DNA metabarcoding unveils multiscale trophic variation in a widespread coastal opportunist

A thorough understanding of ecological networks relies on comprehensive information on trophic relationships among species. Since unpicking the diet of many organisms is unattainable using traditional morphology‐based approaches, the application of high‐throughput sequencing methods represents a rapid and powerful way forward. Here, we assessed the application of DNA metabarcoding with nearly universal primers for the mitochondrial marker cytochrome c oxidase I in defining the trophic ecology of adult brown shrimp, Crangon crangon, in six European estuaries. The exact trophic role of this abundant and widespread coastal benthic species is somewhat controversial, while information on geographical variation remains scant. Results revealed a highly opportunistic behaviour. Shrimp stomach contents contained hundreds of taxa (>1,000 molecular operational taxonomic units), of which 291 were identified as distinct species, belonging to 35 phyla. Only twenty ascertained species had a mean relative abundance of more than 0.5%. Predominant species included other abundant coastal and estuarine taxa, including the shore crab Carcinus maenas and the amphipod Corophium volutator. Jacobs’ selectivity index estimates based on DNA extracted from both shrimp stomachs and sediment samples were used to assess the shrimp's trophic niche indicating a generalist diet, dominated by crustaceans, polychaetes and fish. Spatial variation in diet composition, at regional and local scales, confirmed the highly flexible nature of this trophic opportunist. Furthermore, the detection of a prevalent, possibly endoparasitic fungus (Purpureocillium lilacinum) in the shrimp's stomach demonstrates the wide range of questions that can be addressed using metabarcoding, towards a more robust reconstruction of ecological networks.     

Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring

Given their positioning and biological productivity, estuaries have long represented key providers of ecosystem services and consequently remain under remarkable pressure from numerous forms of anthropogenic impact. The monitoring of fish communities in space and time is one of the most widespread and established approaches to assess the ecological status of estuaries and other coastal habitats, but traditional fish surveys are invasive, costly, labour intensive and highly selective. Recently, the application of metabarcoding techniques, on either sediment or aqueous environmental DNA, has rapidly gained popularity. Here, we evaluate the application of a novel, high‐throughput DNA‐based monitoring tool to assess fish diversity, based on the analysis of the gut contents of a generalist predator/scavenger, the European brown shrimp, Crangon crangon. Sediment and shrimp samples were collected from eight European estuaries, and DNA metabarcoding (using both 12S and COI markers) was carried out to infer fish assemblage composition. We detected 32 teleost species (16 and 20, for 12S and COI, respectively). Twice as many species were recovered using metabarcoding than by traditional net surveys. By comparing and interweaving trophic, environmental DNA and traditional survey‐based techniques, we show that the DNA‐assisted gut content analysis of a ubiquitous, easily accessible, generalist species may serve as a powerful, rapid and cost‐effective tool for large‐scale, routine estuarine biodiversity monitoring.     

Effect of linolenate on photosynthesis by intact spinach chloroplasts I. Inhibition of orthophosphate uptake and of 3-P-glyceraldehyde efflux across the chloroplast envelope

Linolenic acid (C_18:3) inhibited photosynthesis by intact spinachchloroplasts. This inhibition was due neither to a lack of NADPHin chloroplasts nor to a direct inhibition of the enzyme activitiesin the Calvin-Benson cycle. Linolenate inhibited CO₂ fixationand oxygen evolution more effectively than NADP⁺ photoreductionbut did not inhibit the activity of several key enzymes of theCalvin cycle. Linolenate inhibited phosphate influx and 3-phosphoglyceraldehydeefflux across the chloroplast envelope. A hypothesis explainingthe inhibition of photosynthesis by linolenate is presented. ¹ This work is part of a doctoral program which is carried outby L. Mv? Akamba in this laboratory. (Received October 14, 1978; )     

Tuning of DnaK chaperone action by nonnative protein sensor DnaJ and thermosensor GrpE

DnaK, an Hsp70 molecular chaperone, processes its substrates in an ATP-driven cycle, which is controlled by the co-chaperones DnaJ and GrpE. The kinetic analysis of substrate binding and release has as yet been limited to fluorescence-labeled peptides. Here, we report a comprehensive kinetic analysis of the chaperone action with protein substrates. The kinetic partitioning of the (ATP x DnaK) x substrate complexes between dissociation and conversion into stable (ADP x DnaK) x substrate complexes is determined by DnaJ. In the case of substrates that allow the formation of ternary (ATP x DnaK) x substrate x DnaJ complexes, the cis-effect of DnaJ markedly accelerates ATP hydrolysis. This triage mechanism efficiently selects from the (ATP x DnaK) x substrate complexes those to be processed in the chaperone cycle; at 45 degrees C, the fraction of protein complexes fed into the cycle is 20 times higher than that of peptide complexes. The thermosensor effect of the ADP/ATP exchange factor GrpE retards the release of substrate from the cycle at higher temperatures; the fraction of total DnaK in stable (ADP x DnaK) x substrate complexes is 2 times higher at 45 degrees C than at 25 degrees C. Monitoring the cellular situation by DnaJ as nonnative protein sensor and GrpE as thermosensor thus directly adapts the operational mode of the DnaK system to heat shock conditions.     

