Showing papers by "Bo Thamdrup published in 2016"

Ammonium and nitrite oxidation at nanomolar oxygen concentrations in oxygen minimum zone waters

Abstract: A major percentage of fixed nitrogen (N) loss in the oceans occurs within nitrite-rich oxygen minimum zones (OMZs) via denitrification and anammox. It remains unclear to what extent ammonium and nitrite oxidation co-occur, either supplying or competing for substrates involved in nitrogen loss in the OMZ core. Assessment of the oxygen (O2) sensitivity of these processes down to the O2 concentrations present in the OMZ core (<10 nmol⋅L−1) is therefore essential for understanding and modeling nitrogen loss in OMZs. We determined rates of ammonium and nitrite oxidation in the seasonal OMZ off Concepcion, Chile at manipulated O2 levels between 5 nmol⋅L−1 and 20 μmol⋅L−1. Rates of both processes were detectable in the low nanomolar range (5–33 nmol⋅L−1 O2), but demonstrated a strong dependence on O2 concentrations with apparent half-saturation constants (Kms) of 333 ± 130 nmol⋅L−1 O2 for ammonium oxidation and 778 ± 168 nmol⋅L−1 O2 for nitrite oxidation assuming one-component Michaelis–Menten kinetics. Nitrite oxidation rates, however, were better described with a two-component Michaelis–Menten model, indicating a high-affinity component with a Km of just a few nanomolar. As the communities of ammonium and nitrite oxidizers were similar to other OMZs, these kinetics should apply across OMZ systems. The high O2 affinities imply that ammonium and nitrite oxidation can occur within the OMZ core whenever O2 is supplied, for example, by episodic intrusions. These processes therefore compete with anammox and denitrification for ammonium and nitrite, thereby exerting an important control over nitrogen loss.

SAR11 bacteria linked to ocean anoxia and nitrogen loss.

Abstract: Bacteria of the SAR11 clade constitute up to one half of all microbial cells in the oxygen-rich surface ocean. SAR11 bacteria are also abundant in oxygen minimum zones (OMZs), where oxygen falls below detection and anaerobic microbes have vital roles in converting bioavailable nitrogen to N2 gas. Anaerobic metabolism has not yet been observed in SAR11, and it remains unknown how these bacteria contribute to OMZ biogeochemical cycling. Here, genomic analysis of single cells from the world's largest OMZ revealed previously uncharacterized SAR11 lineages with adaptations for life without oxygen, including genes for respiratory nitrate reductases (Nar). SAR11 nar genes were experimentally verified to encode proteins catalysing the nitrite-producing first step of denitrification and constituted ~40% of OMZ nar transcripts, with transcription peaking in the anoxic zone of maximum nitrate reduction activity. These results link SAR11 to pathways of ocean nitrogen loss, redefining the ecological niche of Earth's most abundant organismal group.

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

Abstract: 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.

NC10 bacteria in marine oxygen minimum zones.

Abstract: Bacteria of the NC10 phylum link anaerobic methane oxidation to nitrite denitrification through a unique O2-producing intra-aerobic methanotrophy pathway. A niche for NC10 in the pelagic ocean has not been confirmed. We show that NC10 bacteria are present and transcriptionally active in oceanic oxygen minimum zones (OMZs) off northern Mexico and Costa Rica. NC10 16S rRNA genes were detected at all sites, peaking in abundance in the anoxic zone with elevated nitrite and methane concentrations. Phylogenetic analysis of particulate methane monooxygenase genes further confirmed the presence of NC10. rRNA and mRNA transcripts assignable to NC10 peaked within the OMZ and included genes of the putative nitrite-dependent intra-aerobic pathway, with high representation of transcripts containing the unique motif structure of the nitric oxide (NO) reductase of NC10 bacteria, hypothesized to participate in O2-producing NO dismutation. These findings confirm pelagic OMZs as a niche for NC10, suggesting a role for this group in OMZ nitrogen, methane and oxygen cycling.

