In-depth analysis of N2O fluxes in tropical forest soils of the Congo Basin combining isotope and functional gene analysis

Primary tropical forests generally exhibit large gaseous nitrogen (N) losses, occurring as nitric oxide (NO), nitrous oxide (N2O) or elemental nitrogen (N2). The release of N2O is of particular concern due to its high global warming potential and destruction of stratospheric ozone. Tropical forest soils are predicted to be among the largest natural sources of N2O; however, despite being the world’s second-largest rainforest, measurements of gaseous N-losses from forest soils of the Congo Basin are scarce. In addition, long-term studies investigating N2O fluxes from different forest ecosystem types (lowland and montane forests) are scarce. In this study we show that fluxes measured in the Congo Basin were lower than fluxes measured in the Neotropics, and in the tropical forests of Australia and South East Asia. In addition, we show that despite different climatic conditions, average annual N2O fluxes in the Congo Basin’s lowland forests (0.97 ± 0.53 kg N ha−1 year−1) were comparable to those in its montane forest (0.88 ± 0.97 kg N ha−1 year−1). Measurements of soil pore air N2O isotope data at multiple depths suggests that a microbial reduction of N2O to N2 within the soil may account for the observed low surface N2O fluxes and low soil pore N2O concentrations. The potential for microbial reduction is corroborated by a significant abundance and expression of the gene nosZ in soil samples from both study sites. Although isotopic and functional gene analyses indicate an enzymatic potential for complete denitrification, combined gaseous N-losses (N2O, N2) are unlikely to account for the missing N-sink in these forests. Other N-losses such as NO, N2 via Feammox or hydrological particulate organic nitrogen export could play an important role in soils of the Congo Basin and should be the focus of future research

Drivers of organic molecular signatures in the Amazon River

Author Posting. © American Geophysical Union, 2021. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Global Biogeochemical Cycles 35(6), (2021): e2021GB006938, https://doi.org/10.1029/2021GB006938.As climate-driven El Niño Southern Oscillation (ENSO) events are projected to increase in frequency and severity, much attention has focused on impacts regarding ecosystem productivity and carbon balance in Amazonian rainforests, with comparatively little attention given to carbon dynamics in fluvial ecosystems. In this study, we compared the wet 2012 La Niña period to the following normal hydrologic period in the Amazon River. Elevated water flux during the La Niña period was accompanied by dilution of inorganic ion concentrations. Furthermore, the La Niña period exported 2.77 Tg C yr−1 more dissolved organic carbon (DOC) than the normal period, an increase greater than the annual amount of DOC exported by the Mississippi River. Using ultra-high-resolution mass spectrometry, we detected both intra- and interannual differences in dissolved organic matter (DOM) composition, revealing that DOM exported during the dry season and the normal period was more aliphatic, whereas compounds in the wet season and following the La Niña event were more aromatic, with ramifications for its environmental role. Furthermore, as this study has the highest temporal resolution DOM compositional data for the Amazon River to-date we showed that compounds were highly correlated to a 6-month lag in Pacific temperature and pressure anomalies, suggesting that ENSO events could impact DOM composition exported to the Atlantic Ocean. Therefore, as ENSO events increase in frequency and severity into the future it seems likely that there will be downstream consequences for the fate of Amazon Basin-derived DOM concurrent with lag periods as described here.This work was partially supported by National Science Foundation grant OCE-1464396 to Robert G. M. Spencer and funding from the Harbourton Foundation to Robert G. M. Spencer, R. Max Holmes, and Bernhard Peucker-Ehrenbrink.2021-12-1

The pulse of the Amazon: fluxes of dissolved organic carbon, nutrients, and ions from the world's largest river

