Intracellular nitrate of marine diatoms as a driver of anaerobic nitrogen cycling in sinking aggregates

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

Protocols for Assessing Transformation Rates of Nitrous Oxide in the Water Column

Nitrous oxide (N2O) is a potent greenhouse gas and an ozone destroying substance. Yet, clear step-by-step protocols to measure N2O transformation rates in freshwater and marine environments are still lacking, challenging inter-comparability efforts. Here we present detailed protocols currently used by leading experts in the field to measure water-column N2O production and consumption rates in both marine and other aquatic environments. We present example 15N-tracer incubation experiments in marine environments as well as templates to calculate both N2O production and consumption rates. We discuss important considerations and recommendations regarding (1) precautions to prevent oxygen (O2) contamination during low-oxygen and anoxic incubations, (2) preferred bottles and stoppers, (3) procedures for 15N-tracer addition, and (4) the choice of a fixative. We finally discuss data reporting and archiving. We expect these protocols will make 15N-labeled N2O transformation rate measurements more accessible to the wider community and facilitate future inter-comparison between different laboratories

Small sinking particles control anammox rates in the Peruvian oxygen minimum zone

Anaerobic oxidation of ammonium (anammox) in oxygen minimum zones (OMZs) is a major pathway of oceanic nitrogen loss. Ammonium released from sinking particles has been suggested to fuel this process. During cruises to the Peruvian OMZ in April–June 2017 we found that anammox rates are strongly correlated with the volume of small particles (128–512 µm), even though anammox bacteria were not directly associated with particles. This suggests that the relationship between anammox rates and particles is related to the ammonium released from particles by remineralization. To investigate this, ammonium release from particles was modelled and theoretical encounters of free-living anammox bacteria with ammonium in the particle boundary layer were calculated. These results indicated that small sinking particles could be responsible for ~75% of ammonium release in anoxic waters and that free-living anammox bacteria frequently encounter ammonium in the vicinity of smaller particles. This indicates a so far underestimated role of abundant, slow-sinking small particles in controlling oceanic nutrient budgets, and furthermore implies that observations of the volume of small particles could be used to estimate N-loss across large areas

Enhanced Nitrogen Loss by Eddy-Induced Vertical Transport in the Offshore Peruvian Oxygen Minimum Zone

The eastern tropical South Pacific (ETSP) upwelling region is one of the ocean’s largest sinks of fixed nitrogen, which is lost as N2 via the anaerobic processes of anammox and denitrification. One-third of nitrogen loss occurs in productive shelf waters stimulated by organic matter export as a result of eastern boundary upwelling. Offshore, nitrogen loss rates are lower, but due to its sheer size this area accounts for ~70% of ETSP nitrogen loss. How nitrogen loss and primary production are regulated in the offshore ETSP region where coastal upwelling is less influential remains unclear. Mesoscale eddies, ubiquitous in the ETSP region, have been suggested to enhance vertical nutrient transport and thereby regulate primary productivity and hence organic matter export. Here, we investigated the impact of mesoscale eddies on anammox and denitrification activity using 15N-labelled in situ incubation experiments. Anammox was shown to be the dominant nitrogen loss process, but varied across the eddy, whereas denitrification was below detection at all stations. Anammox rates at the eddy periphery were greater than at the center. Similarly, depth-integrated chlorophyll paralleled anammox activity, increasing at the periphery relative to the eddy center; suggestive of enhanced organic matter export along the periphery supporting nitrogen loss. This can be attributed to enhanced vertical nutrient transport caused by an eddy-driven submesoscale mechanism operating at the eddy periphery. In the ETSP region, the widespread distribution of eddies and the large heterogeneity observed in anammox rates from a compilation of stations suggests that eddy-driven vertical nutrient transport may regulate offshore primary production and thereby nitrogen loss

Two warm, low-density sub-Jovian planets orbiting bright stars in K2 campaigns 13 and 14

