Elemental line scanning of an increment core using EDXRF: From fundamental research to environmental forensics applications

Environmental forensics seeks to determine the responsible parties for contamination from leaks or spills of petroleum or other toxic products. Dendrochemistry contributes to environmental forensics at the intersection of analytical chemistry, tree biology, and environmental responsibility. To be useful, dendrochemistry requires the rigorous application of analytical techniques as well as an understanding of tree biology. The choice of analytical technique is usually driven by tradeoffs among the selection of chemical elements or molecules of interest, sensitivity and discrimination, spatial resolution, ease of sample preparation, availability, sample destructiveness, and cost.One useful solid-state spectroscopic technique for dendrochemical analysis is energy dispersive X-ray fluorescence (EDXRF). This method provides essentially non-destructive, simultaneous detection of a number of elements with an adjustable spatial resolution, typically from 0.1 to 0.3 mm. The most commonly targeted elements are S and Cl as markers for fossil fuels, Cl for solvents, and Pb for leaded gasoline. Other metal elements may also be used as indicators of mining and smelting.For elements that are not normally present in appreciable amounts in wood, the mere presence of the element anywhere in the tree-ring record indicates exposure of the tree to an unusual chemical event or process. Dating the environmental exposure from dendrochemical analysis can be complicated by internal changes in tree chemistry due to wood infection, tree maturation, and wood maturation.     

Real-time PCR approach for detection of environmental sources of Campylobacter strains colonizing broiler flocks

Reducing colonization of poultry flocks by Campylobacter spp. is a key strategy in the control and prevention human campylobacteriosis. Horizontal transmission of campylobacters, from in and around the farm, is the presumed route of flock colonization. However, the identification and prioritization of sources are confounded by the ubiquitous nature of these organisms in the environment, their poor rates of recovery by standard culture methods, and the need for cost-effective and timely methods for strain-specific comparison. A real-time PCR screening test for the strain-specific detection of campylobacters in environmental samples has been developed to address this issue. To enable this approach, fluorescently labeled PCR oligonucleotide probes suitable for a LightCycler-based assay were designed to match a highly variable DNA segment within the flaA short variable region (SVR) of Campylobacter jejuni or C. coli. The capacity of such probes to provide strain-specific tools was investigated by using bacterial cultures and spiked and naturally contaminated poultry fecal and environmental samples. The sensitivity of two representative probes was estimated, by using two different C. jejuni strains, to be 1.3 x 10(2) to 3.7 x 10(2) CFU/ml in bacterial cultures and 6.6 x 10(2) CFU/ml in spiked fecal samples. The specificity of the SVR for C. jejuni and C. coli was confirmed by using a panel of strains comprising other Campylobacter species and naturally contaminated samples. The approach was field tested by sampling the environment and feces of chickens of two adjacently located poultry houses on a conventional broiler farm throughout the life of one flock. All environmental samples were enriched for 2 days, and then DNA was prepared and stored. Where feasible, campylobacter isolates were also recovered and stored for subsequent testing. A strain-specific probe based on the SVR of the strain isolated from the first positive chicken fecal sample was developed. This probe was then used to screen the stored environmental samples by real-time PCR. Pulsed-field gel electrophoresis was used to compare recovered environmental and fecal isolates to assess the specificity of the method. The results established the proof of principle that strain-specific probes, based on the SVR of flaA, can identify a flock-colonizing strain in DNA preparations from enriched environmental cultures. Such a novel strategy provides the opportunity to investigate the epidemiology of campylobacters in poultry flocks and allows targeted biosecurity interventions to be developed. The strategy may also have wider applications for the tracking of specific campylobacter strains in heavily contaminated environments.     