A single and continuous spectrophotometric assay for various lipolytic enzymes, using natural, non-labelled lipid substrates

A rapid, continuous spectrophotometric assay for measuring the amount and activity of several lipolytic enzymes is described. It is based on the metachromatic properties of the cationic dye safranine, and makes use of the fact that an adequate combination of a lipolytic enzyme with one of its substrates leads to a change in the net negative charge at the lipid/water interface, which is monitored by the absorbance change of safranine. Utilizing this method, most lipolytic enzymes can be detected in very low amounts (milliunit or less) in about 1 min without employing radiolabelled lipids or synthetic lipid analogues. Over a wide range of enzyme concentrations, there is a good linearity between the initial hydrolysis rate (determination by the safranine method) and the amount of enzyme. The versatility of the assay is illustrated by examples showing how phospholipase A2, triacylglycerol hydrolase, phospholipase D or phospholipase C (either general or phosphatidylinositol-specific) activities can be detected, either separately or sequentially. Due to its high sensitivity, simplicity, and rapidity, this assay should find its main application in monitoring column effluents during the purification steps of lipolytic enzymes.     

Factors modulating cottongrass seedling growth stimulation to enhanced nitrogen and carbon dioxide: compensatory tradeoffs in leaf dynamics and allocation to meet potassium-limited growth

Eriophorum vaginatum is a characteristic species of northern peatlands and a keystone plant for cutover bog restoration. Understanding the factors affecting E. vaginatum seedling establishment (i.e. growth dynamics and allocation) under global change has practical implications for the management of abandoned mined bogs and restoration of their C-sequestration function. We studied the responses of leaf dynamics, above- and belowground biomass production of establishing seedlings to elevated CO₂ and N. We hypothesised that nutrient factors such as limitation shifts or dilutions would modulate growth stimulation. Elevated CO₂ did not affect biomass, but increased the number of young leaves in spring (+400 %), and the plant vitality (i.e. number of green leaves/total number of leaves) (+3 %), both of which were negatively correlated to [K⁺] in surface porewater, suggesting a K-limited production of young leaves. Nutrient ratios in green leaves indicated either N and K co-limitation or K limitation. N addition enhanced the number of tillers (+38 %), green leaves (+18 %), aboveground and belowground biomass (+99, +61 %), leaf mass-to-length ratio (+28 %), and reduced the leaf turnover (?32 %). N addition enhanced N availability and decreased [K⁺] in spring surface porewater. Increased tiller and leaf production in July were associated with a doubling in [K⁺] in surface porewater suggesting that under enhanced N production is K driven. Both experiments illustrate the importance of tradeoffs in E. vaginatum growth between: (1) producing tillers and generating new leaves, (2) maintaining adult leaves and initiating new ones, and (3) investing in basal parts (corms) for storage or in root growth for greater K uptake. The K concentration in surface porewater is thus the single most important factor controlling the growth of E. vaginatum seedlings in the regeneration of selected cutover bogs.     

Calmodulin is not involved in the regulation of exogenous NADH oxidation by plant mitochondria

The oxidation of exogenous NADH by mitochondria from potato ( Solanum tuberosum L., cv. Bintje) tubers, measured with different electron acceptors, oxygen, cytochrome c , duroquinone and ubiquinone 1, was greatly enhanced under high salt conditions compared to low salt conditions, confirming the stimulatory effect of electrostatic screeening of negative membrane charges by cations. In addition to this nonspecific stimulation, the oxidation of exogenous NADH showed a specific dependence on Ca²⁺. Results presented here suggest that calmodulin was not directly involved in the regulation of exogenous NADH oxidation by potato mitochondria: (1) Calmodulin antagonists were found to inhibit electron flow at several sites in a nonspecific manner. (2) Using a phenothiazine-Affi Gel column, it was not possible to demonstrate the presence of calmodulin in Triton X-100 solubilized mitochondria. (3) Fractions eluted from a calmodulin-Sepharose column with EGTA [ethyleneglycolbis (β-aminoethylether)-N, N, N', N'-tetraacetic acid] did not display any activity related to mitochondrial electron transport, suggesting that NADH dehydrogenase had no specific affinity for calmodulin. The possible indirect involvement of calmodulin in the regulation of exogenous NADH oxidation by Ca²⁺ is discussed.     

Development of Oat Prothylakoids into Thylakoids during Greening Does Not Change Transmembrane Galactolipid Asymmetry but Preserves the Thylakoid Bilayer

The lipase from Rhizopus arrhizus and the lipolytic acyl hydrolase from potato tubers have been used to determine the transmembrane distribution of monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) in prothylakoids and thylakoids from oat (Avena sativa). Both galactolipids were found to be asymmetrically distributed. The molar outside/inside distribution was 70 ± 8/30 ± 8 for MGDG and 10 ± 4/90 ± 4 for DGDG in the prothylakoid membrane. Mature thylakoids presented a similar distribution, i.e. 63 ± 4/37 ± 4 for MGDG and 12 ± 3/88 ± 3 for DGDG. This distribution has been assessed under a variety of different conditions, namely (a) in media favoring thylakoid stacking or unstacking and inducing various membrane surface potentials, (b) in the presence of defatted bovine serum albumin which removed free fatty acids and partially lyso-galactolipids, (c) under various temperature conditions which resulted in different hydrolysis rates and degrees of fluidity of the membrane, and (d) in the presence of different enzyme concentrations which influenced the hydrolysis rate. The above distribution was found to be independent of the type of conditions used. Nonbilayer forming/bilayer forming lipid ratios suggest that both monolayers of the prothylakoid and the inner monolayer of oat thylakoid membranes should display lamellar structures (e.g. ratios <2.5). In contrast the outer monolayer of the thylakoid membrane should display non-lamellar configurations (e.g. ratio >2.5). Thus, it is concluded that the incorporation of chlorophyll-protein complexes into the nascent thylakoid membrane modifies neither the galactolipid nor the phospholipid transmembrane distribution. However, these complexes appear to be crucial to preserve a bilayer configuration to the greening membrane which, otherwise, would adopt nonlamellar structures. The possible origin of galactolipid transversal asymmetry which appears very early during the biogenesis of oat thylakoid membranes is discussed.