Denitrification by sulfur-oxidizing bacteria in a eutrophic lake

Understanding the mechanistic controls of microbial denitrification is of central importance to both environmental microbiology and ecosystem ecology. Loss of nitrate (NO3 −) is often attributed to carbon-driven (heterotrophic) denitrification. However, denitrification can also be coupled to sulfur (S) oxidation by chemolithoautotrophic bacteria. In the present study, we used an in situ stable isotope (15NO3 −) tracer addition in combination with molecular approaches to understand the contribution of sulfur-oxidizing bacteria to the reduction of NO3 − in a eutrophic lake. Samples were incubated across a total dissolved sulfide (H2S) gradient (2 to 95 μM) between the lower epilimnion and the upper hypolimnion. Denitrification rates were low at the top of the chemocline (4.5 m) but increased in the deeper waters (5.0 and 5.5 m), where H2S was abundant. Concomitant with increased denitrification at depths with high sulfide was the production of sulfate (SO4 2−), suggesting that the added NO3 − was used to oxidize H2S to SO4 2−. Alternative nitrate removal pathways, including dissimilatory nitrate reduction to ammonium (DNRA) and anaerobic ammonium oxidation (anammox), did not systematically change with depth and accounted for 1 to 15% of the overall nitrate loss. Quantitative PCR revealed that bacteria of the Sulfurimonas genus that are known denitrifiers increased in abundance in response to NO3 − addition in the treatments with higher H2S. Stoichiometric estimates suggest that H2S oxidation accounted for more than half of the denitrification at the depth with the highest sulfide concentration. The present study provides evidence that microbial coupling of S and nitrogen (N) cycling is likely to be important in eutrophic freshwater ecosystems

Kinematics of chromodynamic multicomponent lattice Boltzmann Simulation with a large density contrast

The utility of an enhanced chromodynamic, color gradient or phase-field multicomponent lattice Boltzmann (MCLB) equation for immiscible fluids with a density difference was demonstrated by Wen et al. [Phys. Rev. E 100, 023301 (2019)] and Ba et al. [Phys. Rev. E 94, 023310 (2016)], who advanced earlier work by Liu et al. [Phys. Rev. E 85, 046309 (2012)] by removing certain error terms in the momentum equations. But while these models' collision scheme has been carefully enhanced by degrees, there is, currently, no quantitative consideration in the macroscopic dynamics of the segregation scheme which is common to all. Here, by analysis of the kinetic-scale segregation rule (previously neglected when considering the continuum behavior) we derive, bound, and test the emergent kinematics of the continuum fluids' interface for this class of MCLB, concurrently demonstrating the circular relationship with—and competition between—the models' dynamics and kinematics. The analytical and numerical results we present in Sec. V confirm that, at the kinetic scale, for a range of density contrast, color is a material invariant. That is, within numerical error, the emergent interface structure is isotropic (i.e., without orientation dependence) and Galilean-invariant (i.e., without dependence on direction of motion). Numerical data further suggest that reported restrictions on the achievable density contrast in rapid flow, using chromodynamic MCLB, originate in the effect on the model's kinematics of the terms deriving from our term F1i in the evolution equation, which correct its dynamics for large density differences. Taken with Ba's applications and validations, this result significantly enhances the theoretical foundation of this MCLB variant, bringing it somewhat belatedly further into line with the schemes of Inamuro et al. [J. Comput. Phys. 198, 628 (2004)] and the free-energy scheme [see, e.g., Phys. Rev. E. 76, 045702(R) (2007), and references therein] which, in contradistinction to the present scheme and perhaps wisely, postulate appropriate kinematics a priori

Impact testing to determine the mechanical properties of articular cartilage in isolation and on bone

The original publication is available at www.springerlink.comNon peer reviewedPostprin

Geomechanical modelling and consequences for fluid-flow in complex rifted settings: A case study in the Otway Basin, Australia

Poster presented at the EGU General Assembly 2019Geomechanical modelling of dilation tendency has been completed on more than 900 faults from nine three dimensional seismic surveys within the Otway Basin, Australia. As the in-situ stress regime within the basin is currently debated, scenarios of normal, strike-slip and reverse regimes of in-situ stress have been modelled. Additionally, the stability of natural fractures from seven wellbore image logs has been modelled under the same scenarios, with the consequences for each explored. NW-SE striking faults that define the basin’s major structural fabric are at critical risk of dilation irrespective of the regime of in-situ stress, while similarly striking fractures require very low (<5MPa under a strike-slip scenario) increases in pore pressure in order to be reactivated. N-S striking and W-E striking faults show lower risks for reactivation although their propensity to dilate is still significant. Our results in part explain why fault seal within the Otway Basin has been historically so poor, and suggest that while natural fracture networks may be optimally oriented for reactivation in order to increase secondary permeability – promising for unconventional prospectively - there is a high associated risk with respect to up-dip contamination along regional faults. This case study also provides insight into possible fluid flow pathways within other more frontier passive margin settings.Hugo Burgin, Khalid Amrouch, David Kulikowski, Simon Holford, and Philippe Robio

The Lotic Intersite Nitrogen Experiments: an example of successful ecological research collaboration

Collaboration is an essential skill for modern ecologists because it brings together diverse expertise, viewpoints, and study systems. The Lotic Intersite Nitrogen eXperiments (LINX I and II), a 17-y research endeavor involving scores of early- to late-career stream ecologists, is an example of the benefits, challenges, and approaches of successful collaborative research in ecology. The scientific success of LINX reflected tangible attributes including clear scientific goals (hypothesis-driven research), coordinated research methods, a team of cooperative scientists, excellent leadership, extensive communication, and a philosophy of respect for input from all collaborators. Intangible aspects of the collaboration included camaraderie and strong team chemistry. LINX further benefited from being part of a discipline in which collaboration is a tradition, clear data-sharing and authorship guidelines, an approach that melded field experiments and modeling, and a shared collaborative goal in the form of a universal commitment to see the project and resulting data products through to completion