Inferring nitrate sources through end member mixing analysis in an intermittent Mediterranean stream

We monitored 24 storms during the period 1998–2002 in order to elucidate whether the origin of nitrate could be inferred from water sources in the catchment. The study was performed in the Fuirosos catchment (10.5 km²) drained by an intermittent stream. Water sources were estimated through end member mixing analysis (EMMA) using chloride, sulfate and dissolved organic carbon as tracers. Three end members were identified in the catchment: event water, hillslope groundwater and riparian groundwater. Streamwater data encompassed the mixing space defined by the end members only during the 12 storms occurred during the wet period (from December to May). Water sources were related to stream nitrate concentrations during 6 of the 12 storms indicating a linkage between hydrological and nitrate sources. However, there was not a consistent pattern of a particular end member being a source of nitrate. EMMA was used to determine expected nitrate concentrations in stream water based on conservative mixing of the different water sources. The effect of the near- and in- stream zones on stream nitrate was inferred by comparing predicted nitrate concentrations to measured stream nitrate concentration. At discharges below 80 l s⁻¹ stream nitrate concentrations were lower than expected from catchment sources in 82% of the cases suggesting nitrate retention in the near stream zones. The trend was the opposite at higher discharges.     

Bromphenol blue: nitrate reductase activity in Nicotiana plumbaginifolia: an immunochemical and genetic approach

NADH: nitrate reductase (EC 1.6.6.1) was purified from Nicotiana plumbaginifolia leaves. As recently observed with nitrate reductase from other sources, this enzyme is able to reduce nitrate using reduced bromphenol blue (rBPB) as the electron donor. In contrast to the physiological NADH-dependent activity, the rBPB-dependent activity is stable in vitro. The latter activity is non-competitively inhibited by NADH. The monoclonal antibody ZM.96(9)25, which inhibits the NADH: nitrate reductase total activity as well as the NADH: cytochrome c reductase and reduced methyl viologen (rMV): nitrate reductase partial activities, has no inhibitory effect on the rBPB: nitrate reductase activity. Conversely, the monoclonal antibody NP.17-7(6) inhibits nitrate reduction with all three electron donors: NADH, MV or BPB. Among various nitrate reductase-deficient mutants, an apoprotein gene mutant (nia. E56) shows reduced terminal activities but a highly increased rBPB:nitrate reductase activity. rBPB:nitrate reductase thus appears to be a new terminal activity of higher plant nitrate reductase and involves specific sites which are not shared by the other activities.     

Intrinsic and environmental drivers of growth in an Alaskan rockfish: an otolith biochronology approach

Otolith growth-increment chronologies provide an approach for evaluating the impacts of both high-frequency (e.g., interannual) and low-frequency (e.g., interdecadal) climate variability on fish growth. A growth-increment biochronology spanning six decades, spanning several warm and cold climate regime periods, was developed for a commercially important species of rockfish, Sebastes polyspinis, in the Gulf of Alaska. To confirm that all increments were correctly identified and placed in time, we borrowed the technique of crossdating from the tree-ring science of dendrochronology, which ensured high data quality. We then used a mixed effects model to partition variance in otolith growth-increment width among intrinsic (e.g., age-related) and extrinsic (e.g., climate-related) factors. This biochronology was contrasted with one recently developed for S. alutus, a closely-related species which exhibited a significant change in growth following the late 1970s North Pacific climate regime shift. Both species generally showed positive relationships between warm climate conditions and growth, though S. polyspinis experienced a relatively smaller step-increase in growth following the regime shift. The new S. polyspinis otolith biochronology represents a long-term record of growth that extends well before biological specimens were first collected in the Gulf of Alaska, providing a potential tool for fisheries managers to evaluate the effects of climate variability on growth and biological reference points.     

Relationships between DOC bioavailability and nitrate removal in an upland stream: An experimental approach

The Catskill Mountains of southeastern New York State have among thehighest rates of atmospheric nitrogen deposition in the United States. Somestreams draining Catskill catchments have shown dramatic increases in nitrateconcentrations while others have maintained low nitrate concentrations. Streamsin which exchange occurs between surface and subsurface (i.e. hyporheic) watersare thought to be conducive to nitrate removal via microbial assimilationand/ordenitrification. Hyporheic exchange was documented in the Neversink River inthesouthern Catskill Mountains, but dissolved organic carbon (DOC) and nitrate(NO₃ ^–) losses along hyporheic flowpaths werenegligible. In this study, Neversink River water was amended with natural,bioavailable dissolved organic carbon (BDOC) (leaf leachate) in a series ofexperimental mesocosms that simulated hyporheic flowpaths. DOC and N dynamicswere examined before and throughout a three week BDOC amendment. In addition,bacterial production, dissolved oxygen demand, denitrification, and sixextracellular enzyme activities were measured to arrive at a mechanisticunderstanding of potential DOC and NO₃ ^– removalalong hyporheic flowpaths. There were marked declines in DOC and completeremoval of nitrate in the BDOC amended mesocosms. Independent approaches wereused to partition NO₃ ^– loss into two fractions:denitrification and assimilation. Microbial assimilation appears to be thepredominant process explaining N loss. These results suggest that variabilityinBDOC may contribute to temporal differences in NO₃ ^–export from streams in the Catskill Mountains.     