Denitrification and DNRA at the Baltic Sea oxic–anoxic interface: Substrate spectrum and kinetics

Abstract: The dependence of denitrification and dissimilatory nitrate reduction to ammonium (DNRA) on different electron donors was tested in the nitrate-containing layer immediately below the oxic–anoxic interface (OAI) at three stations in the central anoxic basins of the Baltic Sea. Additionally, pathways and rates of fixed nitrogen transformation were investigated with 15N incubation techniques without addition of donors. Denitrification and anammox were always detected, but denitrification rates were higher than anammox rates. DNRA occurred at two sites and rates were two orders of magnitude lower than denitrification rates. Separate additions of dissolved organic carbon and sulfide stimulated rates without time lag indicating that both organotrophic and lithotrophic bacterial populations were simultaneously active and that they could carry out denitrification or DNRA. Manganese addition stimulated denitrification and DNRA at one station, but it is not clear whether this was due to a direct or indirect effect. Ammonium oxidation to nitrite was detected on one occasion. During denitrification, the production of nitrous oxide (N2O) was as important as dinitrogen (N2) production. A high ratio of N2O to N2 production at one site may be due to copper limitation, which inhibits the last denitrification step. These data demonstrate the coexistence of a range of oxidative and reductive nitrogen cycling processes at the Baltic OAI and suggest that the dominant electron donor supporting denitrification and DNRA is organic matter. Organotrophic denitrification is more important for nitrogen budgets than previously thought, but the large temporal variability in rates calls for long-term seasonal studies.

Anaerobic Nitrogen Turnover by Sinking Diatom Aggregates at Varying Ambient Oxygen Levels.

Abstract: In the world’s oceans, even relatively low oxygen (O2) levels inhibit anaerobic nitrogen cycling by free-living microbes. Sinking organic aggregates, however, might provide oxygen-depleted microbial hotspots in otherwise oxygenated surface waters. Here we show that sinking diatom aggregates can host anaerobic nitrogen cycling at ambient O2 levels well above the hypoxic threshold. Aggregates were produced from the ubiquitous diatom Skeletonema marinoi and the natural microbial community of seawater. Microsensor profiling through the center of sinking aggregates revealed internal anoxia at ambient 40% air saturation (~100 µmol O2 L-1) and below. Accordingly, anaerobic nitrate turnover inside the aggregates was evident within this range of ambient O2 levels. In incubations with 15N-labeled nitrate, individual Skeletonema aggregates produced NO2- (up to 10.7 nmol N h-1 per aggregate), N2 (up to 7.1 nmol N h-1), NH4+ (up to 2.0 nmol N h-1), and N2O (up to 0.2 nmol N h-1). Intriguingly, nitrate stored inside the diatom cells served as an additional, internal nitrate source for N2 production, which may partially uncouple anaerobic nitrate turnover by diatom aggregates from direct ambient nitrate supply. Sinking diatom aggregates can contribute directly to fixed-nitrogen loss in low-oxygen environments in the ocean and vastly expand the ocean volume in which anaerobic nitrogen turnover is possible, despite relatively high ambient O2 levels. Depending on the extent of intracellular nitrate consumption during the sinking process, diatom aggregates may also be involved in the long-distance export of nitrate to the deep ocean.

High sulfur isotope fractionation associated with anaerobic oxidation of methane in a low-sulfate, iron-rich environment

Abstract: Sulfur isotope signatures provide key information for the study of microbial activity in modern systems and the evolution of the Earth surface redox system. Microbial sulfate reducers shift sulfur isotope distributions by discriminating against heavier isotopes. This discrimination is strain-specific and often suppressed at sulfate concentrations in the lower micromolar range that are typical to freshwater systems and inferred for ancient oceans. Anaerobic oxidation of methane (AOM) is a sulfate-reducing microbial process with a strong impact on global sulfur cycling in modern habitats and potentially in the geological past, but its impact on sulfur isotope signatures is poorly understood, especially in low sulfate environments. We investigated sulfur cycling and 34S fractionation in a low-sulfate freshwater sediment with biogeochemical conditions analogous to Early Earth environments. The zone of highest AOM activity was associated in situ with a zone of strong 34S depletions in the pool of reduced sulfur species, indicating a coupling of sulfate reduction and AOM at sulfate concentrations < 50 µmol L-1. In slurry incubations of AOM-active sediment, the addition of methane stimulated sulfate reduction and induced a bulk sulfur isotope effect of ~29 ‰. Our results imply that sulfur isotope signatures may be strongly impacted by AOM even at sulfate concentrations two orders of magnitude lower than at present oceanic levels. Therefore, we suggest that sulfur isotope fractionation during AOM must be considered when interpreting 34S signatures in modern and ancient environment.

