Microbial manganese and sulfate reduction in Black Sea shelf sediments

The microbial ecology of anaerobic carbon oxidation processes was investigated in Black Sea shelf sediments from mid-shelf with well-oxygenated bottom water to the oxic-anoxic chemocline at the shelf-break. At all stations, organic carbon (Corg) oxidation rates were rapidly attenuated with depth in anoxically incubated sediment. Dissimilatory Mn reduction was the most important terminal electron-accepting process in the active surface layer to a depth of ∼1 cm, while SO42− reduction accounted for the entire Corg oxidation below. Manganese reduction was supported by moderately high Mn oxide concentrations. A contribution from microbial Fe reduction could not be discerned, and the process was not stimulated by addition of ferrihydrite. Manganese reduction resulted in carbonate precipitation, which complicated the quantification of Corg oxidation rates. The relative contribution of Mn reduction to Corg oxidation in the anaerobic incubations was 25 to 73% at the stations with oxic bottom water. In situ, where Mn reduction must compete with oxygen respiration, the contribution of the process will vary in response to fluctuations in bottom water oxygen concentrations. Total bacterial numbers as well as the detection frequency of bacteria with fluorescent in situ hybridization scaled to the mineralization rates. Most-probable-number enumerations yielded up to 105 cells of acetate-oxidizing Mn-reducing bacteria (MnRB) cm−3, while counts of Fe reducers were <102 cm−3. At two stations, organisms affiliated with Arcobacter were the only types identified from 16S rRNA clone libraries from the highest positive MPN dilutions for MnRB. At the third station, a clone type affiliated with Pelobacter was also observed. Our results delineate a niche for dissimilatory Mn-reducing bacteria in sediments with Mn oxide concentrations greater than ∼10 μmol cm−3 and indicate that bacteria that are specialized in Mn reduction, rather than known Mn and Fe reducers, are important in this niche

Pathways of carbon oxidation in continental margin sediments off central Chile

Rates and oxidative pathways of organic carbon mineralization were determined in sediments at six stations on the shelf and slope off Concepcion Bay at 36.5 degrees S. The depth distribution of C oxidation rates was determined to 10 cm from accumulation of dissolved inorganic C in 1-5-d incubations. Pathways of C oxidation were inferred from the depth distributions of the potential oxidants (O-2, NO3-, and oxides of Mn and Fe) and from directly determined rates of SO42- reduction. The study area is characterized by intense seasonal upwelling, and during sampling in late summer the bottom water over the shelf was rich in NO3- and depleted of O-2. Sediments at the four shelf stations were covered by mats of filamentous bacteria of the genera Thioploca and Beggiatoa. Carbon oxidation rates at these sites were extremely high near the sediment surface (> 3 mu mol cm(-3) d(-1)) and decreased exponentially with depth. The process was entirely coupled to SO42- reduction. At the two slope stations where bottom-water O-2 was > 100 mu M, C oxidation rates were 10-fold lower and varied less with depth; C oxidation coupled to the reduction of O-2, NO3-, and Mn oxides combined to yield an estimated 15% of the total C oxidation between 0 and 10 cm. Carbon oxidation through Fe reduction contributed a further 12-29% of the depth-integrated rate, while the remainder of C oxidation was through SO42- reduction. The depth distribution of Fe reduction agreed well with the distribution of poorly crystalline Fe oxides, and as this pool decreased with depth, the importance of SO42- reduction increased. The results point to a general importance of Fe reduction in C oxidation in continental margin sediments. At the shelf stations, Fe reduction was mainly coupled to oxidation of reduced S. These sediments were generally H2S-free despite high SO42- reduction rates, and precipitation of Fe sulfides dominated H2S scavenging during the incubations. A large NO3- pool was associated with the Thioploca, and the shelf sediments were thus enriched in NO3- relative to the bottom water, with maximum concentrations of 3 mu mol cm(-3). The NO3- was consumed during our sediment incubations, but no effects on either C or S cycles could be discerned

Vertical segregation among pathways mediating nitrogen loss (N2 and N2O production) across the oxygen gradient in a coastal upwelling ecosystem

Indexación: ScopusThe upwelling system off central Chile (36.5 S) is seasonally subjected to oxygen (O2)-deficient waters, with a strong vertical gradient in O2 (from oxic to anoxic conditions) that spans a few metres (30-50€m interval) over the shelf. This condition inhibits and/or stimulates processes involved in nitrogen (N) removal (e.g. anammox, denitrification, and nitrification). During austral spring (September 2013) and summer (January 2014), the main pathways involved in N loss and its speciation, in the form of N2 and/or N2O, were studied using 15N-tracer incubations, inhibitor assays, and the natural abundance of nitrate isotopes along with hydrographic information. Incubations were developed using water retrieved from the oxycline (25€m depth) and bottom waters (85€m depth) over the continental shelf off Concepción, Chile. Results of 15N-labelled incubations revealed higher N removal activity during the austral summer, with denitrification as the dominant N2-producing pathway, which occurred together with anammox at all times. Interestingly, in both spring and summer maximum potential N removal rates were observed in the oxycline, where a greater availability of oxygen was observed (maximum O2 fluctuation between 270 and 40€μmol€L'1) relative to the hypoxic bottom waters ( < €20€μmol€O2€L'1). Different pathways were responsible for N2O produced in the oxycline and bottom waters, with ammonium oxidation and dissimilatory nitrite reduction, respectively, as the main source processes. Ammonium produced by dissimilatory nitrite reduction to ammonium (DNiRA) could sustain both anammox and nitrification rates, including the ammonium utilized for N2O production. The temporal and vertical variability of /15N-NO3' confirms that multiple N-cycling processes are modulating the isotopic nitrate composition over the shelf off central Chile during spring and summer. N removal processes in this coastal system appear to be related to the availability and distribution of oxygen and particles, which are a source of organic matter and the fuel for the production of other electron donors (i.e. ammonium) and acceptors (i.e. nitrate and nitrite) after its remineralization. These results highlight the links between several pathways involved in N loss. They also establish that different mechanisms supported by alternative N substrates are responsible for substantial accumulation of N2O, which are frequently observed as hotspots in the oxycline and bottom waters. Considering the extreme variation in oxygen observed in several coastal upwelling systems, these findings could help to understand the ecological and biogeochemical implications due to global warming where intensification and/or expansion of the oceanic OMZs is projected.https://www.biogeosciences.net/14/4795/2017