Assessing the sources and magnitude of diurnal nitrate variability in the San Joaquin River (California) with an in situ optical nitrate sensor and dual nitrate isotopes

1. We investigated diurnal nitrate (NO₃⁻) concentration variability in the San Joaquin River using an in situ optical NO₃⁻ sensor and discrete sampling during a 5‐day summer period characterized by high algal productivity. Dual NO₃⁻ isotopes (δ¹⁵N_NO3 and δ¹⁸O_NO3) and dissolved oxygen isotopes (δ¹⁸O_DO) were measured over 2 days to assess NO₃⁻ sources and biogeochemical controls over diurnal time‐scales. 2. Concerted temporal patterns of dissolved oxygen (DO) concentrations and δ¹⁸O_DO were consistent with photosynthesis, respiration and atmospheric O₂ exchange, providing evidence of diurnal biological processes independent of river discharge. 3. Surface water NO₃⁻ concentrations varied by up to 22% over a single diurnal cycle and up to 31% over the 5‐day study, but did not reveal concerted diurnal patterns at a frequency comparable to DO concentrations. The decoupling of δ¹⁵N_NO3 and δ¹⁸O_NO3 isotopes suggests that algal assimilation and denitrification are not major processes controlling diurnal NO₃⁻ variability in the San Joaquin River during the study. The lack of a clear explanation for NO₃⁻ variability likely reflects a combination of riverine biological processes and time‐varying physical transport of NO₃⁻ from upstream agricultural drains to the mainstem San Joaquin River. 4. The application of an in situ optical NO₃⁻ sensor along with discrete samples provides a view into the fine temporal structure of hydrochemical data and may allow for greater accuracy in pollution assessment.     

Absorption and accumulation of nitrate in plants: influence of environmental factors

Plants adopt various strategies to fulfill their nitrogen nutrition requirement, the most important being the uptake of nitrate from the soil and its subsequent assimilation in to amino acids. The uptake of nitrate is energy dependent and is an active process involving high affinity and low affinity transport systems. The net uptake of the anion depends upon both influx as well as on its passive efflux. When the uptake far exceeds over its assimilation in the plant, there is considerable accumulation of nitrate in the plant parts making them unfit for human and cattle consumption. Various environmental factors affect the uptake and accumulation of nitrate, which along with the genetic component of the plant affecting the net uptake and accumulation of the nitrate, need to be considered and carefully manipulated for effective nitrogen management in the plant, soil and aquatic environment.     

环境雄激素的危害、来源与环境行为

内分泌干扰物(EDCs)因低剂量即可导致严重的生理效应而成为研究的热点,环境雄激素就是典型的内分泌干扰物之一,它主要来源于畜禽粪尿的排放以及造纸厂和城市污水处理厂处理不彻底的废水排放,污染源的连续性排放致使环境雄激素物质在各类环境介质中被不断检出,并导致一些地区出现鱼类的雄性化现象,对环境健康和生态安全构成严重威胁。综述了环境雄激素的暴露危害、主要来源以及环境雄激素在不同环境中的浓度水平和分布特征,介绍了环境雄激素的分析检测手段,阐述了环境雄激素在环境中的迁移、吸附、降解等过程,并对环境雄激素的研究进行了展望。     

Disentangling environmental and host sources of fungal endophyte communities in an experimental beachgrass study

