Chemodenitrification in the cryoecosystem of Lake Vida,Victoria Valley,Antarctica

Lake Vida, in the Victoria Valley of East Antarctica, is frozen, yet harbors liquid brine (~20% salt, >6 times seawater) intercalated in the ice below 16 m. The brine has been isolated from the surface for several thousand years. The brine conditions (permanently dark, ?13.4 °C, lack of O₂, and pH of 6.2) and geochemistry are highly unusual. For example, nitrous oxide (N₂O) is present at a concentration among the highest reported for an aquatic environment. Only a minor ¹⁷O anomaly was observed in N₂O, indicating that this gas was predominantly formed in the lake. In contrast, the ¹⁷O anomaly in nitrate () in Lake Vida brine indicates that approximately half or more of the present is derived from atmospheric deposition. Lake Vida brine was incubated in the presence of ¹⁵N‐enriched substrates for 40 days. We did not detect microbial nitrification, dissimilatory reduction of to ammonium (), anaerobic ammonium oxidation, or denitrification of N₂O under the conditions tested. In the presence of ¹⁵N‐enriched nitrite (), both N₂ and N₂O exhibited substantial ¹⁵N enrichments; however, isotopic enrichment declined with time, which is unexpected. Additions of ¹⁵N– alone and in the presence of HgCl₂ and ZnCl₂ to aged brine at ?13 °C resulted in linear increases in the δ¹⁵N of N₂O with time. As HgCl₂ and ZnCl₂ are effective biocides, we interpret N₂O production in the aged brine to be the result of chemodenitrification. With this understanding, we interpret our results from the field incubations as the result of chemodenitrification stimulated by the addition of ¹⁵N‐enriched and ZnCl₂ and determined rates of N₂O and N₂ production of 4.11–41.18 and 0.55–1.75 nmol L^?1 day^?1, respectively. If these rates are representative of natural production, the current concentration of N₂O in Lake Vida could have been reached between 6 and 465 years. Thus, chemodenitrification alone is sufficient to explain the high levels of N₂O present in Lake Vida.     

Rates and pathways of CH4 oxidation in ferruginous Lake Matano,Indonesia

This study evaluates rates and pathways of methane (CH₄) oxidation and uptake using ¹⁴C‐based tracer experiments throughout the oxic and anoxic waters of ferruginous Lake Matano. Methane oxidation rates in Lake Matano are moderate (0.36 nmol L^?1 day^?1 to 117 μmol L^?1 day^?1) compared to other lakes, but are sufficiently high to preclude strong CH₄ fluxes to the atmosphere. In addition to aerobic CH₄ oxidation, which takes place in Lake Matano's oxic mixolimnion, we also detected CH₄ oxidation in Lake Matano's anoxic ferruginous waters. Here, CH₄ oxidation proceeds in the apparent absence of oxygen (O₂) and instead appears to be coupled to some as yet uncertain combination of nitrate (), nitrite (), iron (Fe) or manganese (Mn), or sulfate () reduction. Throughout the lake, the fraction of CH₄ carbon that is assimilated vs. oxidized to carbon dioxide (CO₂) is high (up to 93%), indicating extensive CH₄ conversion to biomass and underscoring the importance of CH₄ as a carbon and energy source in Lake Matano and potentially other ferruginous or low productivity environments.     

Ordinary stoichiometry of extraordinary microorganisms

All life on Earth seems to be made of the same chemical elements in relatively conserved proportions (stoichiometry). Whether this stoichiometry is conserved in settings that differ radically in physicochemical conditions (extreme environments) from those commonly encountered elsewhere on the planet provides insight into possible stoichiometries for putative life beyond Earth. Here, we report measurements of elemental stoichiometry for extremophile microbes from hot springs of Yellowstone National Park (YNP). Phototrophic and chemotrophic microbes were collected in locations spanning large ranges of temperature (24 °C to boiling), pH (1.6–9.6), redox (0.1–7.2 mg L^?1 dissolved oxygen), and nutrient concentrations (0.01–0.25 mg L^?1 , 0.7–12.9 mg L^?1 , 0.01–42 mg L^?1 NH₄⁺, 0.003–1.1 mg L^?1 P mostly as phosphate). Despite these extreme conditions, the microbial cells sampled had a major and trace element stoichiometry within the ranges commonly encountered for microbes living in the more moderate environments of lakes and surface oceans. The cells did have somewhat high C:P and N:P ratios that are consistent with phosphorus (P) limitation. Furthermore, chemotrophs and phototrophs had similar compositions with the exception of Mo content, which was enriched in cells derived from chemotrophic sites. Thus, despite the extraordinary physicochemical and biological diversity of YNP environments, life in these settings, in a stoichiometric sense, remains much the same as we know it elsewhere.     

