Picoplankton Diel Variability and Estimated Growth Rates in Epipelagic and Mesopelagic Waters of the Central Red Sea

The diel variability of the abundance and cell size of picoplanktonic groups in the central Red Sea was monitored every 2 h in situ on 4 occasions (once per season) from 2015 to 2016. We distinguished Prochlorococcus, low (LF-Syn) and high (HF-Syn) fluorescence Synechococcus, small (Speuk) and large (Lpeuk) picoeukaryotes and two groups of heterotrophic prokaryotes of low (LNA) and high (HNA) nucleic acid content. The diel variability in abundance was less marked than in cell size and more apparent in autotrophs than heterotrophs. Specific growth rates were estimated by an empirical relationship from measurements obtained in bottle incubations of surface and deep samples collected in the winter compared with in situ variations in cell size over 24 h. Autotrophic picoplankton groups generally grew faster (0.23–0.77 d–1) than heterotrophic prokaryotes (0.12–0.50 d–1). Surface to 100 m depth-weighted specific growth rates displayed a clear seasonal pattern for Prochlorococcus, with maxima in winter (0.77 ± 0.07 d–1) and minima in fall (0.52 ± 0.07 d–1). The two groups of Synechococcus peaked in spring, with slightly higher growth rates of LF-Syn (0.57 ± 0.04 d–1) than HF-Syn (0.43 ± 0.04 d–1). Speuk and Lpeuk showed different seasonal patterns, with lower values of the former (0.27 ± 0.02 and 0.37 ± 0.04 d–1, respectively). HNA consistently outgrew LNA heterotrophic prokaryotes, with a higher growth in the epipelagic (0–200 m, 0.36 ± 0.03 d–1) than in the mesopelagic (200–700 m, 0.26 ± 0.03 d–1), while no differences were found for LNA cells (0.19 ± 0.03 d–1 and 0.17 ± 0.02 d–1, respectively). With all data pooled, the mean diel abundances of autotrophic picoplankton in the upper epipelagic and of HNA cells in the epipelagic and mesopelagic layers were significantly correlated with the specific growth rates estimated from cell size variations. Our high-resolution sampling dataset suggests that changes in growth rates underlie the noticeable seasonality of picoplankton recently described in these tropical waters.

Influence of atmospheric deposition on biogeochemical cycles in an oligotrophic ocean system

The surface mixed layer (ML) in the Mediterranean Sea is a well-stratified domain characterized by low macronutrients and low chlorophyll content for almost 6 months of the year. In this study we characterize the biogeochemical cycling of nitrogen (N) in the ML by analyzing simultaneous in situ measurements of atmospheric deposition, nutrients in seawater, hydrological conditions, primary production, heterotrophic prokaryotic production, N2 fixation and leucine aminopeptidase activity. Dry deposition was continuously measured across the central and western open Mediterranean Sea, and two wet deposition events were sampled, one in the Ionian Sea and one in the Algerian Basin. Along the transect, N budgets were computed to compare the sources and sinks of N in the mixed layer. In situ leucine aminopeptidase activity made up 14 % to 66 % of the heterotrophic prokaryotic N demand, and the N2 fixation rate represented 1 % to 4.5 % of the phytoplankton N demand. Dry atmospheric deposition of inorganic nitrogen, estimated from dry deposition of nitrate and ammonium in aerosols, was higher than the N2 fixation rates in the ML (on average 4.8-fold). The dry atmospheric input of inorganic N represented a highly variable proportion of biological N demand in the ML among the stations, 10 %–82 % for heterotrophic prokaryotes and 1 %–30 % for phytoplankton. As some sites were visited on several days, the evolution of biogeochemical properties in the ML and within the nutrient-depleted layers could be followed. At the Algerian Basin site, the biogeochemical consequences of a wet dust deposition event were monitored through high-frequency sampling. Notably, just after the rain, nitrate was higher in the ML than in the nutrient-depleted layer below. Estimates of nutrient transfer from the ML into the nutrient-depleted layer could explain up to a third of the nitrate loss from the ML. Phytoplankton did not benefit directly from the atmospheric inputs into the ML, probably due to high competition with heterotrophic prokaryotes, also limited by N and phosphorus (P) availability at the time of this study. Primary producers decreased their production after the rain but recovered their initial state of activity after a 2 d lag in the vicinity of the deep chlorophyll maximum layer.