Nitrate removal in stream ecosystems measured by 15N addition experiments: Denitrification

We measured denitrification rates using a field 15NO3− tracer-addition approach in a large, cross-site study of nitrate uptake in reference, agricultural, and suburban-urban streams. We measured denitrification rates in 49 of 72 streams studied. Uptake length due to denitrification (SWdenn) ranged from 89 m to 184 km (median of 9050 m) and there were no significant differences among regions or land-use categories, likely because of the wide range of conditions within each region and land use. N2 production rates far exceeded N2O production rates in all streams. The fraction of total NO3− removal from water due to denitrification ranged from 0.5% to 100% among streams (median of 16%), and was related to NH4+ concentration and ecosystem respiration rate (ER). Multivariate approaches showed that the most important factors controlling SWden were specific discharge (discharge / width) and NO3− concentration (positive effects), and ER and transient storage zones (negative effects). The relationship between areal denitrification rate (Uden) and NO3− concentration indicated a partial saturation effect. A power function with an exponent of 0.5 described this relationship better than a Michaelis-Menten equation. Although Uden increased with increasing NO3− concentration, the efficiency of NO3− removal from water via denitrification declined, resulting in a smaller proportion of streamwater NO3− load removed over a given length of stream. Regional differences in stream denitrification rates were small relative to the proximate factors of NO3− concentration and ecosystem respiration rate, and land use was an important but indirect control on denitrification in streams, primarily via its effect on NO3− concentration

Nitrate removal in stream ecosystems measured by 15N addition experiments: Total uptake

We measured uptake length of 15NO3− in 72 streams in eight regions across the United States and Puerto Rico to develop quantitative predictive models on controls of NO3− uptake length. As part of the Lotic Intersite Nitrogen eXperiment II project, we chose nine streams in each region corresponding to natural (reference), suburban-urban, and agricultural land uses. Study streams spanned a range of human land use to maximize variation in NO3− concentration, geomorphology, and metabolism. We tested a causal model predicting controls on NO3− uptake length using structural equation modeling. The model included concomitant measurements of ecosystem metabolism, hydraulic parameters, and nitrogen concentration. We compared this structural equation model to multiple regression models which included additional biotic, catchment, and riparian variables. The structural equation model explained 79% of the variation in log uptake length (SWtot). Uptake length increased with specific discharge (Q/w) and increasing NO3− concentrations, showing a loss in removal efficiency in streams with high NO3− concentration. Uptake lengths shortened with increasing gross primary production, suggesting autotrophic assimilation dominated NO3− removal. The fraction of catchment area as agriculture and suburban-urban land use weakly predicted NO3− uptake in bivariate regression, and did improve prediction in a set of multiple regression models. Adding land use to the structural equation model showed that land use indirectly affected NO3− uptake lengths via directly increasing both gross primary production and NO3− concentration. Gross primary production shortened SWtot, while increasing NO3− lengthened SWtot resulting in no net effect of land use on NO3− removal

Use of divalent metal ions in the DNA cleavage reaction of topoisomerase IV

It has long been known that type II topoisomerases require divalent metal ions in order to cleave DNA. Kinetic, mutagenesis and structural studies indicate that the eukaryotic enzymes utilize a novel variant of the canonical two-metal-ion mechanism to promote DNA scission. However, the role of metal ions in the cleavage reaction mediated by bacterial type II enzymes has been controversial. Therefore, to resolve this critical issue, this study characterized the DNA cleavage reaction of Escherichia coli topoisomerase IV. We utilized a series of divalent metal ions with varying thiophilicities in conjunction with oligonucleotides that replaced bridging and non-bridging oxygen atoms at (and near) the scissile bond with sulfur atoms. DNA scission was enhanced when thiophilic metal ions were used with substrates that contained bridging sulfur atoms. In addition, the metal-ion dependence of DNA cleavage was sigmoidal in nature, and rates and levels of DNA cleavage increased when metal ion mixtures were used in reactions. Based on these findings, we propose that topoisomerase IV cleaves DNA using a two-metal-ion mechanism in which one of the metal ions makes a critical interaction with the 3′-bridging atom of the scissile phosphate and facilitates DNA scission by the bacterial type II enzyme

Spectroscopy and Biosensing with Optically Resonant Dielectric Nanostructures

Resonant dielectric nanoparticles (RDNs) made of materials with large positive dielectric permittivity, such as Si, GaP, GaAs, have become a powerful platform for modern light science, enabling various fascinating applications in nanophotonics and quantum optics. In addition to light localization at the nanoscale, dielectric nanostructures provide electric and magnetic resonant responses throughout the visible and infrared spectrum, low dissipative losses and optical heating, low doping effect and absence of quenching, which are interesting for spectroscopy and biosensing applications. In this review, we present state-of-the-art applications of optically resonant high-index dielectric nanostructures as a multifunctional platform for light-matter interactions. Nanoscale control of quantum emitters and applications for enhanced spectroscopy including fluorescence spectroscopy, surface-enhanced Raman scattering (SERS), biosensing, and lab-on-a-chip technology are surveyed. We describe the theoretical background underlying these effects, overview realizations of specific resonant dielectric nanostructures and hybrid excitonic systems, and outlook the challenges in this field, which remain open to future research