The effect of O2 and pressure on thiosulfate oxidation by Thiomicrospira thermophila

Microbial sulfur cycling in marine sediments often occurs in environments characterized by transient chemical gradients that affect both the availability of nutrients and the activity of microbes. High turnover rates of intermediate valence sulfur compounds and the intermittent availability of oxygen in these systems greatly impact the activity of sulfur‐oxidizing micro‐organisms in particular. In this study, the thiosulfate‐oxidizing hydrothermal vent bacterium Thiomicrospira thermophila strain EPR85 was grown in continuous culture at a range of dissolved oxygen concentrations (0.04–1.9 mM) and high pressure (5–10 MPa) in medium buffered at pH 8. Thiosulfate oxidation under these conditions produced tetrathionate, sulfate, and elemental sulfur, in contrast to previous closed‐system experiments at ambient pressure during which thiosulfate was quantitatively oxidized to sulfate. The maximum observed specific growth rate at 5 MPa pressure under unlimited O₂ was 0.25 hr^?1. This is comparable to the μ_max (0.28 hr^?1) observed at low pH (<6) at ambient pressure when T. thermophila produces the same mix of sulfur species. The half‐saturation constant for O₂ () estimated from this study was 0.2 mM (at a cell density of 10⁵ cells/ml) and was robust at all pressures tested (0.4–10 MPa), consistent with piezotolerant behavior of this strain. The cell‐specific was determined to be 1.5 pmol O₂/cell. The concentrations of products formed were correlated with oxygen availability, with tetrathionate production in excess of sulfate production at all pressure conditions tested. This study provides evidence for transient sulfur storage during times when substrate concentration exceeds cell‐specific and subsequent consumption when oxygen dropped below that threshold. These results may be common among sulfur oxidizers in a variety of environments (e.g., deep marine sediments to photosynthetic microbial mats).     

Isotopically anomalous organic carbon in the aftermath of the Marinoan snowball Earth

Throughout most of the sedimentary record, the marine carbon cycle is interpreted as being in isotopic steady state. This is most commonly inferred via isotopic reconstructions, where two export fluxes (organic carbon and carbonate) are offset by a constant isotopic fractionation of ~25 (termed ). Sedimentary deposits immediately overlying the Marinoan snowball Earth diamictites, however, stray from this prediction. In stratigraphic sections from the Ol Formation (Mongolia) and Sheepbed Formation (Canada), we observe a temporary excursion where the organic matter has anomalously heavy C and is grossly decoupled from the carbonate C. This signal may reflect the unique biogeochemical conditions that persisted in the aftermath of snowball Earth. For example, physical oceanographic modeling suggests that a strong density gradient caused the ocean to remain stratified for about 50,000 years after termination of the Marinoan snowball event, during which time the surface ocean and continental weathering consumed the large atmospheric CO₂ reservoir. Further, we now better understand how C records of carbonate can be post‐depostionally altered and thus be misleading. In an attempt to explain the observed carbon isotope record, we developed a model that tracks the fluxes and isotopic values of carbon between the surface ocean, deep ocean, and atmosphere. By comparing the model output to the sedimentary data, stratification alone cannot generate the anomalous observed isotopic signal. Reproducing the heavy C in organic matter requires the progressively diminishing contribution of an additional anomalous source of organic matter. The exact source of this organic matter is unclear.     