Intracellular Nitrate of Marine Diatoms as a Driver of Anaerobic Nitrogen Cycling in Sinking Aggregates.

Abstract: Diatom-bacteria aggregates are key for the vertical transport of organic carbon in the ocean. Sinking aggregates also represent pelagic microniches with intensified microbial activity, oxygen depletion in the center, and anaerobic nitrogen cycling. Since some of the aggregate-forming diatom species store nitrate intracellularly, we explored the fate of intracellular nitrate and its availability for microbial metabolism within anoxic diatom-bacteria aggregates. The ubiquitous nitrate-storing diatom Skeletonema marinoi was studied as both axenic cultures and laboratory-produced diatom-bacteria aggregates. Stable 15N isotope incubations under dark and anoxic conditions revealed that axenic S. marinoi is able to reduce intracellular nitrate to ammonium that is immediately excreted by the cells. When exposed to a light:dark cycle and oxic conditions, S. marinoi stored nitrate intracellularly in concentrations > 60 mmol L-1 both as free-living cells and associated to aggregates. Intracellular nitrate concentrations exceeded extracellular concentrations by three orders of magnitude. Intracellular nitrate was used up within 2-3 days after shifting diatom-bacteria aggregates to dark and anoxic conditions. Thirty-one percent of the diatom-derived nitrate was converted to nitrogen gas, indicating that a substantial fraction of the intracellular nitrate pool of S. marinoi becomes available to the aggregate-associated bacterial community. Only 5% of the intracellular nitrate was reduced to ammonium, while 59% was recovered as nitrite. Hence, aggregate-associated diatoms accumulate nitrate from the surrounding water and sustain complex nitrogen transformations, including loss of fixed nitrogen, in anoxic, pelagic microniches. Additionally, it may be expected that intracellular nitrate not converted before the aggregates have settled onto the seafloor could fuel benthic nitrogen transformations.

A new diet for methane oxidizers

Abstract: In anoxic marine sediments, consortia of methane-consuming archaea and sulfate-reducing bacteria oxidize methane. Together, they thereby control methane discharge in a metabolism of global importance. During this cooperative interspecies interaction, known as syntrophy, the excess reducing equivalents released by one species feed the second species (see the first figure). The two species only gain energy when they work together. On page 703 of this issue, Scheller et al. ( 1 ) show that these partners can be decoupled in the laboratory. The results help to elucidate the molecular mechanisms that control methane discharge in marine systems.

Isotope fractionation and isotope decoupling during anammox and denitrification in marine sediments

Abstract: To evaluate the relation of isotope fractionation during sedimentary nitrate reduction with sediment reactivity, we measured nitrate and nitrite reduction rates and corresponding isotope changes in marine sediments in the Skagerrak. Our sampling sites encompassed a gradient of reactivity, oxygen consumption, and manganese concentration. Anammox was the main N2-production pathway at the deepest site. For this site, we calculated the intrinsic isotope effect of nitrite consumption by anammox in marine sediments, and found that it is ∼ −20‰, in accordance with culture studies. Denitrification was dominant at shallower sites, which confirms previous studies from whole core incubations. The N-isotope effect of denitrification, 15e, ranged from −12‰ to −16‰. Oxygen isotopes of nitrate were more variable, and the ratio of 18e/15e, was highly variable in all sediments we investigated. At all stations, the oxygen isotope effect was (partly or entirely) decoupled from the nitrogen isotope effect. In denitrification-dominated sediments, this decoupling of oxygen and nitrogen isotopes appeared to be driven by nitrite reoxidation in anoxic sediment incubations, either due to enzymatic reversibility of the respiratory nitrate reductase Nar, or to reversibility on the community level. In anammox-dominated sediments, this effect was also evident in N-isotope changes, likely due to net nitrate production and isotope exchange that is promoted by anammox. These findings suggest that the ratio of 18e/15e in marine environments is more flexible than previously assumed, because enzymatic or community-driven isotope exchange can alter both N and O isotopes, deviating from standard Rayleigh-type fractionation.

