Jack J. Middelburg

Archaeal nitrification in the ocean

Marine Crenarchaeota are the most abundant single group of prokaryotes in the ocean, but their physiology and role in marine biogeochemical cycles are unknown. Recently, a member of this clade was isolated from a sea aquarium and shown to be capable of nitrification, tentatively suggesting that Crenarchaeota may play a role in the oceanic nitrogen cycle. We enriched a crenarchaeote from North Sea water and showed that its abundance, and not that of bacteria, correlates with ammonium oxidation to nitrite. A time series study in the North Sea revealed that the abundance of the gene encoding for the archaeal ammonia monooxygenase alfa subunit (amoA) is correlated with a decline in ammonium concentrations and with the abundance of Crenarchaeota. Remarkably, the archaeal amoA abundance was 1–2 orders of magnitude higher than those of bacterial nitrifiers, which are commonly thought to mediate the oxidation of ammonium to nitrite in marine environments. Analysis of Atlantic waters of the upper 1,000 m, where most of the ammonium regeneration and oxidation takes place, showed that crenarchaeotal amoA copy numbers are also 1–3 orders of magnitude higher than those of bacterial amoA. Our data thus suggest a major role for Archaea in oceanic nitrification.

Impacts of Atmospheric Anthropogenic Nitrogen on the Open Ocean

Increasing quantities of atmospheric anthropogenic fixed nitrogen entering the open ocean could account for up to about a third of the oceans external (nonrecycled) nitrogen supply and up to ∼3% of the annual new marine biological production, ∼0.3 petagram of carbon per year. This input could account for the production of up to ∼1.6 teragrams of nitrous oxide (N2O) per year. Although ∼10% of the oceans drawdown of atmospheric anthropogenic carbon dioxide may result from this atmospheric nitrogen fertilization, leading to a decrease in radiative forcing, up to about two-thirds of this amount may be offset by the increase in N2O emissions. The effects of increasing atmospheric nitrogen deposition are expected to continue to grow in the future.

Major role of marine vegetation on the oceanic carbon cycle

HAL is a multi-disciplinary open access archive for the deposit and dissemination of scientific research documents, whether they are published or not. The documents may come from teaching and research institutions in France or abroad, or from public or private research centers. L’archive ouverte pluridisciplinaire HAL, est destinée au dépôt et à la diffusion de documents scientifiques de niveau recherche, publiés ou non, émanant des établissements d’enseignement et de recherche français ou étrangers, des laboratoires publics ou privés. Major role of marine vegetation on the oceanic carbon cycle C. M. Duarte, J. J. Middelburg, N. Caraco

Mangrove production and carbon sinks: A revision of global budget estimates.

results in a conservative estimate of 218 ± 72 Tg C a 1 . When using the best available estimates of various carbon sinks (organic carbon export, sediment burial, and mineralization), it appears that >50% of the carbon fixed by mangrove vegetation is unaccounted for. This unaccounted carbon sink is conservatively estimated at 112 ± 85 Tg C a 1 , equivalent in magnitude to 30–40% of the global riverine organic carbon input to the coastal zone. Our analysis suggests that mineralization is severely underestimated, and that the majority of carbon export from mangroves to adjacent waters occurs as dissolved inorganic carbon (DIC). CO2 efflux from sediments and creek waters and tidal export of DIC appear to be the major sinks. These processes are quantitatively comparable in magnitude to the unaccounted carbon sink in current budgets, but are not yet adequately constrained with the limited published data available so far.

Stable isotopes and biomarkers in microbial ecology.

The use of biomarkers in combination with stable isotope analysis is a new approach in microbial ecology and a number of papers on a variety of subjects have appeared. We will first discuss the techniques for analysing stable isotopes in biomarkers, primarily gas chromatography-combustion-isotope ratio mass spectrometry, and then describe a number of applications in microbial ecology based on 13C. Natural abundance isotope ratios of biomarkers can be used to study organic matter sources utilised by microorganisms in complex ecosystems and for identifying specific groups of bacteria like methanotrophs. Addition of labelled substrates in combination with biomarker analysis enables direct identification of microbes involved in specific processes and also allows for the incorporation of bacteria into food web studies. We believe that the full potential of the technique in microbial ecology has just started to be exploited.

A simple rate model for organic matter decomposition in marine sediments

Abstract A model is presented for the decomposition of organic matter in marine sediments. The model considers the organic matter as a whole. In this model the first-order rate parameters (k) gradually decrease with time (t) according to logk = −0.95 logt − 0.81 (N= 140; r = 0.987). This equation is found to be valid over eight orders of magnitude and is based on organic carbon versus depth profiles of well-dated cores and laboratory experiments. The predicted continuous decrease in the reactivity of organic matter is consistent with multi-G models and in situ measurements of sulphate reduction. Although all organic carbon versus depth profiles follow the same reactivity decrease with time, their reactivity at the sediment-water interface (i.e., “apparent initial age”) is different. Apparent initial ages calculated on the basis of various experiments and field measurements show consistent trends.

