Nitrogen processes in aquatic ecosystems

Executive summary Nature of the problem (science/management/policy) • Freshwater ecosystems play a key role in the European nitrogen (N) cycle, both as a reactive agent that transfers, stores and processes N loadings from the atmosphere and terrestrial ecosystems, and as a natural environment severely impacted by the increase of these loadings. Approaches • This chapter is a review of major processes and factors controlling N transport and transformations for running waters, standing waters, groundwaters and riparian wetlands. Key findings/state of knowledge • The major factor controlling N processes in freshwater ecosystems is the residence time of water, which varies widely both in space and in time, and which is sensitive to changes in climate, land use and management. • The effects of increased N loadings to European freshwaters include acidification in semi-natural environments, and eutrophication in more disturbed ecosystems, with associated loss of biodiversity in both cases. • An important part of the nitrogen transferred by surface waters is in the form of organic N, as dissolved organic N (DON) and particulate organic N (PON). This part is dominant in semi-natural catchments throughout Europe and remains a significant component of the total N load even in nitrate enriched rivers. • In eutrophicated standing freshwaters N can be a factor limiting or co-limiting biological production, and control of both N and phosphorus (P) loading is oft en needed in impacted areas, if ecological quality is to be restored. Major uncertainties/challenges • The importance of storage and denitrifi cation in aquifers is a major uncertainty in the global N cycle, and controls in part the response of catchments to land use or management changes. In some aquifers, the increase of N concentrations will continue for decades even if efficient mitigation measures are implemented now. • Nitrate retention by riparian wetlands has oft en been highlighted. However, their use for mitigation must be treated with caution, since their effectiveness is difficult to predict, and side effects include increased DON emissions to adjacent open waters, N2O emissions to the atmosphere, and loss of biodiversity. • In fact, the character and specific spatial origins of DON are not fully understood, and similarly the quantitative importance of indirect N2O emissions from freshwater ecosystems as a result of N leaching losses from agricultural soils is still poorly known at the regional scale. • These major uncertainties remain due to the lack of adequate monitoring (all forms of N at a relevant frequency), especially – but not only – in the southern and eastern EU countries. Recommendations (research/policy) • The great variability of transfer pathways, buffering capacity and sensitivity of the catchments and of the freshwater ecosystems calls for site specific mitigation measures rather than standard ones applied at regional to national scale. • The spatial and temporal variations of the N forms, the processes controlling the transport and transformation of N within freshwaters, require further investigation if the role of N in influencing freshwater ecosystem health is to be better understood, underpinning the implementation of the EU Water Framework Directive for European freshwaters.

Using near infrared reflectance spectroscopy (NIRS) to predict the biological parameters of maize silage

The microbial fermentability, ruminal degradability and digestibility of 48 maize silages were determined using in vitro gas production (GP), in situ degradability and in vitro digestibility procedures. The silages were produced from forage maize harvested throughout the summer of 1998, and represent a wide range of physiological maturities. Large variations among samples were observed for all biological parameters, with the exception of in vitro digestibility and the asymptote of in vitro GP. The potential of near infrared reflectance spectroscopy (NIRS) to predict the biological parameters measured was determined by regression of the biological data against the respective spectral profile. NIRS demonstrated only a moderate ability (R-2 > 0.60-0.80) to predict in vitro digestibility, modelled kinetics of gas production (excluding the asymptote of gas production) and the modelled ruminally soluble dry matter (DM) fraction. Calibration statistics for remaining biological parameters were unacceptably poor (R-2 = 0.60). (C) 2004 Elsevier B.V. All rights reserved.

The role of weeds in supporting biological diversity within crop fields

Weeds are major constraints on crop production, yet as part of the primary producers within farming systems, they may be important components of the agroecosystem. Using published literature, the role of weeds in arable systems for other above-ground trophic levels are examined. In the UK, there is evidence that weed flora have changed over the past century, with some species declining in abundance, whereas others have increased. There is also some evidence for a decline in the size of arable weed seedbanks. Some of these changes reflect improved agricultural efficiency, changes to more winter-sown crops in arable rotations and the use of more broad-spectrum herbicide combinations. Interrogation of a database of records of phytophagous insects associated with plant species in the UK reveals that many arable weed species support a high diversity of insect species. Reductions in abundances of host plants may affect associated insects and other taxa. A number of insect groups and farmland birds have shown marked population declines over the past 30 years. Correlational studies indicate that many of these declines are associated with changes in agricultural practices. Certainly reductions in food availability in winter and for nestling birds in spring are implicated in the declines of several bird species, notably the grey partridge, Perdix perdix . Thus weeds have a role within agroecosystems in supporting biodiversity more generally. An understanding of weed competitivity and the importance of weeds for insects and birds may allow the identification of the most important weed species. This may form the first step in balancing the needs for weed control with the requirements for biodiversity and more sustainable production methods.

