Molecular profiling of soil animal diversity in natural ecosystems: Incongruence of molecular and morphological results

A major problem facing ecologists is obtaining a complete picture of the highly complex soil community. While DNA-based methods are routinely used to assess prokaryote community structure and diversity in soil, approaches for measuring the total faunal community are not yet available. This is due to difficulties such as designing primers specific to a range of soil animals while excluding other eukaryotes. Instead, scientists use laborious and specialized taxonomic methods for extracting and identifying soil fauna. We examined this problem using DNA sequencing to profile soil animal diversity across two Alaskan ecosystems and compare the results with morphological analyses. Of 5267 sequences, representing 549 operational taxonomic units (OTU), only 18 OTUs were common to both sites. Representatives included 8 phyla, dominated by arthropods and nematodes. This is the most comprehensive molecular analysis of soil fauna to date, and provides a tool to rapidly assess a missing component of soil biodiversity.     

Effect of removal of logging residue on nutrient leaching and nutrient pools in the soil after clearcutting in a Norway spruce stand

Following clearcutting applying the conventional stem-only harvesting method in a Norway spruce (Picea abies (L.) Karst.) stand and different levels of removal of logging residue, the nutrient fluxes from the heaps of logging residue and from the O horizon were monitored over four growing seasons and the soil nutrient pools were determined. Three levels of removal of logging residue were carried out using (i) conventional stem-only harvesting (no residues removed); (ii) residues removed; and (iii) removal of branches (foliage left on site). The heaps of logging residue were a minor source of inorganic N entering the soil in the water percolating through the heaps, but they were a significant source of organic N, P, Ca, Mg, and especially K. Nutrient fluxes from the O horizon were in general greater under the heaps of logging residue as compared to soils without overlying logging residue. The leaching of inorganic N from the O horizon under the heaps of logging residue resulted in a net loss of these compounds, while the O horizon without overlying logging residue gained N. The removal of logging residue significantly decreased the extractable K pools in the soil while it or conversely, the presence of residue heaps had no significant effect on the pools of organic matter and the pools of N, P, Ca, and Mg in the O horizon and in the 0–10 cm soil layer. The results show that the short-term effects of logging residue on nutrient dynamics in the soil can be complex and difficult to interpret in terms of site productivity as there are changes in the nutrient fluxes, which imply the opposite effects on site productivity. However, the results do indicate that, in the short-term, the removal of logging residue does not impair pools of N in the soil nor site productivity on sites where the availability of N limits productivity.     

Improved Detection of Domoic Acid Using Covalently Immobilised Antibody Fragments

Antibody molecules, and antibody fragments in particular, have enormous potential in the development of biosensors for marine monitoring. Conventional immobilisation approaches used in immunoassays typically yield unstable and mostly incorrectly oriented antibodies, however, resulting in reduced detection sensitivities for already low concentration analytes. The 2H12 anti-domoic acid scFv antibody fragment was engineered with cysteine-containing linkers of two different lengths, distal to the antigen binding pocket, for covalent and correctly oriented immobilisation of the scFvs on functionalised solid supports. The Escherichia coli-produced, cysteine-engineered scFvs dimerised in solution and demonstrated similar efficiencies of covalent immobilisation on maleimide-activated plates and minimal non-covalent attachment. The covalently attached scFvs exhibited negligible leaching from the support under acidic conditions that removed almost 50% of the adsorbed wildtype fragment, and IC₅₀s for domoic acid of 270 and 297 ng/mL compared with 1126 and 1482 ng/mL, respectively, for their non-covalently adsorbed counterparts. The expression and immobilisation approach will facilitate the development of stable, reusable biosensors with increased stability and detection sensitivity for marine neurotoxins.