Disentangling the ecological factors that contribute to the assembly of the microbial symbiont communities within eukaryotic hosts is an ongoing challenge. Broadly speaking, symbiont propagules arrive either from external sources in the environment or from internal sources within the same host individual. To understand the relative importance of these propagule sources to symbiont community assembly, we characterized symbiotic fungal endophyte communities within the roots of three species of beachgrass in a field experiment. We manipulated two aspects of the external environment, successional habitat and physical disturbance. To determine the role of internal sources of propagules for endophyte community assembly, we used beachgrass individuals with different pre‐existing endophyte communities. Endophyte species richness and community composition were characterized using culture‐based and next‐generation sequencing approaches. Our results showed that external propagule sources associated with successional habitat, but not disturbance, were particularly important for colonization of most endophytic taxa. In contrast, internal propagule sources played a minor role for most endophytic taxa but were important for colonization by the dominant taxon Microdochium bolleyi. Our findings highlight the power of manipulative field experiments to link symbiont community assembly to its underlying ecological processes, and to ultimately improve predictions of symbiont community assembly across environments.     

Using a nitrogen and oxygen isotopic approach to identify nitrate sources and cycling in the Wei River of northwestern China

The Wei River is the largest tributary of the Yellow River in China. To understand the sources and cycling of nitrate in the Wei River, we determined the concentrations and nitrogen and oxygen isotopic values of nitrate from water samples. Our results revealed that NO₃^?-N dominated the inorganic N and ranged from 0.1 to 8.8 mg/L (averaging 3.3 mg/L). Although this NO₃^?-N concentration does not exceed the World Health Organization's drinking water standard of 10 mg/L, the NO₃^?-N content of most water samples exceeded 3 mg/L, indicating poor water quality. The NO₃^?-N concentrations and δ¹⁵N-NO₃^? values demonstrate that there are significant differences in the spatial distribution of nitrogen between the tributaries and the main stream of the Wei River. In addition, a negative linear relationship (r² = 0.63) between NO₃^?-N concentrations and δ¹⁸O-NO₃^? values suggests mixing between two distinct sources (fertilizer and manure or sewage). Furthermore, we infer that the main source of nitrate is not manure or sewage itself, but rather the nitrification of NH₄⁺ in manure and sewage. Finally, no obvious denitrification processes were observed. These results expand our understanding of sewage as a major source of nitrate to the Wei River, emphasizing the role of nitrification.     

Microbial nitrate respiration--genes, enzymes and environmental distribution

Nitrate is a key node in the network of the assimilatory and respiratory nitrogen pathways. As one of the ‘fixed’ forms of nitrogen, nitrate plays an essential role in both nature and industry. For bacteria, it is both a nitrogen source and an electron acceptor. In agriculture and wastewater treatment, nitrate respiration by microorganisms is an important issue with respect to economics, greenhouse gas emission and public health. Several microbial processes compete for nitrate: denitrification, dissimilatory nitrate reduction to ammonium and anaerobic ammonium oxidation. In this review we provide an up to date overview of the organisms, genes and enzymes involved in nitrate respiration. We also address the molecular detection of these processes in nature. We show that despite rapid progress in the experimental and genomic analyses of pure cultures, knowledge on the mechanism of nitrate reduction in natural ecosystems is still largely lacking.     

Post-translational regulation of nitrate reductase: mechanism, physiological relevance and environmental triggers

Assimilatory nitrate reductase (NR) of higher plants is a most interesting enzyme, both from its central function in plant primary metabolism and from the complex regulation of its expression and control of catalytic activity and degradation. Here, present knowledge about the mechanism of post-translational regulation of NR is summarized and the properties of the regulatory enzymes involved (protein kinases, protein phosphatases and 14-3-3-binding proteins) are described. It is shown that light and oxygen availability are the major external triggers for the rapid and reversible modulation of NR activity, and that sugars and/or sugar phosphates are the internal signals which regulate the protein kinase(s) and phosphatase. It is also demonstrated that stress factors like nitrate deficiency and salinity have remarkably little direct influence on the NR activation state. Further, changes in NR activity measured in vitro are not always associated with changes in nitrate reduction rates in vivo, suggesting that NR can be under strong substrate limitation. The degradation and half-life of the NR protein also appear to be affected by NR phosphorylation and 14-3-3 binding, as NR activation always correlates positively with its stability. However, it is not known whether the molecular form of NR in vivo affects its susceptibility to proteolytic degradation, or whether factors that affect the NR activation state also independently affect the activity or induction of the NR protease(s). A second and potentially important function of NR, the production of nitric oxide (NO) from nitrite is briefly described, but it remains to be determined whether NR produces NO for pathogen/stress signalling in vivo.     

