Nutritional importance of benthic bacteria for deep-sea nematodes from the Arctic ice margin: Results of an isotope tracer experiment

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Present nitrogen and carbon dynamics in the Scheldt estuary using a novel 1-D model

A 1-D, pelagic, reactive-transport model of a completely mixed, turbid, heterotrophic estuary – the Scheldt estuary – is presented. The model resolves major carbon and nitrogen species and oxygen, as well as pH. The model features two organic matter degradation pathways, oxic mineralisation and denitrification, and includes primary production as well as nitrification. Apart from advective-dispersive transport along the length axis, the model also describes O<sub>2</sub>, CO<sub>2</sub>, and N<sub>2</sub> air-water exchange. The aim of this study is to present a model which is as simple as possible but still fits the data well enough to determine the fate and turnover of nutrients entering the estuary and their spatial patterns in the years 2000 to 2004. Nitrification is identified as one of the most important processes in the estuary, consuming a comparable amount of oxygen as oxic mineralisation (1.7 Gmol O<sub>2</sub> y<sup>−1</sup> vs. 2.7 Gmol O<sub>2</sub> y<sup>−1</sup>). About 10% of the 2.5 Gmol of nitrogen entering the estuary per year is lost within the estuary due to denitrification. Nitrogen and carbon budgets are compared to budgets from the seventies and eighties, showing that nitrification activity has peaked in the eighties, while denitrification steadily declined. Our model estimates an average CO<sub>2</sub> emission of 3.3 Gmol y<sup>−1</sup> in the years 2001 to 2004, which is a comparatively low estimate in the context of previous estimates of CO<sub>2</sub> export from the Scheldt estuary

Balance of assimilative and dissimilative nitrogen processes in a diatom-rich tidal flat sediment

Tidal flat sediments are subject to repetitive mixing and resuspension events. In a short-term (24 h) <sup>15</sup>N-labelling experiment, we investigated reactive nitrogen cycling in a tidal flat sediment following an experimentally induced resuspension event. We focused on (a) the relative importance of assimilatory versus dissimilatory processes and (b) the role of benthic microalgae therein. <sup>15</sup>N-labelled substrate was added to homogenized sediment, and <sup>15</sup>N was subsequently traced into sediment and dissolved inorganic nitrogen (DIN) pools. Integration of results in a N-cycle model allowed us to quantify the proportion of major assimilatory and dissimilatory processes in the sediment. <br><br> Upon sediment disturbance, rates of dissimilatory processes like nitrification and denitrification were very high, but declined rapidly towards a steady state. Once this was reached, the balance between assimilation and dissimilation in this tidal mudflat was mainly dependent on the nitrogen source: nitrate was utilized almost exclusively dissimilatory via denitrification, whereas ammonium was rapidly assimilated, with about a quarter of this assimilation due to benthic microalgae (BMA). Benthic microalgae significantly affected the nitrogen recycling balance in sediments, because in the absence of BMA activity the recovering sediment turned from a net ammonium sink to a net source. <br><br> The driving mechanisms for assimilation or dissimilation accordingly appear to be ruled to a large extent by external physical forcing, with the entire system being capable of rapid shifts following environmental changes. Assimilatory pathways gain importance under stable conditions, with a substantial contribution of BMA to total assimilation

A Bayesian compositional estimator for microbial taxonomy based on biomarkers

Determination of microbial taxonomy based on lipid or pigment spectra requires use of a compositional estimator. We present a new approach based on Bayesian inference and an implementation in the open software platform R. The Bayesian Compositional Estimator (BCE) aims not only to obtain a maximum likelihood solution, but also to provide a complete estimate of the taxonomic composition, including probability distributions and dependencies between estimated values. BCE results are compared with those obtained with CHEMTAX. The BCE has not only a similar accuracy, but also extracts more information from the data, the most obvious being standard deviation and covariance estimates

Potential uptake of dissolved organic matter by seagrasses and macroalgae

Dissolved organic nitrogen (DON) acts as a large reservoir of fixed nitrogen. Whereas DON utilization is common in the microbial community, little is known about utilization by macrophytes. We investigated the ability of the coexisting temperate marine macrophytes Zostera noltii, Cymodocea nodosa, and Caulerpa prolifera to take up nitrogen and carbon from small organic substrates of different molecular complexities (urea, glycine, L-leucine, and L-phenylalanine) and from dissolved organic matter (DOM) derived from algal and bacterial cultures (substrates with a complex composition). In addition to inorganic nitrogen, nitrogen from small organic substrates could be taken up in significant amounts by all macrophytes. Substrate uptake by the aboveground tissue differed from that of the belowground tissue. No relationships between carbon and nitrogen uptake of small organics were found. The preference for individual organic substrates was related to their structural complexity and C:N ratio. Uptake of algae-derived organic nitrogen was of similar magnitude as inorganic nitrogen, and was preferred over bacteria-derived nitrogen. These results add to the growing evidence that direct or quick indirect DON utilization may be more widespread among aquatic macrophytes than traditionally thought.This research was supported by the regional government of Andalusia project FUNDIV (P07-RNM-2516), the Spanish Project CTM2008-00012/MAR, a European Reintegration Grant (MERG-CT-2007-205675), a travel grant from Schure-Beijerinck-Popping Fund (SBP/JK/2007-32) and the Netherlands Organization for Scientific Research. Thanks to Fidel Echevarrìa Navas (Director of CACYTMAR) for granting us access to facilities, and to Bas Koutstaal for helping with sample processing. We also thank the anonymous reviewers for their valuable comments which significantly improved this manuscript