Rapid analysis of organic carbon and nitrogen in particulate materials

Abstract A method for rapid determination of organic carbon and nitrogen in natural particulate materials is described. The procedure allows the determination of 60 samples per day by a single analyst. It involves the determination of carbon and nitrogen using an automatic CN-analyzer following the partitioning of inorganic and organic carbon phase by acidification with 25% HCl in situ within silver sample cups. The technique eliminates reweighing procedures, losses of organic and inorganic compounds (except carbonates and sulphides) and is free from matrix interferences. Extensive testing and application showed long-term precisions for organic carbon and nitrogen of about 3%. The accuracy is excellent, irrespective of the calcium carbonate content of the sample.

Chemical processes affecting the mobility of major, minor, and trace elements during weathering of granitic rocks

Abstract The behaviour of 38 major and trace elements as well as changes in the mineralogy have been examined in 10 weathering profiles developing on some Portuguese granitic rocks. Element mobilities are calculated from geochemical data normalized with respect to Ti in the fresh parent rock. Chemical elements are divided into two groups, immobile and mobile, on the basis of their geochemical distribution during weathering. Elements that are immobile during weathering are Zr, Hf, Fe, Al, Th, Nb, Sc and the REE. Very mobile are Ca, Na, P, K, Sr, Ba, Rb, Mg and Si. Mobile elements are derived mainly from leachable minerals such as feldspars, micas and apatites, whereas immobile elements are either concentrated in resistate phases or strongly adsorbed by secondary minerals. The geochemical behaviour of Mn, Cr, V, Fe and Ce is very dependent on redox conditions. Redox transformations of these elements can be used to set limits on the oxidation state of a weathering suite. The REE are mobilized or fractionated during late stages of weathering, but not during moderate stages of weathering. This fractionation is caused by selective leaching of rocks composed of both stable and unstable minerals containing REE.

A model of early diagenetic processes from the shelf to abyssal depths

Abstract We present a numerical model of sedimentary early diagenetic processes that includes oxic and anoxic mineralization. The model belongs to the new wave of early diagenesis models that account for depth-dependent bioturbation and porosity profiles; it can be used both for calculating steady-state conditions and transient simulation. It was developed to reproduce the cycling of carbon, oxygen, and nitrogen along the ocean margin; it resolves the sediment-depth profiles of carbon, oxygen, nitrate, ammonium, and other reduced substances. Organic carbon is modeled as two degradable fractions with different first-order degradation rates and nitrogen:carbon ratios, to account for the decreasing reactivity and N/C ratio of the organic matter with depth into the sediment. The consumption of oxygen and nitrate as terminal electron acceptors is explicitly modeled, and mineralization is limited both by carbon (first order kinetics) and by oxidant availability (Michaelis-Menten type kinetics). Nitrification and oxic mineralization are decoupled, which allows the description of ammonium profiles. Mineralization processes using other oxidants (manganese oxides, iron oxides, sulphate) are lumped into one process, where degradation is only carbon limited; the terminal electron acceptors are not explicitly modeled, only the production of reduced substances is described. These substances are in part permanently removed (e.g., pyrite formation below the bioturbation zone) and partly diffuse towards the oxic layer where they react with oxygen. The values of several parameters were constrained using literature-derived relationships. The model was calibrated on a dataset obtained from the literature, which relates the magnitude of the different pathways to total organic carbon mineralization. The influence of carbon flux, bioturbation, sedimentation rate, bottomwater concentrations of oxygen, and nitrate and carbon degradability on the different mineralization pathways is examined. The relative contribution of the oxic mineralization in the model is significantly depressed under high organic flux, under low bottomwater oxygen conditions and when the bioturbation increases; higher carbon degradability has only a small positive effect, while sedimentation rate is relatively unimportant. Denitrification is mainly influenced by the nitrate concentration in the overlying bottomwater.

Sediment organic carbon burial in agriculturally eutrophic impoundments over the last century

The OC buried in these lakes originates in both autochthonous and allochthonous production. These analyses suggest that OC sequestration in moderate to large impoundments may be double the rate assumed in previous analyses. Extrapolation suggests that they may bury 4 times as much carbon (C) as the world’s oceans. The world’s farm ponds alone may bury more OC than the oceans and 33% as much as the world’s rivers deliver to the sea.