Nitrous oxide and dinitrogen emissions from urine-affected soil under controlled conditions

A ¹⁵N labelling technique was used to measure N₂O and N₂ emissions from an undisturbed grassland soil treated with cow urine and held at 30 cm water tension and 20°C in a laboratory. Large emissions of dinitrogen were detected immediately following urine application to pasture. These coincided with a rapid and large increase in soil water-soluble carbon levels, some of this increase being attributed to solubilization of soil organic matter by high pH and ammonia concentrations. Emissions of nitrous oxide generally increased with time in contrast to dinitrogen fluxes which decreased as time progressed. Estimated losses of N₂O and N₂ over a 30 day period were between 1 to 5% and 30 to 65% of the urine N applied plus N mineralized from soil organic matter, respectively. Most of the N₂ and N₂O originated from denitrification with nitrification-denitrification being of minor significance as a source of N₂O. Comparisons of the ¹⁵N enrichments in the soil mineral N pools and the evolved N₂O suggested that much of the N₂O was produced in the 5–8 cm zone of the soil. It is concluded that established grassland soils contain large amounts of readily-oxidizable organic carbon which may be used by soil denitrifying organisms when nitrate is non-limiting and soil redox potential is lowered due to high rates of biological activity and high soil moisture contents. ei]{gnR}{fnMerckx}     

Inferring evolutionarily significant units of bacterial diversity from broad environmental surveys of single-locus data

By far the greatest challenge for diversity studies is to characterize the diversity of prokaryotes, which probably encompasses billions of species, most of which are unculturable. Recent advances in theory and analysis have focused on multi-locus approaches and on combined analysis of molecular and ecological data. However, broad environmental surveys of bacterial diversity still rely on single-locus data, notably 16S ribosomal DNA, and little other detailed information. Evolutionary methods of delimiting species from single-locus data alone need to consider population genetic and macroevolutionary theories for the expected levels of interspecific and intraspecific variation. We discuss the use of a recent evolutionary method, based on the theory of coalescence within independently evolving populations, compared with a traditional approach that uses a fixed threshold divergence to delimit species.     

Sequence-based species delimitation for the DNA taxonomy of undescribed insects

Cataloging the very large number of undescribed species of insects could be greatly accelerated by automated DNA based approaches, but procedures for large-scale species discovery from sequence data are currently lacking. Here, we use mitochondrial DNA variation to delimit species in a poorly known beetle radiation in the genus Rivacindela from arid Australia. Among 468 individuals sampled from 65 sites and multiple morphologically distinguishable types, sequence variation in three mtDNA genes (cytochrome oxidase subunit 1, cytochrome b, 16S ribosomal RNA) was strongly partitioned between 46 or 47 putative species identified with quantitative methods of species recognition based on fixed unique ("diagnostic") characters. The boundaries between groups were also recognizable from a striking increase in branching rate in clock-constrained calibrated trees. Models of stochastic lineage growth (Yule models) were combined with coalescence theory to develop a new likelihood method that determines the point of transition from species-level (speciation and extinction) to population-level (coalescence) evolutionary processes. Fitting the location of the switches from speciation to coalescent nodes on the ultrametric tree of Rivacindela produced a transition in branching rate occurring at 0.43 Mya, leading to an estimate of 48 putative species (confidence interval for the threshold ranging from 47 to 51 clusters within 2 logL units). Entities delimited in this way exhibited biological properties of traditionally defined species, showing coherence of geographic ranges, broad congruence with morphologically recognized species, and levels of sequence divergence typical for closely related species of insects. The finding of discontinuous evolutionary groupings that are readily apparent in patterns of sequence variation permits largely automated species delineation from DNA surveys of local communities as a scaffold for taxonomy in this poorly known insect group.     

What can phylogenetics tell us about speciation in the Cape flora?

The spectacular diversity of the Cape flora has promoted wide speculation on the evolutionary processes behind its origins, but until recently these ideas could not be tested rigorously due to the almost complete absence of a fossil record for the region. Now, molecular phylogenetic approaches, combined with analyses of ecological and biogeographical information, offer the potential to test key hypotheses about speciation of so-called Cape clades of flowering plants. We outline the main theories and how they might be tested by phylogenetic approaches. One conclusion is that population level studies of particular species complexes are now needed to complement the growing volume of phylogenetic information for Cape clades and to provide better understanding of mechanisms of population divergence in the Cape. Another is that comparisons between Cape and non-Cape clades are needed to confirm whether speciation is indeed faster in the Cape region. An alternative possibility, that extinction rates are lower, should also be considered in these comparisons. By virtue of the ongoing, coordinated efforts by a global team of botanists, the Cape is now uniquely placed for exploring the origins and assembly of a regional assemblage or biome.     