The effect of rock composition on cyanobacterial weathering of crystalline basalt and rhyolite

The weathering of volcanic rocks contributes significantly to the global silicate weathering budget, effecting carbon dioxide drawdown and long‐term climate control. The rate of chemical weathering is influenced by the composition of the rock. Rock‐dwelling micro‐organisms are known to play a role in changing the rate of weathering reactions; however, the influence of rock composition on bio‐weathering is unknown. Cyanobacteria are known to be a ubiquitous surface taxon in volcanic rocks. In this study, we used a selection of fast and slow growing cyanobacterial species to compare microbial‐mediated weathering of bulk crystalline rocks of basaltic and rhyolitic composition, under batch conditions. Cyanobacterial growth caused an increase in the pH of the medium and an acceleration of rock dissolution compared to the abiotic controls. For example, Anabaena cylindrica increased the linear release rate () of Ca, Mg, Si and K from the basalt by more than fivefold (5.21–12.48) and increased the pH of the medium by 1.9 units. Although A. cylindrica enhanced rhyolite weathering, the increase in was less than threefold (2.04–2.97) and the pH increase was only 0.83 units. The values obtained with A. cylindrica were at least ninefold greater with the basalt than the rhyolite, whereas in the abiotic controls, the difference was less than fivefold. Factors accounting for the slower rate of rhyolite weathering and lower biomass achieved are likely to include the higher content of quartz, which has a low rate of weathering and lower concentrations of bio‐essential elements, such as, Ca, Fe and Mg, which are known to be important in controlling cyanobacterial growth. We show that at conditions where weathering is favoured, biota can enhance the difference between low and high Si‐rock weathering. Our data show that cyanobacteria can play a significant role in enhancing rock weathering and likely have done since they evolved on the early Earth.     

Soil nitrogen dynamics in switchgrass seeded to a marginal cropland in South Dakota

The potential ecological impacts of switchgrass (Panicum virgatum L.), as a biofuel feedstock, have been assessed under different environmental conditions. However, limited information is available in understanding the integrated analysis of nitrogen (N) dynamics including soil nitrate (), nitrous oxide (N₂O) emissions, and leaching under switchgrass land management. The specific objective was to explore N dynamics for 2009 through 2015 in switchgrass seeded to a marginally yielding cropland based on treatments of N fertilization rate (N rate; low, 0; medium, 56; high, 112 kg N ha^?1) and landscape position (shoulder, backslope, and footslope). Our findings indicated that N rate impacted soil (0–5 cm depth) and surface N₂O fluxes but did not impact leaching during the observed years. Medium N (56 kg N ha^?1) was the optimal rate for increasing biomass yield with reduced environmental problems. Landscape position impacted the N dynamics. At the footslope position, soil , soil leaching, and N₂O fluxes were higher than the other landscape positions. Soil N₂O fluxes and leaching had downward trends over the observed years. Growing switchgrass on marginally yielding croplands can store soil N, reduce N losses via leaching, and mitigate N₂O emissions from soils to the atmosphere over the years. Switchgrass seeded on marginally yielding croplands can be beneficial in reducing N losses and can be grown as a sustainable bioenergy crop on these marginal lands.     

Predicting soils and environmental impacts associated with switchgrass for bioenergy production: a DAYCENT modeling approach

Switchgrass (Panicum virgatum L.) production has the potential to improve soils and the environment. However, little is known about the long‐term future assessment of soil and environmental impacts associated with switchgrass production. In this study, soil organic carbon (SOC), soil nitrate (), water‐filled pore space (WFPS), carbon dioxide (CO₂) and nitrous oxide (N₂O) fluxes, and biomass yield from switchgrass field were predicted using DAYCENT models for 2016 through 2050. Measured data for model calibration and validation at this study site managed with nitrogen fertilization rates (N rates) (low, 0 kg N ha^?1; medium, 56 kg N ha^?1; and high, 112 kg N ha^?1) and landscape positions (shoulder and footslope) for switchgrass production were collected from the previously published studies. Modeling results showed that the N fertilization can enhance SOC and soil NO₃^?, but increase soil N₂O and CO₂ fluxes. In this study, medium N fertilization was the optimum rate for enhancing switchgrass yield and reducing negative impact on the environment. Footslope position can be beneficial for improving SOC, , and yield, but contribute higher greenhouse gas (GHG) emissions compared to those of the shoulder. An increase in temperature and decrease in precipitation (climate scenarios) may reduce soil , WFPS, and N₂O flux. Switchgrass production can improve and maintain SOC and , and reduce N₂O and CO₂ fluxes over the predicted years. These findings indicate that switchgrass could be a sustainable bioenergy crop on marginally yielding lands for improving soils without significant negative impacts on the environment in the long run.     