We report the discovery of two planets transiting the bright stars HD 89345 (EPIC 248777106, $V=9.376$, $K=7.721$) in K2 Campaign 14 and HD 286123 (EPIC 247098361, $V=9.822$, $K=8.434$) in K2 Campaign 13. Both stars are G-type stars, one of which is at or near the end of its main sequence lifetime, and the other that is just over halfway through its main sequence lifetime. HD 89345 hosts a warm sub-Saturn (0.66 $R_J$, 0.11 $M_J$, $T_\mathrm{eq}=1100$ K) in an 11.81-day orbit. The planet is similar in size to WASP-107b, which falls in the transition region between ice giants and gas giants. HD 286123 hosts a Jupiter-sized, low-mass planet (1.06 $R_J$, 0.39 $M_J$, $T_\mathrm{eq}=1000$ K) in an 11.17-day, mildly eccentric orbit, with $e=0.255\pm0.035$. Given that they orbit relatively evolved main-sequence stars and have orbital periods longer than 10 days, these planets are interesting candidates for studies of gas planet evolution, migration, and (potentially) re-inflation. Both planets have spent their entire lifetimes near the proposed stellar irradiation threshold at which giant planets become inflated, and neither shows any sign of radius inflation. They probe the regime where inflation begins to become noticeable and are valuable in constraining planet inflation models. In addition, the brightness of the host stars, combined with large atmospheric scale heights of the planets, makes these two systems favorable targets for transit spectroscopy to study their atmospheres and perhaps provide insight into the physical mechanisms that lead to inflated hot Jupiters.Comment: 16 pages, 12 figures; accepted for publication in A

Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300T)

Sebaldella termitidis (Sebald 1962) Collins and Shah 1986, is the only species in the genus Sebaldella within the fusobacterial family ‘Leptotrichiaceae’. The sole and type strain of the species was first isolated about 50 years ago from intestinal content of Mediterranean termites. The species is of interest for its very isolated phylogenetic position within the phylum Fusobacteria in the tree of life, with no other species sharing more than 90% 16S rRNA sequence similarity. The 4,486,650 bp long genome with its 4,210 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project

The influence of light on nitrogen cycling and the primary nitrite maximum in a seasonally stratified sea

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Progress In Oceanography 91 (2011): 545–560, doi:10.1016/j.pocean.2011.09.001.In the seasonally stratified Gulf of Aqaba Red Sea, both NO2- release by phytoplankton and NH4+ oxidation by nitrifying microbes contributed to the formation of a primary nitrite maximum (PNM) over different seasons and depths in the water column. In the winter and during the days immediately following spring stratification, NO2- formation was strongly correlated (R2=0.99) with decreasing irradiance and chlorophyll, suggesting that incomplete NO3- reduction by light limited phytoplankton was a major source of NO2-. However, as stratification progressed, NO2- continued to be generated below the euphotic depth by microbial NH4+ oxidation, likely due to differential photoinhibition of NH4+ and NO2- oxidizing populations. Natural abundance stable nitrogen isotope analyses revealed a decoupling of the δ15N and δ18O in the combined NO3- and NO2- pool, suggesting that assimilation and nitrification were co-occurring in surface waters. As stratification progressed, the δ15N of particulate N below the euphotic depth increased from -5‰ to up to +20‰. N uptake rates were also influenced by light; based on 15N tracer experiments, assimilation of NO3-, NO2-, and urea was more rapid in the light (434±24, 94±17, and 1194±48 nmol N L-1 day-1 respectively) than in the dark (58±14, 29±14, and 476±31 nmol N L-1 day-1 respectively). Dark NH4+ assimilation was 314±31 nmol N L-1 day-1, while light NH4+ assimilation was much faster, resulting in complete consumption of the 15N spike in less than 7 hour from spike addition. The overall rate of coupled urea mineralization and NH¬4+ oxidation (14.1±7.6 nmol N L-1 day-1) was similar to that of NH¬4+ oxidation alone (16.4±8.1 nmol N L-1 day-1), suggesting that for labile dissolved organic N compounds like urea, mineralization was not a rate limiting step for nitrification. Our results suggest that assimilation and nitrification compete for NH4+ and that N transformation rates throughout the water column are influenced by light over diel and seasonal cycles, allowing phytoplankton and nitrifying microbes to contribute jointly to PNM formation. We identify important factors that influence the N cycle throughout the year, including light intensity, substrate availability, and microbial community structure. These processes could be relevant to other regions worldwide where seasonal variability in mixing depth and stratification influence the contributions of phytoplankton and non-photosynthetic microbes to the N cycle.This research was supported under the North Atlantic Treaty Organization (NATO) Science for Peace Grant SfP 982161 to AP and AFP, a grant from the Koret Foundation to AP, a National Science Foundation Biological Oceanography grant to AP, the Israel Science Foundation grant 135/05 to AFP, and research grant 8330-06 from the Geological Society of America to KRMM