Accelerated belowground C cycling in a managed agriforest ecosystem exposed to elevated carbon dioxide concentrations

We investigated the effects of three elevated atmospheric CO₂ levels on a Populus deltoides plantation at Biosphere 2 Laboratory in Oracle Arizona. Stable isotopes of carbon have been used as tracers to separate the carbon present before the CO₂ treatments started (old C), from that fixed after CO₂ treatments began (new C). Tree growth at elevated [CO₂] increased inputs to soil organic matter (SOM) by increasing the production of fine roots and accelerating the rate of root C turnover. However, soil carbon content decreased as [CO₂] in the atmosphere increased and inputs of new C were not found in SOM. Consequently, the rates of soil respiration increased by 141% and 176% in the 800 and 1200 μL L^?1 plantations, respectively, when compared with ambient [CO₂] after 4 years of exposure. However, the increase in decomposition of old SOM (i.e. already present when CO₂ treatments began) accounted for 72% and 69% of the increase in soil respiration seen under elevated [CO₂]. This resulted in a net loss of soil C at a rate that was between 10 and 20 times faster at elevated [CO₂] than at ambient conditions. The inability to retain new and old C in the soil may stem from the lack of stabilization of SOM, allowing for its rapid decomposition by soil heterotrophs.     

Encoded metal nanoparticle-based molecular beacons for multiplexed detection of DNA

In this paper we describe a molecular beacon format assay in which encoded nanowire particles are used to achieve multiplexing. We demonstrate this principle with the detection of five viral pathogens; Hepatitis A virus, Hepatitis C virus, West Nile Virus, Human Immune Deficiency virus and Severe Acute Respiratory Syndrome virus. Oligonucleotides are designed complementary to a target sequence of interest containing a 3′ universal fluorescence dye. A 5′ thiol causes the oligonucleotides to self-assemble onto the metal nanowire. The single-stranded oligonucleotide contains a self-complementary hairpin stem sequence of 10 bases that forces the 3′ fluorophore to come into contact with the metallic nanowire surface, thereby quenching the fluorescence. Upon addition of target DNA, there is hybridization with the complementary oligonucleotides. The resulting DNA hybrid is rigid, unfolds the hairpin structure, and causes the fluorophore to be moved away from the surface such that it is no longer quenched. By using differently encoded nanowires, each conjugated with a different oligonucleotide sequence, multiplexed DNA assays are possible using a single fluorophore, from a multiplexed RT-PCR reaction.     

Vegetation quality and habitat selection by European haresLepus europaeus in a pastural landscape

European haresLepus europaeus Pallas, 1778 have lower population densities and body condition in pastural landscapes than in arable landscapes, but reasons for this are not understood. The aim of this study was to determine whether forage quality is low in pastural landscapes during certain seasons. We carried out chemical analysis of the nutritional quality of 5 habitat types to determine whether hares select high quality habitats, and whether nutritional quality explains seasonal differences in range sizes of hares in pastural landscapes. Hares did not tend to select habitats of high nutritional quality (protein, fat or energy) over those of lower quality. Hares did not increase active range size as the overall energy content of forage at the study site decreased; seasonal differences in active range size were not explained by nutritional quality. Differences may be explained by behavioural changes related to breeding. Pastural habitat is fairly stable in terms of nutritional quality through the year, and results suggest that poor forage quality is unlikely to be responsible for the poor body condition of hares in pastural landscapes. Hares in these landscapes are more likely to be limited by habitat quality in terms of cover than by forage.     

Roles of Aquaporins in Root Responses to Irrigation

Due to current environmental issues concerning the use of water for irrigation, the improvement of crop water-use efficiency and a reduction in water consumption has become a priority. New irrigation methods that reduce water use, while still maintaining production have been developed. To optimise these techniques knowledge of above- and below-ground plant physiological responses is necessary. During growth, plant roots are exposed to cycles of wetting and drying in normal rain-fed and irrigation situations. This review concentrates on the below-ground aspects, in particular the water permeability of roots. Significant research has been conducted on the root anatomy and hydraulic conductivity of desert plants subjected to wetting and drying. Major intrinsic proteins (MIPs), most of which show aquaporin (water-channel) activity are likely to be involved in balancing the water relations of the plants during water deficit. However, many MIPs seem to allow permeation of other small neutral solutes and some may allow permeation of ions under certain conditions. The ability of the plant to rapidly respond to rewetting may be important in maintaining productivity. It has been suggested that aquaporins may be involved in this rapid response. The down-regulation of the aquaporins during dry conditions can also limit water loss to the soil, and intrinsic sensitivity of aquaporins to water potential is shown here to be very strong in some cases (NOD26). However, the response of aquaporins in various plant species to water deficits has been quite varied. Another component of aquaporin regulation in response to various stresses (hypoxia/anoxia, salinity and chilling) may be related to redistribution of flow to more favourable regions of the soil. Some irrigation techniques may be triggering these responses. Diurnal fluctuations of root hydraulic conductance that is related to aquaporin expression seem to match the expected transpirational demands of the shoot, and it remains to be seen if shoot-to-root signalling may be important in regulation of root aquaporins. If so, canopy management typical of horticultural crops may impact on root hydraulic conductance. An understanding of the regulation of aquaporins may assist in the development of improved resistance to water stress and greater efficiency of water use by taking into account where and when roots best absorb water.     