In vitro biological activity of tannins from Acacia and other tree fruits: Correlations with colorimetric and gravimetric phenolic assays

This Study was designed to investigate impact of tannins on in vitro ruminal fermentation parameters as well as relationships between concentration and in vitro biological activity of tannins present in tree fruits. Dry and mature fruits of known phenolic content harvested from Acacia nilotica, A. erubescens, A. erioloba, A. sieberiana, Piliostigima thonningii and Dichrostachys cinerea tree species were fermented with rumen fluid in vitro with or without polyethylene glycol (PEG). Correlation between in vitro biological activity and phenolic concentration was determined. Polyethylene glycol inclusion increased Cumulative gas production from all fruit substrates. The largest Increase (225%) after 48 h incubation was observed in D. cinerea fruits while the least (12.7%) increase was observed in A. erubescens fruits. Organic matter degradability (48 h) was increased by PEG inclusion for all tree species except A. erubescens and P. thonningii. For D. cinerea fruits, colorimetric assays were poorly correlated to Increases In gas production due to PEG treatment. Ytterbium precipitable phenolics (YbPh) were also poorly correlated with response to PEG for A. erioloba and P. thonningii fruits. However, YbPh were strongly and positively correlated to the increase In Cumulative gas production due to PEG for A. erubescens and A. nilotica. Folin-Ciocalteau assayed phenolics (SPh) were not correlated to response to PEG in P. thonningii and A. sieberiana. It was Concluded that the PEG effect oil in vitro fermentation was closely related to some measures of phenolic concentration but the relationships varied with tree species.

Organic dairy production: A review

Organic farming aims to create an integrated, humane, environmentally and economically sustainable agricultural system. For organic dairy systems, the fulfilment of these aims requires the understanding and integration of a number of systems components including land use (mixed or dairy only) and stocking rate; grassland and forage production, including quantity and quality; potential milk yield and milk quality; animal nutrition (largely farm based) and health; environmental sustainability such as farm nutrient balance; the financial status of the farm, including enterprise performance, fixed costs and labour use, and farm income and profit; and finally the policy environment in which organic dairy systems operate. This review discusses worldwide research undertaken into each of these key components of organic dairy production systems. As converting organic dairy systems are often considerably different to established organic systems, both the converting and developed organic dairy system are discussed in this paper.

Degree of oxidation of low density lipoprotein affects expression of CD36 and PPAR gamma, but not cytokine production, by human monocyte-macrophages

Oxidized low-density lipoprotein (oxLDL) exhibits many atherogenic effects, including the promotion of monocyte recruitment to the arterial endothelium and the induction of scavenger receptor expression. However, while atherosclerosis involves chronic inflammation within the arterial intima, it is unclear whether oxLDL alone provides a direct inflammatory stimulus for monocyte-macrophages. Furthermore, oxLDL is not a single, well-defined entity, but has structural and physical properties which vary according to the degree of oxidation. We tested the hypothesis that the biological effects of oxLDL will vary according to its degree of oxidation and that some species of oxLDL will have atherogenic properties, while other species may be responsible for its inflammatory activity. The atherogenic and inflammatory properties of LDL oxidized to predetermined degrees (mild, moderate and extensive oxidation) were investigated in a single system using human monocyte-derived macrophages. Expression of CD36 mRNA was up-regulated by mildly- and moderately-oxLDL, but not highly-oxLDL. The expression of the transcription factor, proliferator-activated receptor-gamma (PPARgamma), which has been proposed to positively regulate the expression of CD36, was increased to the greatest degree by highly-oxLDL. However, the DNA binding activity of PPARgamma was increased only by mildly- and moderately-oxLDL. None of the oxLDL species appeared to be pro-inflammatory towards monocytes, either directly or indirectly through mediators derived from lymphocytes, regardless of the degree of oxidation. (C) 2003 Published by Elsevier Science Ireland Ltd.