Biophysical analysis of the dynamics of calmodulin interactions with neurogranin and Ca2+/calmodulin‐dependent kinase II

Calmodulin (CaM) functions depend on interactions with CaM‐binding proteins, regulated by . Induced structural changes influence the affinity, kinetics, and specificities of the interactions. The dynamics of CaM interactions with neurogranin (Ng) and the CaM‐binding region of /calmodulin‐dependent kinase II (CaMKII_290−309) have been studied using biophysical methods. These proteins have opposite dependencies for CaM binding. Surface plasmon resonance biosensor analysis confirmed that and CaM interact very rapidly, and with moderate affinity ( ). Calmodulin‐CaMKII_290−309 interactions were only detected in the presence of , exhibiting fast kinetics and nanomolar affinity ( ). The CaM–Ng interaction had higher affinity under ‐depleted ( and k ₋₁ = 1.6 × 10⁻¹s⁻¹) than ‐saturated conditions ( ). The IQ motif of Ng (Ng₂₇₋₅₀) had similar affinity for CaM as Ng under ‐saturated conditions ( ), but no interaction was seen under ‐depleted conditions. Microscale thermophoresis using fluorescently labeled CaM confirmed the surface plasmon resonance results qualitatively, but estimated lower affinities for the Ng ( ) and CaMKII_290−309( ) interactions. Although CaMKII_290−309 showed expected interaction characteristics, they may be different for full‐length CaMKII. The data for full‐length Ng, but not Ng₂₇₋₅₀, agree with the current model on Ng regulation of /CaM signaling.     

Differential responses of two wetland graminoids to high ammonium at different pH values

Enhanced soil ammonium () concentrations in wetlands often lead to graminoid dominance, but species composition is highly variable. Although is readily taken up as a nutrient, several wetland species are known to be sensitive to high concentrations or even suffer toxicity, particularly at low soil pH. More knowledge about differential graminoid responses to high availability in relation to soil pH can help to better understand vegetation changes. The responses of two wetland graminoids, Juncus acutiflorus and Carex disticha, to high (2 mmol·l^?1) versus control (20 μmol·l^?1) concentrations were tested in a controlled hydroponic set up, at two pH values (4 and 6). A high concentration did not change total biomass for these species at either pH, but increased C allocation to shoots and increased P uptake, leading to K and Ca limitation, depending on pH treatment. More than 50% of N taken up by C. disticha was invested in N‐rich amino acids with decreasing C:N ratio, but only 10% for J. acutiflorus. Although both species appeared to be well adapted to high loadings in the short term, C. disticha showed higher classic detoxifying responses that are early warning indicators for decreased tolerance in the long term. In general, the efficient aboveground biomass allocation, P uptake and N detoxification explain the competitive strength of wetland graminoids at the expense of overall biodiversity at high loading. In addition, differential responses to enhanced affect interspecific competition among graminoids and lead to a shift in vegetation composition.     

RISK OF POPULATION EXTINCTION FROM FIXATION OF NEW DELETERIOUS MUTATIONS

The fixation of new deleterious mutations is analyzed for a randomly mating population of constant size with no environmental or demographic stochasticity. Mildly deleterious mutations are far more important in causing loss of fitness and eventual extinction than are lethal and semilethal mutations in populations with effective sizes, N_e, larger than a few individuals. If all mildly deleterious mutations have the same selection coefficient, s against heterozygotes and 2s against homozygotes, the mean time to extinction, , is asymptotically proportional to for 4N_es > 1. Nearly neutral mutations pose the greatest risk of extinction for stable populations, because the magnitude of selection coefficient that minimizes is about ? = 0.4/N_e. The influence of variance in selection coefficients among mutations is analyzed assuming a gamma distribution of s, with mean and variance . The mean time to extinction increases with variance in selection coefficients if is near ?, but can decrease greatly if is much larger than ?. For a given coefficient of variation of , the mean time to extinction is asymptotically proportional to for . When s is exponentially distributed, (c = 1) is asymptotically proportional to . These results in conjunction with data on the rate and magnitude of mildly deleterious mutations in Drosophila melanogaster indicate that even moderately large populations, with effective sizes on the order of N_e = 10³, may incur a substantial risk of extinction from the fixation of new mutations.     