Riparian roots through time, space and disturbance

Riparian zones are landscape features adjacent to streams and are widely recognized as important in reducing erosion and filtering groundwater. Few studies directly investigate rooting dynamics of riparian areas, and little information exists concerning riparian root densities, biomass, depth profiles, changes through time, or vulnerability to disturbance. This study examined spatial and temporal patterns in root systems in streamsides influenced by season, hydrologic regime, vegetative composition, and ice storm disturbance in the eastern Adirondacks, New York. Sequential root cores and in-growth cores were collected from June 2000 through August 2001 in a riparian area with minimal ice storm damage adjacent to a third-order stream. Data were used to assess seasonal trends in root biomass and to provide a reference for spatial comparisons. The biomass and surface area of roots collected in the reference site cores were compared with cores collected at nine additional riparian sites differing in degree of canopy damage from the January 1998 ice storm. Average root biomass at the reference site was 1330 g/m², comparable to or greater than values reported for terrestrial and other riparian systems. Root biomass varied seasonally with a maximum root biomass in August, 2000; this result was not repeated the following year after the water table inundated much of the rooting zone in mid-June. Root biomass was spatially variable on a range of scales. Although the maximum root surface area occurred in the upper 10 cm, root biomass peaked at 20–30 cm belowground, unlike observations from most other root studies where the maximum root biomass has been found in the top 10 cm. Areas severely damaged by the ice storm had significantly less root biomass and surface area than areas with low damage. This study demonstrates that root biomass in riparian areas is highly dynamic over time, space, and across disturbance sites. Our findings suggest that the spatial variability in root densities has direct implications for riparian vulnerability to erosion.     

The effects of foliar pubescence and nutrient enrichment on arthropod communities of Metrosideros polymorpha (Myrtaceae)

Abstract.  1. Nutrient resource availability and host-plant foliar pubescence both influence arthropod food webs, but multifactor studies are needed to understand their interdependence and relative importance. Arthropods were sampled by clipping foliage from Metrosideros polymorpha (Myrtaceae) trees of pubescent, glabrous, and intermediate leaf forms on fertilised and unfertilised plots.
2. Fertilisation decreased leaf mass per area (LMA) but did not change the relative mass of pubescence within leaf morphological classes.
3. Fertilisation increased densities of individuals in four taxonomic orders, densities of individuals and species of all trophic levels, and the biomass of Collembola and Homoptera. Herbivore relative diversity (Shannon H ') also increased with fertilisation, but detritivore diversity declined due to increasing dominance of Salina celebensis (Schaeffer) (Collembola).
4. Detritivore density, driven again by S. celebensis , increased with decreasing leaf pubescence, but Heteroptera and Acari were most abundant on the intermediate pubescence class, and Psocoptera density and biomass increased with increasing pubescence. Trophic-level species density did not change with leaf morphological class, but relative diversity of all arthropods and of detritivores increased with increasing pubescence.
5. Both resource availability and leaf pubescence affected Metrosideros arthropod communities. However, the pervasive positive influence of fertilisation did not translate to compositional shifts, and there were no interactions with leaf morphological class. In contrast, the effects of leaf pubescence on arthropod density, biomass, and diversity were more restricted taxonomically, and non-parametric manova and redundancy analyses demonstrated significant differentiation in community composition on the pubescent morphology.     