Increased temperature sensitivity of net DOC production from ombrotrophic peat due to water table draw-down.

The production and release of dissolved organic carbon (DOC) from peat soils is thought to be sensitive to changes in climate, specifically changes in temperature and rainfall. However, little is known about the actual rates of net DOC production in response to temperature and water table draw-down, particularly in comparison to carbon dioxide (CO2) fluxes. To explore these relationships, we carried out a laboratory experiment on intact peat soil cores under controlled temperature and water table conditions to determine the impact and interaction of each of these climatic factors on net DOC production. We found a significant interaction (P < 0.001) between temperature, water table draw-down and net DOC production across the whole soil core (0 to −55 cm depth). This corresponded to an increase in the Q10 (i.e. rise in the rate of net DOC production over a 10 °C range) from 1.84 under high water tables and anaerobic conditions to 3.53 under water table draw-down and aerobic conditions between −10 and − 40 cm depth. However, increases in net DOC production were only seen after water tables recovered to the surface as secondary changes in soil water chemistry driven by sulphur redox reactions decreased DOC solubility, and therefore DOC concentrations, during periods of water table draw-down. Furthermore, net microbial consumption of DOC was also apparent at − 1 cm depth and was an additional cause of declining DOC concentrations during dry periods. Therefore, although increased temperature and decreased rainfall could have a significant effect on net DOC release from peatlands, these climatic effects could be masked by other factors controlling the biological consumption of DOC in addition to soil water chemistry and DOC solubility. These findings highlight both the sensitivity of DOC release from ombrotrophic peat to episodic changes in water table draw-down, and the need to disentangle complex and interacting controls on DOC dynamics to fully understand the impact of environmental change on this system.