Potential and expression of carbohydrate utilization by marine fungi in the global ocean

Background Most of the research on the cycling of carbon in the open-ocean has focused on heterotrophic prokaryotes and eukaryotic phytoplankton, but the role of pelagic fungi remains largely enigmatic. Methods Here, we performed a global-ocean multi-omics analysis of all pelagic fungal carbohydrate-active enzymes (CAZymes), key enzymes in the carbon cycling. We studied the occurrence, expression, diversity, functional classification, and taxonomic affiliation of the genes encoding all pelagic fungal CAZymes from the epi- and mesopelagic realm. Results Pelagic fungi are active in carbohydrate degradation as indicated by a high ratio of CAZymes transcripts per gene. Dothideomycetes in epipelagic and the Leotiomycetes in mesopelagic waters (both from the phylum Ascomycota) are the main pelagic fungi responsible for carbohydrate degradation in the ocean. The abundance, expression, and diversity of fungal CAZymes were higher in the mesopelagic than in the epipelagic waters, in contrast to the distribution pattern of prokaryotic CAZymes. Conclusions Our results reveal a widespread utilization of different types of CAZymes by pelagic fungi, uncovering an active and hitherto largely unexplored participation of fungi in the pelagic C cycling, where pelagic prokaryotes and fungi occupy different ecological niches, and fungi becoming relatively more important with depth.

DOM Biological Lability in an Estuarine System in Two Contrasting Periods

Estuarine processes play a key role in determining the amount and quality of land-derived dissolved organic matter (DOM) reaching the oceans. Microbial-mediated reactions can affect the concentration, quality, and bioavailability of DOM within an estuary. In this study, we investigated biological DOM removal in a small estuary and its variability in two contrasting seasons (spring and autumn) characterized by natural differences in the concentration and quality of the riverine DOM. Two incubation experiments were carried out using natural DOM and heterotrophic prokaryotes community collected at the estuary in March and September. Dissolved organic carbon (DOC) concentration, DOM fluorescence, and the heterotrophic prokaryotes abundance (HPA) showed marked differences between the two seasons. These parameters were followed through time for up to two months. Despite the marked differences in the initial conditions, the DOC removal rates were surprisingly similar in the two periods (16 µM DOC month−1 in March and 18 µM DOC month−1 in September), with the biggest removal in the first 48 h. The trend of fluorescent DOM (FDOM) during the incubation showed marked differences between the two periods. In March, the net removal of all the FDOM components was observed consistently with the decrease in DOC; whereas, in September, the net production of humic-like substances was observed.

Influence of atmospheric deposition on biogeochemical cycles in an oligotrophic ocean system