Control of Substrate Specificity by Active-Site Residues in Nitrobenzene Dioxygenase

Nitrobenzene 1,2-dioxygenase from Comamonas sp. strain JS765 catalyzes the initial reaction in nitrobenzene degradation, forming catechol and nitrite. The enzyme also oxidizes the aromatic rings of mono- and dinitrotoluenes at the nitro-substituted carbon, but the basis for this specificity is not understood. In this study, site-directed mutagenesis was used to modify the active site of nitrobenzene dioxygenase, and the contribution of specific residues in controlling substrate specificity and enzyme performance was evaluated. The activities of six mutant enzymes indicated that the residues at positions 258, 293, and 350 in the α subunit are important for determining regiospecificity with nitroarene substrates and enantiospecificity with naphthalene. The results provide an explanation for the characteristic specificity with nitroarene substrates. Based on the structure of nitrobenzene dioxygenase, substitution of valine for the asparagine at position 258 should eliminate a hydrogen bond between the substrate nitro group and the amino group of asparagine. Up to 99% of the mononitrotoluene oxidation products formed by the N258V mutant were nitrobenzyl alcohols rather than catechols, supporting the importance of this hydrogen bond in positioning substrates in the active site for ring oxidation. Similar results were obtained with an I350F mutant, where the formation of the hydrogen bond appeared to be prevented by steric interference. The specificity of enzymes with substitutions at position 293 varied depending on the residue present. Compared to the wild type, the F293Q mutant was 2.5 times faster at oxidizing 2,6-dinitrotoluene while retaining a similar K_m for the substrate based on product formation rates and whole-cell kinetics.     

Semen displacement as a sperm competition strategy

Using a sample of 652 college students, we examined several implications of the hypothesis that the shape of the human penis evolved to enable males to substitute their semen for those of their rivals. The incidence of double mating by females appears sufficient to make semen displacement adaptive (e.g., one in four females acknowledge infidelity, one in eight admit having sex with two or more males in a 24-hour period, and one in 12 report involvement in one or more sexual threesomes with two males). We also document several changes in post-ejaculatory behavior (e.g., reduced thrusting, penis withdrawal, loss of an erection) which may have evolved to minimize displacement of the male’s own semen. Consistent with predictions derived from a theoretical model (Gallup and Burch 2006), we discovered that most females report waiting at least 48 hours following an instance of infidelity before resuming sex with their in-pair partners.     

Making water flow: a comparison of the hydrodynamic characteristics of 12 different benthic biological flumes

Flume tanks are becoming increasingly important research tools in aquatic ecology, to link biological to hydrodynamical processes. There is no such thing as a “standard flume tank”, and no flume tank is suitable for every type of research question. A series of experiments has been carried out to characterise and compare the hydrodynamic characteristics of 12 different flume tanks that are designed specifically for biological research. These facilities are part of the EU network BioFlow. The flumes could be divided into four basic design types: straight, racetrack, annular and field flumes. In each facility, two vertical velocity profiles were measured: one at 0.05 m s⁻¹ and one at 0.25 m s⁻¹. In those flumes equipped with Acoustic Doppler Velocimeters (ADV), time series were also recorded for each velocity at two heights above the bottom: 0.05 m and 20% of the water depth. From these measurements turbulence characteristics, such as TKE and Reynolds stress, were derived, and autocorrelation spectra of the horizontal along-stream velocity component were plotted. The flume measurements were compared to two sets of velocity profiles measured in the field.Despite the fact that some flumes were relatively small, turbulence was fully developed in all channels. Straight and racetrack flumes generally produced boundary layers with a clearly definable logarithmic layer, similar to measurements in the field taken under steady flow conditions. The two annular flumes produced relatively thin boundary layers, presumably due to secondary flows developing in the curved channels. The profiles in the field flumes also differed considerably from the expected log profile. This may either have been due the construction of the flume, or due to unsteady conditions during measurement. Constraints imposed by the different flume designs on the suitability for different types of boundary layer research, as well as scaling issues are discussed.     

Expression of HvHMA2 in tobacco modifies Zn–Fe–Cd homeostasis

HvHMA2 is a plasma membrane P_1B-ATPase from barley that functions in Zn/Cd root-to-shoot transport. To assess the usefulness of HvHMA2 for modifying the metal content in aerial plant parts, it was expressed in tobacco under the CaMV35S promoter. Transformation with HvHMA2 did not produce one unique pattern of Zn and Cd accumulation; instead it depended on external metal supply. Thus Zn and Cd root-to-shoot translocation was facilitated, but not at all applied Zn/Cd concentrations. Metal uptake was restricted in HvHMA2-transformed plants and the level in the shoot was not enhanced. It was shown that HvHMA2 localizes to the plasma membrane of tobacco cells, and overloads the apoplast with Zn, which could explain the overall decrease in metal uptake observed. Despite the lower levels in the shoot, HvHMA2 transformants showed increased Zn sensitivity. Moreover, introduction of HvHMA2 into tobacco interfered with Fe metabolism and Fe accumulation was modified in HvHMA2-transformants in a Zn- and Cd-concentration dependent manner. The results indicate that ectopic expression of the export protein HvHMA2 in tobacco interferes with tobacco metal Zn–Cd–Fe cross-homeostasis, inducing internal mechanisms regulating metal uptake and tolerance.