Literature sources for primary environmental science teachers

With school days seemingly getting shorter and packed with more and more obligations, teachers integrate core subjects like science and reading in the hopes of delivering a curriculum that is meaningful and content rich. Using trade books, primary teachers can develop and deliver science content designed to introduce students to proenvironmental behaviors built around the Next Generation Science Earth and Human Activity Standard, Human Impacts on Earth Systems, ESS3-C. The Next Generation Science standards call for integrating literacy skills and science to develop knowledge of scientific topics. This article shares ideas on how primary teachers can use a variety of children’s literature as a foundation to inspire young students to take small steps toward developing proenvironmental behaviors. Under an umbrella of three environmental themes, proenvironmental behavior, trash, and water pollution, the article describes key concepts, vocabulary, and activities designed to develop a mindfulness of proenvironmental behaviors for each selected text. While texts and learning experiences are intentionally focused on young learners (Kindergarten/first grade), they can be adapted and used in all primary grades.     

Response of conifer seedlings to nitrate and ammonium sources of nitrogen

Summary Differences in growth responses of Douglas fir, western hemlock, Sitka spruce, and white spruce to nitrate and ammonium N sources were examined in sand culture and artificial soil culture. Effects of the two forms of N on growth, needle area, and N uptake of three Douglas fir halb-sib progenies were examined in a second sand culture. Response of Douglas fir to the two forms of N was followed over two years in nursery soil of different pH levels. In sand culture 1 mean seedling dry weight of all species, except hemlock, was greatest when ammonium N and nitrate N were provided in equal amounts. In all species, except Sitka spruce, ammonium alone resulted in greater growth than nitrate alone. Use of ammonium N resulted in greater growth of all species, than was obtained with nitrate N, at pH values in the region 5.4 and 7.5 in artificial soil culture. Only Douglas fir showed substantial differences due to N source below pH 5. Growth of all species was greater at pH 5.4 than at 7.5 in each N source treatment. Growth of Douglas fir seedlings was greatest with ammonium N and least with nitrate N in sand culture 2. Supply of nitrate and ammonium in equal proportions resulted in intermediate growth. Leaf area/plant weight ratio was unaffected by N source. Analysis of nutrient solutions showed appreciable nitrification of ammonium N during the 7 days between solution changes. In the three greenhouse experiments, with little exception, increase in proportion of ammonium in N supply resulted in increase of seedling tissue N concentration. This effect was more pronounced in roots than shoots. Total N uptake by ammonium fed seedlings was about double the N uptake of nitrate fed seedlings in sand culture 2. Nursery grown Douglas fir seedlings showed greater growth response to ammonium sulphate than to calcium nitrate, and this appeared due entirely to form of N supply in the first year. A similar response in the second year was partly due to greater soil acidification by ammonium sulphate. Compared with calcium nitrate, ammonium sulphate increased N concentration of one-year old shoots, but this difference was not detected by foliar analysis of two-year old seedlings.     

Ammonium and nitrate as nitrogen sources in two Eriophorum species

Summary We compared ammonium and nitrate nutrition in Eriophorum scheuchzeri and E. vaginatum, two Alaskan sedges that are native to high- and low-fertility sites, respectively. When grown in solution culture, the two species were similar in their kinetics of NH _inf4 ^sup+ NO _inf3 ^sup- absorption: at nitrogen concentrations below 50 M, net NH _inf4 ^sup+ and NO _inf3 ^sup- were absorbed at similar rates, but at higher concentrations, net uptake of NO _inf3 ^sup- was significantly faster than that of NH _inf4 ^sup+ . The two species also showed similar abilities to assimilate NO _inf3 ^sup- . Growth of E. vaginatum under NO _inf3 ^sup- nutrition was only slightly less than that under NH _inf4 ^sup+ . The observed similarities between these species from contrasting edaphic habitats indicate that factors other than tissue-specific rates of nitrogen acquisition and assimilation may underlie local adaptation to soil N fertility. Moreover, the capacity of these species to exploit NO _inf3 ^sup- as a N source supports the view that NO _inf3 ^sup- availability may be significant even in wet, acidic, arctic soils.