Author Posting. © American Geophysical Union, 2021. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Global Biogeochemical Cycles 35(4), (2021): e2020GB006895, https://doi.org/10.1029/2020GB006895.The Amazon River drains a diverse tropical landscape greater than 6 million km2, culminating in the world's largest export of freshwater and dissolved constituents to the ocean. Here, we present dissolved organic carbon (DOC), organic and inorganic nitrogen (DON, DIN), orthophosphate (PO43−), and major and trace ion concentrations and fluxes from the Amazon River using 26 samples collected over three annual hydrographs. Concentrations and fluxes were predominantly controlled by the annual wet season flood pulse. Average DOC, DON, DIN, and PO43− fluxes (±1 s.d.) were 25.5 (±1.0), 1.14 (±0.05), 0.82 (±0.03), and 0.063 (±0.003) Tg yr−1, respectively. Chromophoric dissolved organic matter absorption (at 350 nm) was strongly correlated with DOC concentrations, resulting in a flux of 74.8 × 106 m−2 yr−1. DOC and DON concentrations positively correlated with discharge while nitrate + nitrite concentrations negatively correlated, suggesting mobilization and dilution responses, respectively. Ammonium, PO43−, and silica concentrations displayed chemostatic responses to discharge. Major and trace ion concentrations displayed clockwise hysteresis (except for chloride, sodium, and rubidium) and exhibited either dilution or chemostatic responses. The sources of weathered cations also displayed seasonality, with the highest proportion of carbonate- and silicate-derived cations occurring during peak and baseflow, respectively. Finally, our seasonally resolved weathering model resulted in an average CO2 consumption yield of (3.55 ± 0.11) × 105 mol CO2 km−2 yr−1. These results represent an updated and temporally refined quantification of dissolved fluxes that highlight the strong seasonality of export from the world's largest river and set a robust baseline against which to gauge future change.This work was supported by a grant from the Harbourton Foundation to R. G. M. Spencer and R. M. Holmes. T. W. Drake was supported by ETH Zurich core funding to J. Six. R. G. M. Spencer was additionally supported by NSF OCE-1333157.2021-09-1

Capillary filling with wall corrugations] Capillary filling in microchannels with wall corrugations: A comparative study of the Concus-Finn criterion by continuum, kinetic and atomistic approaches

We study the impact of wall corrugations in microchannels on the process of capillary filling by means of three broadly used methods - Computational Fluid Dynamics (CFD), Lattice-Boltzmann Equations (LBE) and Molecular Dynamics (MD). The numerical results of these approaches are compared and tested against the Concus-Finn (CF) criterion, which predicts pinning of the contact line at rectangular ridges perpendicular to flow for contact angles theta > 45. While for theta = 30, theta = 40 (no flow) and theta = 60 (flow) all methods are found to produce data consistent with the CF criterion, at theta = 50 the numerical experiments provide different results. Whilst pinning of the liquid front is observed both in the LB and CFD simulations, MD simulations show that molecular fluctuations allow front propagation even above the critical value predicted by the deterministic CF criterion, thereby introducing a sensitivity to the obstacle heigth.Comment: 25 pages, 8 figures, Langmuir in pres

Mammals adjust diel activity across gradients of urbanization

Time is a fundamental component of ecological processes. How animal behavior changes over time has been explored through well-known ecological theories like niche partitioning and predator–prey dynamics. Yet, changes in animal behavior within the shorter 24-hr light–dark cycle have largely gone unstudied. Understanding if an animal can adjust their temporal activity to mitigate or adapt to environmental change has become a recent topic of discussion and is important for effective wildlife management and conservation. While spatial habitat is a fundamental consideration in wildlife management and conservation, temporal habitat is often ignored. We formulated a temporal resource selection model to quantify the diel behavior of 8 mammal species across 10 US cities. We found high variability in diel activity patterns within and among species and species-specific correlations between diel activity and human population density, impervious land cover, available greenspace, vegetation cover, and mean daily temperature. We also found that some species may modulate temporal behaviors to manage both natural and anthropogenic risks. Our results highlight the complexity with which temporal activity patterns interact with local environmental characteristics, and suggest that urban mammals may use time along the 24-hr cycle to reduce risk, adapt, and therefore persist, and in some cases thrive, in human-dominated ecosystems

