrophic bacteria (FCB) and purple photoorganoheterotrophic bacteria (PPB) are two interesting microbial guilds to process carbohydrate-rich wastewaters. Their interaction has been studied in axenic pure cultures or co-cultures. Little is known about their metabolic interactions in open cultures. We aimed to harness the competitive and syntrophic interactions between PPB and FCB in mixed cultures. We studied the effect of reactor regimes (batch or continuous, CSTR) and illumination modes (continuous irradiation with infrared light, dark, or light/dark diel cycles) on glucose conversions and the ecology of the process. In batch, FCB outcompeted (>80%) PPB, under both dark and infrared light conditions. In CSTR, three FCB populations of Enterobacteriaceae, Lachnospiraceae and Clostridiaceae were enriched (>70%), while Rhodobacteraceae relatives of PPB made 30% of the community. Fermentation products generated from glucose were linked to the dominant FCB. Continuous culturing at a dilution rate of 0.04 h-1 helped maintain FCB and PPB in syntrophy: FCB first fermented glucose into volatile fatty acids and alcohols, and PPB grew on fermentation products. Direct supply of carboxylates like acetate under infrared light enriched for PPB (60%) independent of reactor regimes. Ecological engineering of FCB- and PPB-based biorefineries can help treat and valorize carbohydrate-based waste feedstocks.

Seasonal and diel cycles of fin whale acoustic occurrence near Elephant Island, Antarctica

This study investigates the relevance of the Elephant Island (EI) region for Southern Hemisphere fin whales ( Balaenoptera physalus ) in their annual life cycle. We collected 3 years of passive acoustic recordings (January 2013 to February 2016) northwest of EI to calculate time series of fin whale acoustic indices, daily acoustic occurrence, spectrograms, as well as the abundance of their 20 Hz pulses. Acoustic backscatter strength, sea ice concentration and chlorophyll-a composites provided concurrent environmental information for graphic comparisons. Acoustic interannual, seasonal and diel patterns together with visual information and literature resources were used to define the period of occupancy and to infer potential drivers for their behaviour. Spectral results suggest that these fin whales migrate annually to and from offshore central Chile. Acoustic data and visual information reveal their arrival at EI in December to feed without producing their typical 20 Hz pulse. For all 3 years, acoustic activity commences in February, peaks in May and decreases in August, in phase with the onset of their breeding season. Our results emphasize the importance of EI for fin whales throughout most of the year. Our recommendation is to consider EI for establishing a marine protected area to expedite the recovery of this vulnerable species.

Daily rhythms in the transcriptomes of the human parasite Schistosoma mansoni

The consequences of the earth’s daily rotation have led to 24-hour biological rhythms in most organisms. Parasites have daily rhythms, which, when in synchrony with host rhythms, optimize their fitness. Using round-the-clock transcriptomics of male and female Schistosoma mansoni blood flukes we have discovered the first 24-hour molecular oscillations in a metazoan parasite, and gained insight into its daily rhythms. We show that expression of ∼2% of its genes followed diel cycles. Rhythmic processes, in synchrony in both sexes, included a night-time stress response and a day-time metabolic ‘rush hour’. These 24hr rhythms may be driven by host rhythms and/or generated by an intrinsic circadian clock. However, canonical core clock genes are lacking, suggesting an unusual oscillatory mechanism or loss of a functional clock. The daily rhythms in biology identified here, may promote within-host survival and between-host transmission, and are important for the development and delivery of therapeutics against schistosomiasis.