A sluggish mid‐Proterozoic biosphere and its effect on Earth's redox balance

The possibility of low but nontrivial atmospheric oxygen (O₂) levels during the mid‐Proterozoic (between 1.8 and 0.8 billion years ago, Ga) has important ramifications for understanding Earth's O₂ cycle, the evolution of complex life and evolving climate stability. However, the regulatory mechanisms and redox fluxes required to stabilize these O₂ levels in the face of continued biological oxygen production remain uncertain. Here, we develop a biogeochemical model of the C‐N‐P‐O₂‐S cycles and use it to constrain global redox balance in the mid‐Proterozoic ocean–atmosphere system. By employing a Monte Carlo approach bounded by observations from the geologic record, we infer that the rate of net biospheric O₂ production was Tmol year^?1 (1σ), or ~25% of today's value, owing largely to phosphorus scarcity in the ocean interior. Pyrite burial in marine sediments would have represented a comparable or more significant O₂ source than organic carbon burial, implying a potentially important role for Earth's sulphur cycle in balancing the oxygen cycle and regulating atmospheric O₂ levels. Our statistical approach provides a uniquely comprehensive view of Earth system biogeochemistry and global O₂ cycling during mid‐Proterozoic time and implicates severe P biolimitation as the backdrop for Precambrian geochemical and biological evolution.     

Nitrogen fixation by the diazotroph Cylindrospermopsis raciborskii (Cyanophyceae)

Nitrogen fixation has been proposed as a mechanism that allows the diazotrophic cyanobacterium, Cylindrospermopsis raciborskii, to bloom in nitrogen‐limited freshwater systems. However, it is unclear whether dinitrogen fixation (N₂ fixation) can supplement available dissolved inorganic nitrogen (DIN) for growth, or only provides minimum nitrogen (N) for cell maintenance under DIN deplete conditions. Additionally, the rate at which cells can switch between DIN use and N₂ fixation is unknown. This study investigated N₂ fixation under a range of nitrate concentrations. Cultures were grown with pretreatments of nitrate replete (single dose 941 μmol  · L^?1) and N‐free conditions and then either received a single dose of 941 μmol  · L^?1 (N941), 118 μmol  · L^?1 (N118) or 0 N. Heterocysts appeared from days 3 to 5 when treatments of high were transferred to N free media (N941:N0), and from day 5 in N941 transferred to N118 treatments. Conversely, transferring cells from N0 to N941 resulted in heterocysts being discarded from day 3 and day 5 for N0:N118. Heterocyst appearance correlated with a detectable rate of N₂ fixation and up‐regulation of nifH gene expression, the discard of heterocysts occurred after sequential reduction of nifH expression and N₂ fixation. Nitrate uptake rates were not affected by pretreatment, suggesting no regulation or saturation of this uptake pathway. These data demonstrate that for C. raciborskii, N₂ fixation is regulated by the production or discard of heterocysts. In conclusion, this study has shown that N₂ fixation only provides enough N to support relatively low growth under N‐limited conditions, and does not supplement available nitrate to increase growth rates.     

Nitrate or ammonium: Influences of nitrogen source on the physiology of a green alga

In freshwaters, algal species are exposed to different inorganic nitrogen (N_i) sources whose incorporation varies in biochemical energy demand. We hypothesized that due to the lesser energy requirement of ammonium ()‐use, in contrast to nitrate ()‐use, more energy remains for other metabolic processes, especially under CO₂‐ and phosphorus (P_i) limiting conditions. Therefore, we tested differences in cell characteristics of the green alga Chlamydomonas acidophila grown on or under covariation of CO₂ and P_i‐supply in order to determine limitations, in a full‐factorial design. As expected, results revealed higher carbon fixation rates for ‐grown cells compared to growth with under low CO₂ conditions. ‐grown cells accumulated more of the nine analyzed amino acids, especially under P_i‐limited conditions, compared to cells provided with . This is probably due to a slower protein synthesis in cells provided with . In contrast to our expectations, compared to ‐grown cells ‐grown cells had higher photosynthetic efficiency under P_i‐limitation. In conclusion, growth on the N_i‐source did not result in a clearly enhanced C_i‐assimilation, as it was highly dependent on P_i and CO₂ conditions (replete or limited). Results are potentially connected to the fact that C. acidophila is able to use only CO₂ as its inorganic carbon (C_i) source.     

