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

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

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

Coupled nitrification and N2 gas production as a cryptic process in oxic riverbeds.

The coupling between nitrification and N2 gas production to recycle ammonia back to the atmosphere is a key step in the nitrogen cycle that has been researched widely. An assumption for such research is that the products of nitrification (nitrite or nitrate) mix freely in the environment before reduction to N2 gas. Here we show, in oxic riverbeds, that the pattern of N2 gas production from ammonia deviates by ~3- to 16-fold from that predicted for denitrification or anammox involving nitrite or nitrate as free porewater intermediates. Rather, the patterns match that for a coupling through a cryptic pool, isolated from the porewater. A cryptic pool challenges our understanding of a key step in the nitrogen cycle and masks our ability to distinguish between sources of N2 gas that 20 years' research has sought to identify. Our reasoning suggests a new pathway or a new type of coupling between known pathways in the nitrogen cycle

Isotope fractionation and sulfur metabolism by pure and enrichment cultures of elemental sulfur-disproportionating bacteria

We have explored the sulfur metabolism and accompanying fractionation of sulfur isotopes during the disproportionation of elemental sulfur by seven different enrichments and three pure bacterial cultures. Cultures were obtained from both marine and freshwater environments. In all cases appreciable fractionation accompanied elemental sulfur disproportionation, with two ranges of fractionation observed. All cultures except Desulfobulbus propionicus produced sulfide depleted in S-34 by between 5.5 and 6.9 per mil (avg of 6.3 per mi) and sulfate enriched in S-34 by between 17.1 and 20.2 per mil (avg of 18.8 per ml). The narrow range of fractionations suggests a conserved biochemistry for the disproportionation of elemental sulfur by many different marine and freshwater bacteria. Fractionations accompanying elemental sulfur disproportionation by Db. propionicus were nearly twice as great as the others, suggesting a different cellular level pathway of sulfur processing by this organism. In nearly every case pyrite formation accompanied the disproportionation of elemental sulfur. By using sulfur isotopes as a tracer of sulfur source, we could identify that pyrite formed both by the addition of elemental sulfur to FeS and from reaction between FeS and H2S. Both processes were equally fast and up to 10(4)-10(5) times faster than expected from the reported kinetics of inorganic pyrite-formation reactions. We speculate that bacteria may have enhanced rates of pyrite formation in our experimental systems. The organisms explored here have different strategies for growth and survival, and they may be active in environments ranging from dissolved sulfide-poor suboxic sediments to interfaces supporting steep opposing gradients of oxygen and sulfide. A large environmental range, combined with high bacterial numbers, significant isotope fractionations, and a possible role in pyrite formation, make elemental sulfur-disproportionating bacteria potentially significant actors in the sedimentary cycling of sulfur compounds

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

Benthic nitrogen cycling in the North Sea

We present new data on the rates of sedimentary denitrification and its component processes (canonical denitrification, anammox and dissimilatory nitrate reduction to ammonium) for intertidal and subtidal sites in the North Sea using nitrogen isotope addition methods. We find overall average denitrification rates of 6.3 (range 0.4-10.6) µmol m-2h-1, similar to those previously reported for this region and other temperate shelf environments. We find canonical denitrification to be the dominant (>90%) process of the three. At the subtidal sites, most of the denitrification is supported by nitrate generated within the sediments, while at the intertidal site the main source is from the water column. We go on to consider the impact of these rates on nitrogen cycling within the North Sea region and compare the sediment core incubation rate results to estimates derived from modelling approaches. Model rates are somewhat higher than those directly measured and we consider possible reasons for this

Temperature dependence of microbial degradation of organic matter in marine sediments:polysaccharide hydrolysis, oxygen consumption, and sulfate reduction

The temperature dependence of representative initial and terminal steps of organic carbon remineralization was measured at 2 temperate sites with annual temperature ranges of 0 to 30°C and 4 to 15°C and 2 Arctic sites with temperatures of 2.6 and –1.7°C. Slurried sediments were incubated in a temperature gradient block spanning a temperature range of ca 45°C. The initial step of organic carbon remineralization, macromolecule hydrolysis, was measured via the enzymatic hydrolysis of fluorescently labeled polysaccharides. The terminal steps of organic carbon remineralization were monitored through consumption of oxygen and reduction of 35SO42–. At each of the 4 sites, the temperature response of the initial step of organic carbon remineralization was similar to that of the terminal steps. Although optimum temperatures were always well above ambient environmental temperatures, optimum temperatures generally decreased with decreasing environmental temperatures. Activity at 5°C as a percentage of highest activity was highest in the Arctic sites and lowest in the warmest temperate site. The highest potential rates of substrate hydrolysis were measured in the Arctic, while the highest rates of oxygen consumption and sulfate reduction were measured at the warmest temperate site. Potential rates of extracellular enzymatic hydrolysis (at least for this class of pullulanase enzymes) do not appear to limit organic carbon turnover in the Arctic. These results suggest that organic carbon turnover in the cold Arctic is not intrinsically slower than carbon turnover in temperate environments; sedimentary metabolism in Arctic sediments may be controlled more by organic matter supply than by temperature