Technologies for biological containment of GM and Non-GM crops

International Perspective The development of GM technology continues to expand into increasing numbers of crops and conferred traits. Inevitably, the focus remains on the major field crops of soybean, maize, cotton, oilseed rape and potato with introduced genes conferring herbicide tolerance and/or pest resistance. Although there are comparatively few GM crops that have been commercialised to date, GM versions of 172 plant species have been grown in field trials in 31 countries. European Crops with Containment Issues Of the 20 main crops in the EU there are four for which GM varieties are commercially available (cotton, maize for animal feed and forage, and oilseed rape). Fourteen have GM varieties in field trials (bread wheat, barley, durum wheat, sunflower, oats, potatoes, sugar beet, grapes, alfalfa, olives, field peas, clover, apples, rice) and two have GM varieties still in development (rye, triticale). Many of these crops have hybridisation potential with wild and weedy relatives in the European flora (bread wheat, barley, oilseed rape, durum wheat, oats, sugar beet and grapes), with escapes (sunflower); and all have potential to cross-pollinate fields non-GM crops. Several fodder crops, forestry trees, grasses and ornamentals have varieties in field trials and these too may hybridise with wild relatives in the European flora (alfalfa, clover, lupin, silver birch, sweet chestnut, Norway spruce, Scots pine, poplar, elm, Agrostis canina, A. stolonifera, Festuca arundinacea, Lolium perenne, L. multiflorum, statice and rose). All these crops will require containment strategies to be in place if it is deemed necessary to prevent transgene movement to wild relatives and non-GM crops. Current Containment Strategies A wide variety of GM containment strategies are currently under development, with a particular focus on crops expressing pharmaceutical products. Physical containment in greenhouses and growth rooms is suitable for some crops (tomatoes, lettuce) and for research purposes. Aquatic bioreactors of some non-crop species (algae, moss, and duckweed) expressing pharmaceutical products have been adopted by some biotechnology companies. There are obvious limitations of the scale of physical containment strategies, addressed in part by the development of large underground facilities in the US and Canada. The additional resources required to grow plants underground incurs high costs that in the long term may negate any advantage of GM for commercial productioNatural genetic containment has been adopted by some companies through the selection of either non-food/feed crops (algae, moss, duckweed) as bio-pharming platforms or organisms with no wild relatives present in the local flora (safflower in the Americas). The expression of pharmaceutical products in leafy crops (tobacco, alfalfa, lettuce, spinach) enables growth and harvesting prior to and in the absence of flowering. Transgenically controlled containment strategies range in their approach and degree of development. Plastid transformation is relatively well developed but is not suited to all traits or crops and does not offer complete containment. Male sterility is well developed across a range of plants but has limitations in its application for fruit/seed bearing crops. It has been adopted in some commercial lines of oilseed rape despite not preventing escape via seed. Conditional lethality can be used to prevent flowering or seed development following the application of a chemical inducer, but requires 100% induction of the trait and sufficient application of the inducer to all plants. Equally, inducible expression of the GM trait requires equally stringent application conditions. Such a method will contain the trait but will allow the escape of a non-functioning transgene. Seed lethality (‘terminator’ technology) is the only strategy at present that prevents transgene movement via seed, but due to public opinion against the concept it has never been trialled in the field and is no longer under commercial development. Methods to control flowering and fruit development such as apomixis and cleistogamy will prevent crop-to-wild and wild-to-crop pollination, but in nature both of these strategies are complex and leaky. None of the genes controlling these traits have as yet been identified or characterised and therefore have not been transgenically introduced into crop species. Neither of these strategies will prevent transgene escape via seed and any feral apomicts that form are arguably more likely to become invasives. Transgene mitigation reduces the fitness of initial hybrids and so prevents stable introgression of transgenes into wild populations. However, it does not prevent initial formation of hybrids or spread to non-GM crops. Such strategies could be detrimental to wild populations and have not yet been demonstrated in the field. Similarly, auxotrophy prevents persistence of escapes and hybrids containing the transgene in an uncontrolled environment, but does not prevent transgene movement from the crop. Recoverable block of function, intein trans-splicing and transgene excision all use recombinases to modify the transgene in planta either to induce expression or to prevent it. All require optimal conditions and 100% accuracy to function and none have been tested under field conditions as yet. All will contain the GM trait but all will allow some non-native DNA to escape to wild populations or to non-GM crops. There are particular issues with GM trees and grasses as both are largely undomesticated, wind pollinated and perennial, thus providing many opportunities for hybridisation. Some species of both trees and grass are also capable of vegetative propagation without sexual reproduction. There are additional concerns regarding the weedy nature of many grass species and the long-term stability of GM traits across the life span of trees. Transgene stability and conferred sterility are difficult to trial in trees as most field trials are only conducted during the juvenile phase of tree growth. Bio-pharming of pharmaceutical and industrial compounds in plants Bio-pharming of pharmaceutical and industrial compounds in plants offers an attractive alternative to mammalian-based pharmaceutical and vaccine production. Several plantbased products are already on the market (Prodigene’s avidin, β-glucuronidase, trypsin generated in GM maize; Ventria’s lactoferrin generated in GM rice). Numerous products are in clinical trials (collagen, antibodies against tooth decay and non-Hodgkin’s lymphoma from tobacco; human gastric lipase, therapeutic enzymes, dietary supplements from maize; Hepatitis B and Norwalk virus vaccines from potato; rabies vaccines from spinach; dietary supplements from Arabidopsis). The initial production platforms for plant-based pharmaceuticals were selected from conventional crops, largely because an established knowledge base already existed. Tobacco and other leafy crops such as alfalfa, lettuce and spinach are widely used as leaves can be harvested and no flowering is required. Many of these crops can be grown in contained greenhouses. Potato is also widely used and can also be grown in contained conditions. The introduction of morphological markers may aid in the recognition and traceability of crops expressing pharmaceutical products. Plant cells or plant parts may be transformed and maintained in culture to produce recombinant products in a contained environment. Plant cells in suspension or in vitro, roots, root cells and guttation fluid from leaves may be engineered to secrete proteins that may be harvested in a continuous, non-destructive manner. Most strategies in this category remain developmental and have not been commercially adopted at present. Transient expression produces GM compounds from non-GM plants via the utilisation of bacterial or viral vectors. These vectors introduce the trait into specific tissues of whole plants or plant parts, but do not insert them into the heritable genome. There are some limitations of scale and the field release of such crops will require the regulation of the vector. However, several companies have several transiently expressed products in clinical and pre-clinical trials from crops raised in physical containment.