Characterisation of Mal d 1-related genes in <Emphasis Type="Italic">Malus</Emphasis>

It has been suggested that there are at least 15 Mal d 1-related (PR10) genes in one genotype of apple (Malus×domestica Borkh.). We sequenced cDNA libraries of cultivar Royal Gala and identified 12 members of the Mal d 1 family, including the previously reported Mal d 1b and Mal d 1d, an allelic variant of the previously reported Mal d 1a. Eight Mal d 1 gene products were expressed in tree-ripened fruit, in either the cortex or the skin, and most of these were also expressed in leaves in response to challenge with Venturia inaequalis—a fungal disease of apple. Mal d 1 gene products were identified from a large number of different tissues. Degree of ripeness as measured by standard parameters was shown not to predict either the amount of protein able to bind to a specific monoclonal antibody 5H8, previously shown to bind to an allergenic epitope in Mal d 1b and a/d, or the amount of Mal d 1 mRNA present. Mal d 1d and Mal d 1b were the most highly expressed isoforms in Royal Gala, particularly in the skin of fruit, and these isoforms were also predominant in other cultivars and species of apple. Genotypes, however, differed in relative predominance of Mal d 1b and Mal d 1d. The predominantly expressed Mal d 1 genes in ripe apple fruit were translated in vivo into proteins and proteins binding to the antibody were found in all cultivars and species examined. New Mal d 1 proteins were identified that bound to the 5H8 antibody. At least two new subfamilies have been identified, and while some structural differences are predicted between groups of isoforms, the P-loop motif is identical in all except two isoforms. A role in intracellular signalling in plants is suggested and in vitro expression of the isoforms should help in assessing their relative roles in disease, allergic responses, senescence and nucleotide-, cytokinin- and brassinosteroid-binding.     

Nitrogen mineralisation and plant nitrogen acquisition in a nitrogen-limited calcareous grassland

A field study measured the rate of soil mineral N supply and its effects on plant biomass and N accumulation in a 13-year-old, naturally regenerating, calcareous grassland. Gross rates of N mineralisation (2 μg g⁻¹ day⁻¹, i.e. 0.69 kg ha⁻¹ day⁻¹), assessed using ¹⁵N pool dilution, were at the lower end of the range previously reported for grasslands. Weekly additions of liquid N fertiliser ([NH₄]₂SO₄, NH₄NO₃ or KNO₃) and, to a lesser extent the addition of water, increased plant growth substantially, demonstrating that the primary constraint to plant growth was low N availability. In plants that had received NO₃⁻, the activity of the inducible enzyme nitrate reductase in shoots initially increased in proportion to the amount of NO₃⁻ supplied. However, as above-ground herbage accumulated, nitrate reductase activity declined to similar low levels in all treatments, despite the continuance of the constant NO₃⁻ additions. The decline in NR specific activity reflected declining tissue NO₃⁻ concentrations, although total plant NRA may have remained constant during the period of study. The study has shown that plant growth is limited by low N mineralisation rates and indeed the soil is a sink for much added N. Low water availability provides an additional constraint on N mineralisation in this calcareous grassland soil. Any disturbances in the N cycle which increase the availability of mineral N will result in a substantial increase in plant growth within this ecosystem.     

Maximum axial root growth pressure in pea seedlings: effects of measurement techniques and cultivars

Values of the maximum axial growth pressure (σ_max) of seedling pea (Pisum sativum L.) roots reported in the literature, obtained using different apparatuses and cultivars, range from 0.3 MPa to 1.3 MPa. To investigate possible reasons for this large range, we studied the effect of apparatus and cultivar on measurements of σ_max in peas. We describe four types of apparatus which can be used to measure axial root growth force and hence σ_max, and used them to measure σ_max in seedling pea roots using cultivar Meteor. Two of these apparatuses were also used to compare σ_max for three pea cultivars (Helka, Meteor and Greenfeast). Both cultivar and apparatus significantly affected σ_max , but there were greater differences between apparatuses than between the three cultivars. Estimating root cross-sectional area from the diameter of cross-sections, rather than from in situ measurements (i.e. measurements made with the root still in place in the apparatus) may explain these differences. This revised version was published online in June 2006 with corrections to the Cover Date.