DNA topoisomerases participate in fragility of the oncogene RET

Fragile site breakage was previously shown to result in rearrangement of the RET oncogene, resembling the rearrangements found in thyroid cancer. Common fragile sites are specific regions of the genome with a high susceptibility to DNA breakage under conditions that partially inhibit DNA replication, and often coincide with genes deleted, amplified, or rearranged in cancer. While a substantial amount of work has been performed investigating DNA repair and cell cycle checkpoint proteins vital for maintaining stability at fragile sites, little is known about the initial events leading to DNA breakage at these sites. The purpose of this study was to investigate these initial events through the detection of aphidicolin (APH)-induced DNA breakage within the RET oncogene, in which 144 APHinduced DNA breakpoints were mapped on the nucleotide level in human thyroid cells within intron 11 of RET, the breakpoint cluster region found in patients. These breakpoints were located at or near DNA topoisomerase I and/or II predicted cleavage sites, as well as at DNA secondary structural features recognized and preferentially cleaved by DNA topoisomerases I and II. Co-treatment of thyroid cells with APH and the topoisomerase catalytic inhibitors, betulinic acid and merbarone, significantly decreased APH-induced fragile site breakage within RET intron 11 and within the common fragile site FRA3B. These data demonstrate that DNA topoisomerases I and II are involved in initiating APH-induced common fragile site breakage at RET, and may engage the recognition of DNA secondary structures formed during perturbed DNA replication

Variable Mutation Rates as an Adaptive Strategy in Replicator Populations

For evolving populations of replicators, there is much evidence that the effect of mutations on fitness depends on the degree of adaptation to the selective pressures at play. In optimized populations, most mutations have deleterious effects, such that low mutation rates are favoured. In contrast to this, in populations thriving in changing environments a larger fraction of mutations have beneficial effects, providing the diversity necessary to adapt to new conditions. What is more, non-adapted populations occasionally benefit from an increase in the mutation rate. Therefore, there is no optimal universal value of the mutation rate and species attempt to adjust it to their momentary adaptive needs. In this work we have used stationary populations of RNA molecules evolving in silico to investigate the relationship between the degree of adaptation of an optimized population and the value of the mutation rate promoting maximal adaptation in a short time to a new selective pressure. Our results show that this value can significantly differ from the optimal value at mutation-selection equilibrium, being strongly influenced by the structure of the population when the adaptive process begins. In the short-term, highly optimized populations containing little variability respond better to environmental changes upon an increase of the mutation rate, whereas populations with a lower degree of optimization but higher variability benefit from reducing the mutation rate to adapt rapidly. These findings show a good agreement with the behaviour exhibited by actual organisms that replicate their genomes under broadly different mutation rates

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure

Natural Selection Fails to Optimize Mutation Rates for Long-Term Adaptation on Rugged Fitness Landscapes

The rate of mutation is central to evolution. Mutations are required for adaptation, yet most mutations with phenotypic effects are deleterious. As a consequence, the mutation rate that maximizes adaptation will be some intermediate value. Here, we used digital organisms to investigate the ability of natural selection to adjust and optimize mutation rates. We assessed the optimal mutation rate by empirically determining what mutation rate produced the highest rate of adaptation. Then, we allowed mutation rates to evolve, and we evaluated the proximity to the optimum. Although we chose conditions favorable for mutation rate optimization, the evolved rates were invariably far below the optimum across a wide range of experimental parameter settings. We hypothesized that the reason that mutation rates evolved to be suboptimal was the ruggedness of fitness landscapes. To test this hypothesis, we created a simplified landscape without any fitness valleys and found that, in such conditions, populations evolved near-optimal mutation rates. In contrast, when fitness valleys were added to this simple landscape, the ability of evolving populations to find the optimal mutation rate was lost. We conclude that rugged fitness landscapes can prevent the evolution of mutation rates that are optimal for long-term adaptation. This finding has important implications for applied evolutionary research in both biological and computational realms

Global carbon dioxide efflux from rivers enhanced by high nocturnal emissions

Carbon dioxide (CO2) emissions to the atmosphere from running waters are estimated to be four times greater than the total carbon (C) flux to the oceans. However, these fluxes remain poorly constrained because of substantial spatial and temporal variability in dissolved CO2 concentrations. Using a global compilation of high-frequency CO2 measurements, we demonstrate that nocturnal CO2 emissions are on average 27% (0.9 gC m−2 d−1) greater than those estimated from diurnal concentrations alone. Constraints on light availability due to canopy shading or water colour are the principal controls on observed diel (24 hour) variation, suggesting this nocturnal increase arises from daytime fixation of CO2 by photosynthesis. Because current global estimates of CO2 emissions to the atmosphere from running waters (0.65–1.8 PgC yr−1) rely primarily on discrete measurements of dissolved CO2 obtained during the day, they substantially underestimate the magnitude of this flux. Accounting for night-time CO2 emissions may elevate global estimates from running waters to the atmosphere by 0.20–0.55 PgC yr−1