Local management and landscape drivers of pollination and biological control services in a Kenyan agro-ecosystem

Arthropods that have a direct impact on crop production (i.e. pests, natural enemies and pollinators) can be influenced by both local farm management and the context within which the fields occur in the wider landscape. However, the contributions and spatial scales at which these drivers operate and interact are not fully understood, particularly in the developing world. The impact of both local management and landscape context on insect pollinators and natural enemy communities and on their capacity to deliver related ecosystem services to an economically important tropical crop, pigeonpea was investigated. The study was conducted in nine paired farms across a gradient of increasing distance to semi-native vegetation in Kibwezi, Kenya. Results show that proximity of fields to semi-native habitats negatively affected pollinator and chewing insect abundance. Within fields, pesticide use was a key negative predictor of pollinator, pest and foliar active predator abundance. On the contrary, fertilizer application significantly enhanced pollinator and both chewing and sucking insect pest abundance. At a 1 km spatial scale of fields, there were significant negative effects of the number of semi-native habitat patches within fields dominated by mass flowering pigeonpea on pollinators abundance. For service provision, a significant decline in fruit set when insects were excluded from flowers was recorded. This study reveals the interconnections of pollinators, predators and pests with pigeonpea crop. For sustainable yields and to conserve high densities of both pollinators and predators of pests within pigeonpea landscapes, it is crucial to target the adoption of less disruptive farm management practices such as reducing pesticide and fertilizer inputs.

Universal scaling of production rates across mammalian lineages

Over many millions of years of independent evolution, placental, marsupial and monotreme mammals have diverged conspicuously in physiology, life history and reproductive ecology. The differences in life histories are particularly striking. Compared with placentals, marsupials exhibit shorter pregnancy, smaller size of offspring at birth and longer period of lactation in the pouch. Monotremes also exhibit short pregnancy, but incubate embryos in eggs, followed by a long period of post-hatching lactation. Using a large sample of mammalian species, we show that, remarkably, despite their very different life histories, the scaling of production rates is statistically indistinguishable across mammalian lineages. Apparently all mammals are subject to the same fundamental metabolic constraints on productivity, because they share similar body designs, vascular systems and costs of producing new tissue.

Sensitivity analysis of an ocean carbon cycle model in the North Atlantic: an investigation of parameters affecting the air-sea CO2 flux, primary production and export of detritus

The sensitivity of the biological parameters in a nutrient-phytoplankton-zooplankton-detritus (NPZD) model in the calculation of the air-sea CO2 flux, primary production and detrital export is analysed. We explore the effect on these outputs of variation in the values of the twenty parameters that control ocean ecosystem growth in a 1-D formulation of the UK Met Office HadOCC NPZD model used in GCMs. We use and compare the results from one-at-a-time and all-at-a-time perturbations performed at three sites in the EuroSITES European Ocean Observatory Network: the Central Irminger Sea (60° N 40° W), the Porcupine Abyssal Plain (49° N 16° W) and the European Station for Time series in the Ocean Canary Islands (29° N 15° W). Reasonable changes to the values of key parameters are shown to have a large effect on the calculation of the air-sea CO2 flux, primary production, and export of biological detritus to the deep ocean. Changes in the values of key parameters have a greater effect in more productive regions than in less productive areas. The most sensitive parameters are generally found to be those controlling well-established ocean ecosystem parameterisations widely used in many NPZD-type models. The air-sea CO2 flux is most influenced by variation in the parameters that control phytoplankton growth, detrital sinking and carbonate production by phytoplankton (the rain ratio). Primary production is most sensitive to the parameters that define the shape of the photosynthesis-irradiance curve. Export production is most sensitive to the parameters that control the rate of detrital sinking and the remineralisation of detritus.

Biological significance of short-chain fatty acid metabolism by the intestinal microbiome

Purpose of review Evidence suggests that short-chain fatty acids (SCFAs) derived from microbial metabolism in the gut play a central role in host homeostasis. The present review describes the current understanding and physiological implications of SCFAs derived from microbial metabolism of nondigestible carbohydrates. Recent findings Recent studies indicate a role for SCFAs, in particular propionate and butyrate, in the metabolic and inflammatory disorders such as obesity, diabetes and inflammatory bowel diseases, through the activation of specific G-protein-coupled receptors and modification of transcription factors. Established prebiotics, such as fructooligosaccharides and galactooligosaccharides, which support the growth of Bifidobacteria, mainly mediate acetate production. Thus, recent identification of prebiotics which are able to stimulate the production of propionate and butyrate by benign saccharolytic populations in the colon is of interest. Summary Manipulation of saccharolytic fermentation by prebiotic substrates is beginning to provide information on structure–function relationships relating to the production of SCFAs, which have multiple roles in host homeostasis.