The surface mixed layer (ML) in the Mediterranean Sea is a well stratified domain characterized by low macro-nutrient and low chlorophyll content, during almost 6 months of the year. Nutrient dynamics in the ML depend on allochthonous inputs, through atmospheric deposition and on biological recycling. Here we characterize the biogeochemical cycling of N in the ML by combining simultaneous in situ measurements of atmospheric deposition, nutrients, hydrological conditions, primary production, heterotrophic prokaryotic production, N2 fixation and leucine aminopeptidase activity. The measurements were conducted along a 4300 km transect across the central and western open Mediterranean Sea in spring 2017. Dry deposition was measured on a continuous basis while two wet deposition events were sampled, one in the Ionian Sea and one in the Algerian basin. Along the transect, N budgets were computed to compare sources and sinks of N in the mixed layer. On average, phytoplankton N demand was 2.9 fold higher (range 1.5–8.1) than heterotrophic prokaryotic N demand. In situ leucine aminopeptidase activity contributed from 14 to 66 % of heterotrophic prokaryotic N demand, and N2 fixation rate represented 1 to 4.5 % of the phytoplankton N demand. Dry atmospheric deposition of inorganic nitrogen, estimated from dry deposition of (nitrate + ammonium) in aerosols, was higher than N2 fixation rates in the ML (on average 4.8 fold). The dry atmospheric input of inorganic N represented a highly variable proportion of biological N demand in the ML, 10–82 % for heterotrophic prokaryotes and 1–30 % for phytoplankton. Stations visited for several days allowed following the evolution of biogeochemical properties in the ML and within the nutrient depleted layers. At the site in the Algerian Basin and on a basis of high frequency sampling of CTD casts before and after a wet dust deposition event, different scenarios were considered to explain a delayed appearance of peaks in dissolved inorganic phosphate in comparison to nitrate within the ML. After the rain, nitrate was higher in the ML than in the nutrient depleted layer below. Estimates of nutrient transfer from the ML to the nutrient depleted layer could explain 1/3 of the nitrate fate out of the ML. Luxury consumption of P by heterotrophic prokaryotes, further transferred in the microbial food web, and remineralized by grazers, is one explanation for the delayed phosphate peak of DIP. The second explanation is a transfer from ML to the nutrient depleted layer below through adsorption/desorption processes on particles. Phytoplankton did not benefit directly from atmospheric inputs in the ML, probably due to a high competition with heterotrophic prokaryotes, also limited by N and P availability at the time of this study. Primary producers, in competition for nutrients with heterotrophic prokaryotes, decreased their production after the rain, recovering their initial state of activity after 2 days lag in the vicinity of the deep chlorophyll maximum layer.

Linking extracellular enzymes to phylogeny indicates a predominantly particle-associated lifestyle of deep-sea prokaryotes

Heterotrophic prokaryotes express extracellular hydrolytic enzymes to cleave large organic molecules before taking up the hydrolyzed products. According to foraging theory, extracellular enzymes should be cell associated in dilute systems such as deep sea habitats, but secreted into the surrounding medium in diffusion-limited systems. However, extracellular enzymes in the deep sea are found mainly dissolved in ambient water rather than cell associated. In order to resolve this paradox, we conducted a global survey of peptidases and carbohydrate-active enzymes (CAZymes), two key enzyme groups initiating organic matter assimilation, in an integrated metagenomics, metatranscriptomics, and metaproteomics approach. The abundance, percentage, and diversity of genes encoding secretory processes, i.e., dissolved enzymes, consistently increased from epipelagic to bathypelagic waters, indicating that organic matter cleavage, and hence prokaryotic metabolism, is mediated mainly by particle-associated prokaryotes releasing their extracellular enzymes into diffusion-limited particles in the bathypelagic realm.

Biological lability of Dissolved Organic Matter released by phytoplankton

<p>Phytoplankton is the primary source of Dissolved Organic Matter (DOM) to the oceans. DOM is mainly released by extracellular exudation and used by heterotrophic prokaryotes to synthesise biomass and recycle inorganic nutrients. DOM released by phytoplankton is mainly composed by carbohydrates, proteins and lipids that are thought to be labile and by humic substances that are thought to be recalcitrant and thus resistant to bacterial degradation. There are a lot of uncertainties regarding the biological lability of exudates and the role of DOM released by phytoplankton in the marine carbon cycle. In this study, cultures of the diatom P. tricornutum were produced under axenic conditions and Dissolved Organic Carbon (DOC) concentration, Excitation-Emission matrices (EEMs) and cell density were measured with time in order to follow the release of DOM during the different growth phases. Exudates were then inoculated with a marine microbial community for 24 days, DOC removal and FDOM transformation were followed with time in the exudates and in the permeate (< 3k Da; Low Molecular Weight, LMW) and retentate (> 3k Da; High Molecular Weight, HMW) fractions. Heterotrophic prokaryotes abundance was also followed during the incubations. Our results show that ~75% of the total DOC pool was LMW. After 24 days, 28% of the initial DOC pool was removed. Fluorescence indicate high lability of protein-like molecules and degradation of bigger proteins into smaller peptides before their removal. The production of humic-like and flavin-like substances was also observed.</p><p> </p>