The Arabidopsis root stele transporter NPF2.3 contributes to nitrate translocation to shoots under salt stress

In most plants, constitutes the major source of nitrogen, and its assimilation into amino acids is mainly achieved in shoots. Furthermore, recent reports have revealed that reduction of translocation from roots to shoots is involved in plant acclimation to abiotic stress. NPF2.3, a member of the NAXT (nitrate excretion transporter) sub‐group of the NRT1/PTR family (NPF) from Arabidopsis, is expressed in root pericycle cells, where it is targeted to the plasma membrane. Transport assays using NPF2.3‐enriched Lactococcus lactis membranes showed that this protein is endowed with transport activity, displaying a strong selectivity for against Cl^?. In response to salt stress, translocation to shoots is reduced, at least partly because expression of the root stele transporter gene NPF7.3 is decreased. In contrast, NPF2.3 expression was maintained under these conditions. A loss‐of‐function mutation in NPF2.3 resulted in decreased root‐to‐shoot translocation and reduced shoot content in plants grown under salt stress. Also, the mutant displayed impaired shoot biomass production when plants were grown under mild salt stress. These mutant phenotypes were dependent on the presence of Na⁺ in the external medium. Our data indicate that NPF2.3 is a constitutively expressed transporter whose contribution to translocation to the shoots is quantitatively and physiologically significant under salinity.     

Evaluating interactions between space‐use sharing and defence under increasing density conditions for the group‐territorial Red‐cockaded Woodpecker Leuconotopicus borealis

Information about how bird species respond to increasing density conditions through either space‐use sharing or increased territoriality, and how those changes affect fitness, is essential for effective conservation planning. We used a case study of endangered Red‐cockaded Woodpeckers Leuconotopicus borealis (RCW) to address these questions. We documented over 36 000 locations from 44 RCW groups in three density conditions on two sites in South Carolina, USA, between April 2013 and March 2015. The frequency of neighbouring group interactions differed among density conditions and was highest for high‐density groups. RCW home‐ranges and core‐areas were larger under low‐density conditions ( = 88.4 ha,  = 21.0 ha) than under medium ( = 68.29 ha,  = 16.6 ha) and high‐density ( = 76.3 ha,  = 18.6 ha) conditions. Neighbouring RCWs maintained overlapping home‐ranges with nearly exclusive core‐areas across density conditions, but overlap tended to increase as neighbouring group density increased. Under high‐density conditions, home‐range overlap correlated inversely with clutch size (β ± se = ?0.19 ± 0.09), nestling production (β ± se = ?0.37 ± 0.09) and fledgling production (β ± se = ?0.34 ± 0.08). Our results indicate that RCWs dedicate more effort to territorial defence under high‐density conditions, potentially at the expense of greater foraging efficiency and time allocated to reproduction, as evidenced by reduced fitness. Large home‐range overlap indicated limited territoriality farther away from cavity trees, but the existence of exclusive core‐areas suggests that RCW groups defend habitat closer to cavity trees. Thiessen partitions used to allocate critical foraging habitat offered comprehensive habitat protection for RCW but appear flawed for spatially explicit habitat assessments because they do not accurately delineate space used by individual RCW groups.     

Energy transfer rate and electron–phonon coupling properties in Eu3+‐doped nanophosphors

A series of controllable emissions SrWO₄:Eu³⁺ and charge‐compensated SrWO₄: (m = 0.01 or 0.20) phosphors was successfully prepared via a simple co‐precipitation method. The energy transfer mechanism was studied based on the Huang's theory. A low magnitude of Huang‐Rhys factor (10^?2) was calculated using phonon sideband spectra. The Judd–Ofelt parameters Ω_λ (λ = 2, 4 and 6) of Eu³⁺‐activated SrWO₄ doped with charge compensation were obtained. The calculated Commission Internationale de l'Eclairage chromaticity coordinates were found to be about (0.67, 0.33) for SrWO₄: and charge‐compensated SrWO₄: phosphors, which coincided with the National Television Standard Committee system standard values for red. A white light emission was obtained under 362 nm excitation. The correlated color temperature was computed by a simple equation to characterize light sources. Thus, warm white light‐emitting diodes with higher Ra can be constructed by combining as‐prepared high efficiency, low correlated color temperature and high color purity phosphor.     