How body mass and lifestyle affect juvenile biomass production in placental mammals

In mammals, the mass-specific rate of biomass production during gestation and lactation, here called maternal productivity, has been shown to vary with body size and lifestyle. Metabolic theory predicts that post-weaning growth of offspring, here termed juvenile productivity, should be higher than maternal productivity, and juveniles of smaller species should be more productive than those of larger species. Furthermore because juveniles generally have similar lifestyles to their mothers, across species juvenile and maternal productivities should be correlated. We evaluated these predictions with data from 270 species of placental mammals in 14 taxonomic/lifestyle groups. All three predictions were supported. Lagomorphs, perissodactyls and artiodactyls were very productive both as juveniles and as mothers as expected from the abundance and reliability of their foods. Primates and bats were unproductive as juveniles and as mothers, as expected as an indirect consequence of their low predation risk and consequent low mortality. Our results point the way to a mechanistic explanation for the suite of correlated life-history traits that has been called the slow–fast continuum.

Molecular insights of p47phox phosphorylation dynamics in the regulation of NADPH oxidase activation and superoxide production

Phagocyte superoxide production by a multicomponent NADPH oxidase is important in host defense against microbial invasion. However inappropriate NADPH oxidase activation causes inflammation. Endothelial cells express NADPH oxidase and endothelial oxidative stress due to prolonged NADPH oxidase activation predisposes many diseases. Discovering the mechanism of NADPH oxidase activation is essential for developing novel treatment of these diseases. The p47phox is a key regulatory subunit of NADPH oxidase; however, due to the lack of full protein structural information, the mechanistic insight of p47phox phosphorylation in NADPH oxidase activation remains incomplete. Based on crystal structures of three functional domains, we generated a computational structural model of the full p47phox protein. Using a combination of in silico phosphorylation, molecular dynamics simulation and protein/protein docking, we discovered that the C-terminal tail of p47phox is critical for stabilizing its autoinhibited structure. Ser-379 phosphorylation disrupts H-bonds that link the C-terminal tail to the autoinhibitory region (AIR) and the tandem Src homology 3 (SH3) domains, allowing the AIR to undergo phosphorylation to expose the SH3 pocket for p22phox binding. These findings were confirmed by site-directed mutagenesis and gene transfection of p47phox_/_ coronary microvascular cells. Compared with wild-type p47phoxcDNAtransfected cells, the single mutation of S379A completely blocked p47phox membrane translocation, binding to p22phox and endothelial O2 . production in response to acute stimulation of PKC. p47phox C-terminal tail plays a key role in stabilizing intramolecular interactions at rest. Ser-379 phosphorylation is a molecular switch which initiates p47phox conformational changes and NADPH oxidase-dependent superoxide production by cells.

Production of acid whey hydrolysates applying an integrative process: effect of calcium on process performance

High ionic calcium concentration and the absence of caseinmacropeptides (CMP) in acid whey could influence the production of angiotensin-I-converting enzyme (ACE)-inhibitory hydrolysate and its bioactivity through the application of the integrative process. Therefore, the aim of the present study was to produce a hydrolysate from acid whey applying the integrative process. Process performance was evaluated based on protein adsorption capacity and conversion in relation to ACE-inhibitory activity (ACEi%) and ionic calcium concentration. Hydrolysates with high potency of their biological activity were produced (IC50 = 206-353 μg mL-1). High ionic calcium concentration in acid whey contributed to ACE-inhibitory activity. However, low β-lactoglobulin adsorption and conversion was observed. Optimisation of the resin volume increased the adsorption of β-lactoglobulin significantly but with lower selectivity. The changes in conversion value were not significant even at higher concentration of enzyme. Several ACE inhibitors derived from β-lactoglobulin that were identified before in sweet whey hydrolysates such as, IIAEKT, IIAE, IVTQ, LIVTQ, LIVTQT, LDAQ and LIVT were found. New peptides such as, SNICNI and ECCHGD derived from α-lactalbumin and BSA respectively were identified.