Rates of N2 production and diversity and abundance of functional genes associated with denitrification and anaerobic ammonium oxidation in the sediment of the Amundsen Sea Polynya, Antarctica

Abstract: A combination of molecular microbiological analyses and metabolic rate measurements was conducted to elucidate the diversity and abundance of denitrifying and anaerobic ammonium oxidation (anammox) bacteria and the nitrogen gas (N2) production rates in sediment underlying the highly productive polynya (Stns. 10 and 17) and the sea-ice zone on the outer shelf (Stn. 83) of the Amundsen Sea, Antarctica. Despite the high water column productivity, the N2 production rates by denitrification (0.04–0.31 nmol N cm−3 sed. h−1) and anammox (0.13–0.26 nmol N cm−3 sed. h−1) were lower than those measured in other polar regions. In contrast, gene copy number (106–107 copies cm−3 of nirS and nosZ genes targeting denitirifiers and 105–107 copies cm−3 of 16S rRNA genes related to anammox bacteria) of the two bacterial groups at Stn. 17 was similar compared to those of other organic-rich environments. The majority of the nirS sequences were affiliated with Gammaproteobacteria (54% and 61% of the total nirS gene at Stns. 17 and 83, respectively), which were closely related to Pseudomonas aeruginosa. Most nosZ sequences (92% and 72% of the total nosZ genes at Stns. 17 and 83, respectively) were related to the Alphaproteobacteria, which were closely related to Ruegeria pomeroyi and Roseobacter denitrificans. Most (98%) of the sequences related to anammox bacteria were affiliated with Candidatus Scalindua at Stn. 17. Consequently, despite the low metabolic activity, the abundance and composition of most denitrifying and anammox bacteria detected from the ASP were similar to those reported from a variety of marine environments. Our results further imply that increased labile organic matter production resulting from a shift of the phytoplankton community from Phaeocystis to diatoms in response to rapid melting of sea ice stimulates metabolic activities of the denitrifying and anammox bacteria, thereby enhancing the N removal process in the ASP.

Anaerobic methane oxidation in an East African great lake (Lake Kivu)

Abstract: . This study investigates methane (CH4) oxidation in the water column of Lake Kivu, a deep meromictic tropical lake containing large quantities of CH4 in the anoxic deep waters. Depth profiles of dissolved gases (CH4 and nitrous oxide (N2O)) and of the different potential electron acceptors for anaerobic methane oxidation (AOM) (nitrate, sulfate, iron and manganese) were determined during six field campaigns between June 2011 and August 2014. Bacterial abundance all along the vertical profiles was also determined by flow cytometry during three field campaigns, and denitrification measurements based on stable isotopes were performed twice. Incubation experiments were performed to quantify CH4 oxidation and nitrate consumption rates, with a focus on AOM, without and with an inhibitor of sulfate-reducing bacteria activity (molybdate). Nitrate consumption rates were measured in these incubations. Substantial CH4 oxidation activity was observed in oxic and anoxic waters, and in the upper anoxic waters of Lake Kivu, CH4 is a major electron donor to sustain anaerobic metabolic processes coupled to AOM. The maximum aerobic and anaerobic CH4 oxidation rates were estimated to 27 ± 2 and 16 ± 8 µmol L−1 d−1, respectively. We observed a decrease of AOM rates when molybdate was added for half of the measurements, strongly suggesting the occurrence of AOM linked to sulfate reduction, but an increase of AOM rates was observed for the other half. Nitrate reduction rates and dissolved manganese production rates tended to be higher with the addition of molybdate, but the maximum rates of 0.6 ± 0.02 and 11 ± 2 µmol L−1 d−1, respectively, were never high enough to explain AOM rates observed at the same depths. We also put in evidence a difference in relative importance of aerobic and anaerobic CH4 oxidation between the seasons, with a higher importance of aerobic oxidation when the oxygenated layer was thicker (in dry season).