Variance component tests of multivariate mediation effects under composite null hypotheses

Mediation effects of multiple mediators are determined by two associations: one between an exposure and mediators (‐) and the other between the mediators and an outcome conditional on the exposure (‐). The test for mediation effects is conducted under a composite null hypothesis, that is, either one of the ‐ and ‐ associations is zero or both are zeros. Without accounting for the composite null, the type 1 error rate within a study containing a large number of multimediator tests may be much less than the expected. We propose a novel test to address the issue. For each mediation test , , we examine the ‐ and ‐ associations using two separate variance component tests. Assuming a zero‐mean working distribution with a common variance for the element‐wise ‐ (and ‐) associations, score tests for the variance components are constructed. We transform the test statistics into two normally distributed statistics under the null. Using a recently developed result, we conduct hypothesis tests accounting for the composite null hypothesis by adjusting for the variances of the normally distributed statistics for the ‐ and ‐ associations. Advantages of the proposed test over other methods are illustrated in simulation studies and a data application where we analyze lung cancer data from The Cancer Genome Atlas to investigate the smoking effect on gene expression through DNA methylation in 15 114 genes.     

Effective number of breeders provides a link between interannual variation in stream flow and individual reproductive contribution in a stream salmonid

The effective number of breeders that give rise to a cohort (N_b) is a promising metric for genetic monitoring of species with overlapping generations; however, more work is needed to understand factors that contribute to variation in this measure in natural populations. We tested hypotheses related to interannual variation in N_b in two long‐term studies of brook trout populations. We found no supporting evidence for our initial hypothesis that reflects (defined as the number of adults in a population at the time of reproduction). was stable relative to and did not follow trends in abundance (one stream negative, the other positive). We used stream flow estimates to test the alternative hypothesis that environmental factors constrain N_b. We observed an intermediate optimum autumn stream flow for both (R² = 0.73, P = 0.02) and full‐sibling family evenness (R² = 0.77, P = 0.01) in one population and a negative correlation between autumn stream flow and full‐sib family evenness in the other population (r = ?0.95, P = 0.02). Evidence for greater reproductive skew at the lowest and highest autumn flow was consistent with suboptimal conditions at flow extremes. A series of additional tests provided no supporting evidence for a related hypothesis that density‐dependent reproductive success was responsible for the lack of relationship between N_b and N_C (so‐called genetic compensation). This work provides evidence that N_b is a useful metric of population‐specific individual reproductive contribution for genetic monitoring across populations and the link we provide between stream flow and N_b could be used to help predict population resilience to environmental change.     

Environmental factors function as constraints on soil nitrous oxide fluxes in bioenergy feedstock cropping systems

Nitrous oxide (N₂O) is a potent greenhouse gas and major component of the net global warming potential of bioenergy feedstock cropping systems. Numerous environmental factors influence soil N₂O production, making direct correlation difficult to any one factor of N₂O fluxes under field conditions. We instead employed quantile regression to evaluate whether soil temperature, water‐filled pore space (WFPS), and concentrations of soil nitrate () and ammonium () determined upper bounds for soil N₂O flux magnitudes. We collected data over 6 years from a range of bioenergy feedstock cropping systems including no‐till grain crops, perennial warm‐season grasses, hybrid poplar, and polycultures of tallgrass prairie species each with and without nitrogen (N) addition grown at two sites. The upper bounds for soil N₂O fluxes had a significant and positive correlation with all four environmental factors, although relatively large fluxes were still possible at minimal values for nearly all factors. The correlation with was generally weaker, suggesting it is less important than in driving large fluxes. Quantile regression slopes were generally lower for unfertilized perennials than for other systems, but this may have resulted from a perpetual state of nitrogen limitation, which prevented other factors from being clear constraints. This framework suggests efforts to reduce concentrations of in the soil may be effective at reducing high‐intensity periods—”hot moments”—of N₂O production.