Dissimilatory nitrate reduction to ammonium coupled to Fe(II) oxidation in sediments of a periodically hypoxic estuary

Estuarine sediments are critical for the remediation of large amounts of anthropogenic nitrogen (N) loading via production of N₂ from nitrate by denitrification. However, nitrate is also recycled within sediments by dissimilatory nitrate reduction to ammonium (DNRA). Understanding the factors that influence the balance between denitrification and DNRA is thus crucial to constraining coastal N budgets. A potentially important factor is the availability of different electron donors (organic carbon, reduced iron and sulfur). Both denitrification and DNRA may be linked to ferrous iron oxidation, however the contribution of Fe(II)-fueled nitrate reduction in natural environments is practically unknown. This study investigated how nitrate-dependent Fe²⁺ oxidation affects the partitioning between nitrate reduction pathways using ¹⁵N-tracing methods in sediments along the salinity gradient of the periodically hypoxic Yarra River estuary, Australia. Increased dissolved Fe²⁺ availability resulted in significant enhancement of DNRA rates from around 10–20% total nitrate reduction in control incubations to over 40% in those with additional Fe²⁺, at several sites. Increases in DNRA at some locations were accompanied by reductions in denitrification. Significant correlations were observed between Fe²⁺ oxidation and DNRA rates, with reaction ratios corresponding to the stoichiometry of Fe²⁺-dependent DNRA. Our results provide experimental evidence for a direct coupling of DNRA to Fe²⁺ oxidation across an estuarine gradient, suggesting that Fe²⁺ availability may exert substantial control on the balance between retention and removal of bioavailable N. Thus, DNRA linked to Fe²⁺ oxidation may be of general importance to environments with Fe-rich sediments

Challenges in using allylthiourea and chlorate as specific nitrification inhibitors

Allylthiourea (ATU) and chlorate (ClO 3 −) are often used to selectively inhibit nitritation and nitratation. In this work we identified challenges with use of these compounds in inhibitory assays with filter material from a biological rapid sand filter for groundwater treatment. Inhibition was investigated in continuous-flow lab-scale columns, packed with filter material from a full-scale filter and supplied with NH 4 + or NO 2 −. ATU concentrations of 0.1–0.5 mM interfered with the indophenol blue method for NH 4 + quantification leading to underestimation of the measured NH 4 + concentration. Interference was stronger at higher ATU levels and resulted in no NH 4 + detection at 0.5 mM ATU. ClO 3 − at typical concentrations for inhibition assays (1–10 mM) inhibited nitratation by less than 6%, while nitritation was instead inhibited by 91% when NH 4 + was supplied. On the other hand, nitratation was inhibited by 67–71% at 10–20 mM ClO 3 − when NO 2 − was supplied, suggesting significant nitratation inhibition at higher NO 2 − concentrations. No chlorite (ClO 2 −) was detected in the effluent, and thus we could not confirm that nitritation inhibition was caused by ClO 3 − reduction to ClO 2 −. In conclusion, ATU and ClO 3 − should be used with caution in inhibition assays, because analytical interference and poor selectivity for the targeted process may affect the experimental outcome and compromise result interpretation. </p

Seasonal carbon cycling in a Greenlandic fjord: an integrated pelagic and benthic study

Climate change is expected to have a pronounced effect on biogeochemical cycling in Arctic fjords, but current insight on the biogeochemical functioning of these systems is limited. Here, we present seasonal data on primary production, export of particulate organic carbon (POC), and the coupling to benthic biogeochemistry in Kobbefjord (SW Greenland). Primary production and associated POC export from the photic zone showed marked seasonality, with annual integrated values of 7.2 and 19.9 mol C m-2 yr-1, respectively. This discrepancy, the isotopic signature, and C:N ratio of the sedimentating material suggested substantial import of marine POC from outside the fjord. At least 52% of the POC export reached the sediment, but the seasonality in pelagic productivity was not reflected in the sediment biogeochemistry, showing only moderate variation. Benthic mineralization and burial of organic carbon amounted to 3.2 and 5.3 mol C m-2 yr-1, respectively. Sulfate reduction was the most prominent mineralization pathway, accounting for 69% of the benthic mineralization, while denitrification accounted for 2%. Overall, the carbon mineralization and burial in Kobbefjord were significantly higher than previously observed in other more northerly Arctic fjords. Data compilation from Arctic fjords suggests proportional increases in surface production, POC export, benthic mineralization and burial of organic material with increasing duration of the ice-free period. Thus, the projected decline in ice coverage in higher Arctic Greenlandic fjords will, as a first approximation, entail proportional increases in productivity, mineralization, and burial of organic carbon in the fjords, which will thus become similar to present-day southerly systems

Nitrous oxide as a function of oxygen and archaeal gene abundance in the North Pacific

Natural Environment Research Council (NERC) (NE/E01559X/1)