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

Nitrogen removal in marine environments: recent findings and future research challenges

Respiratory reduction of nitrate (denitrification) is recognized as the most important process converting biologically available (fixed) nitrogen to N2. In current N cycle models, a major proportion of global marine denitrification (50–70%) is assumed to take place on the sea floor, particularly in organic rich continental margin sediments. Recent observations indicate that present conceptual views of denitrification and pathways of nitrate reduction and N2 formation are incomplete. Alternative N cycle pathways, particularly in sediments, include anaerobic ammonium oxidation to nitrite, nitrate and N2 by Mn-oxides, and anaerobic ammonium oxidation coupled to nitrite reduction and subsequent N2 mobilization. The discovery of new links and feedback mechanisms between the redox cycles of, e.g., C, N, S, Mn and Fe casts doubt on the present general understanding of the global N cycle. Recent models of the oceanic N budget indicate that total inputs are significantly smaller than estimated fixed N removal. The occurrence of alternative N reaction pathways further exacerbates the apparent imbalance as they introduce additional routes of N removal. In this contribution, we give a brief historical background of the conceptual understanding of N cycling in marine ecosystems, emphasizing pathways of aerobic and anaerobic N mineralization in marine sediments, and the implications of recently recognized metabolic pathways for N removal in marine environments

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

Rates of carbonate cementation associated with sulphate reduction in DSDP/ODP sediments: implications for the formation of concretions

DSDP/ODP porewater profiles in organic carbon-bearing (<5% org. C) sediments commonly show decreases in Ca2+ concentrations and increases in alkalinity over depths where sulphate is being removed by microbial reduction. These Ca2+ depletion profiles represent the combined effect of diffusion, advection and reaction (addition by ion exchange and removal by precipitation mainly as CaCO3 and/or dolomite). A diagenetic model has been used to estimate the rate constant (k) for Ca2+ removal by precipitation during sulphate depletion over depths of 15-150 m, assuming first order kinetics. The rate constants for Ca2+ removal range from 10(-14) to 10(-11) s(-1) in 19 DSDP/ODP sediments, which span a range of bottom water temperatures (0-10 degreesC), lithologies (calcareous to clastic) and sedimentation rates (0.001-0.4 cm year(-1)). Values of k correlate with sedimentation rate (omega) such that log k=1.16 log omega-10.3, indicating that faster rates of Ca2+ removal occur at higher sedimentation rates where there are also higher degrees of saturation with respect to CaCO3 and dolomite. Depth-integrated masses of Ca2+ removed (<100 mumol cm(-2)) during sulphate depletion over these depth ranges are equivalent to a dispersed phase of approximately 1.5 wt.% CaCO3 or 3 wt.% dolomite in a compacted sediment. The complete occlusion of sediment porosity observed in concretions with isotopic signatures suggesting carbonate sourced from sulphate reduction therefore requires more time (a depositional hiatus), more rapid sulphate reduction (possibly by anaerobic methane oxidation) and/or the continued transport of isotopically light carbonate to the concretion site after sulphate reduction has ceased

Three manganese oxide-rich marine sediments harbor similar communities of acetate-oxidizing manganese-reducing bacteria

Dissimilatory manganese reduction dominates anaerobic carbon oxidation in marine sediments with high manganese oxide concentrations, but the microorganisms responsible for this process are largely unknown. In this study, the acetate-utilizing manganese-reducing microbiota in geographically well-separated, manganese oxide-rich sediments from Gullmar Fjord (Sweden), Skagerrak (Norway) and Ulleung Basin (Korea) were analyzed by 16S rRNA-stable isotope probing (SIP). Manganese reduction was the prevailing terminal electron-accepting process in anoxic incubations of surface sediments, and even the addition of acetate stimulated neither iron nor sulfate reduction. The three geographically distinct sediments harbored surprisingly similar communities of acetate-utilizing manganese-reducing bacteria: 16S rRNA of members of the genera Colwellia and Arcobacter and of novel genera within the Oceanospirillaceae and Alteromonadales were detected in heavy RNA-SIP fractions from these three sediments. Most probable number (MPN) analysis yielded up to 10(6) acetate-utilizing manganese-reducing cells cm(−3) in Gullmar Fjord sediment. A 16S rRNA gene clone library that was established from the highest MPN dilutions was dominated by sequences of Colwellia and Arcobacter species and members of the Oceanospirillaceae, supporting the obtained RNA-SIP results. In conclusion, these findings strongly suggest that (i) acetate-dependent manganese reduction in manganese oxide-rich sediments is catalyzed by members of taxa (Arcobacter, Colwellia and Oceanospirillaceae) previously not known to possess this physiological function, (ii) similar acetate-utilizing manganese reducers thrive in geographically distinct regions and (iii) the identified manganese reducers differ greatly from the extensively explored iron reducers in marine sediments