DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet.

Ecological understanding of the role of consumer-resource interactions in natural food webs is limited by the difficulty of accurately and efficiently determining the complex variety of food types animals have eaten in the field. We developed a method based on DNA metabarcoding multiplexing and next-generation sequencing to uncover different taxonomic groups of organisms from complex diet samples. We validated this approach on 91 faeces of a large omnivorous mammal, the brown bear, using DNA metabarcoding markers targeting the plant, vertebrate and invertebrate components of the diet. We included internal controls in the experiments and performed PCR replication for accuracy validation in postsequencing data analysis. Using our multiplexing strategy, we significantly simplified the experimental procedure and accurately and concurrently identified different prey DNA corresponding to the targeted taxonomic groups, with ≥ 60% of taxa of all diet components identified to genus/species level. The systematic application of internal controls and replication was a useful and simple way to evaluate the performance of our experimental procedure, standardize the selection of sequence filtering parameters for each marker data and validate the accuracy of the results. Our general approach can be adapted to the analysis of dietary samples of various predator species in different ecosystems, for a number of conservation and ecological applications entailing large-scale population level diet assessment through cost-effective screening of multiple DNA metabarcodes, and the detection of fine dietary variation among samples or individuals and of rare food items.

Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate.

Palaeoenvironments and former climates are typically inferred from pollen and macrofossil records. This approach is time-consuming and suffers from low taxonomic resolution and biased taxon sampling. Here, we test an alternative DNA-based approach utilizing the P6 loop in the chloroplast trnL (UAA) intron; a short (13-158 bp) and variable region with highly conserved flanking sequences. For taxonomic reference, a whole trnL intron sequence database was constructed from recently collected material of 842 species, representing all widespread and/or ecologically important taxa of the species-poor arctic flora. The P6 loop alone allowed identification of all families, most genera (>75%) and one-third of the species, thus providing much higher taxonomic resolution than pollen records. The suitability of the P6 loop for analysis of samples containing degraded ancient DNA from a mixture of species is demonstrated by high-throughput parallel pyrosequencing of permafrost-preserved DNA and reconstruction of two plant communities from the last glacial period. Our approach opens new possibilities for DNA-based assessment of ancient as well as modern biodiversity of many groups of organisms using environmental samples.

Ultrastructural alterations in Fusarium sambucinum and Heterobasidion annosum treated with aluminum chloride and sodium metabisulfite.

Aluminum chloride (AlCl(3)) and sodium metabisulfite (Na(2)S(2)O(5)) have received increasing attention as antifungal agents for the control of plant diseases. In an effort to understand their toxic action on fungi, ultrastructural changes and membrane damage in Fusarium sambucinum (Ascomycota) and Heterobasidion annosum (Basidiomycota) in response to salt exposure was investigated using transmission electron microscopy. Conidial membrane damage was quantified using SYTOX Green stain, which only enters altered membranes. The results showed that mortality of the conidia was generally closely associated with SYTOX stain absorption in F. sambucinum treated with Na(2)S(2)O(5) and in H. annosum treated with AlCl(3) or Na(2)S(2)O(5), suggesting that these salts cause membrane alterations. For both fungi, ultrastructural alterations in conidia treated with AlCl(3) and Na(2)S(2)O(5) included membrane retraction, undulation, and invagination. At higher concentrations or exposure periods to the salts, loss of membrane integrity, cytoplasmic leakage, and cell rupture were observed. Ultrastructural alterations and increased SYTOX stain absorption in salt-treated conidia appear consistent with a mode of action where AlCl(3) and Na(2)S(2)O(5) alter membrane integrity and permeability.

Post-glacial history of the dominant alpine sedge Carex curvula in the European Alpine System inferred from nuclear and chloroplast markers.

The alpine sedge Carex curvula ssp. curvula is a clonal, dominant graminoid found in the European Alps, the Carpathians, the Pyrenees and in some of the Balkan Mountains. It is a late-successional species of acidophilous alpine meadows that occurs on sites that were covered by ice during the last glacial maximum (LGM). By applying the amplified fragment length polymorphism (AFLP) fingerprinting and chloroplast DNA (cpDNA) sequencing, we attempted to identify the recolonization routes followed by the species after the last ice retreat. We relied on the genetic diversity of 37 populations covering the entire distributional range of the species. As a wind-pollinated species, C. curvula is characterized by a low level of population genetic differentiation. Nuclear and chloroplast data both support the hypothesis of a long-term separation of Eastern (Balkans and Carpathians) and Western (Alps and Pyrenees) lineages. In the Alps, a continuum of genetic depauperation from the east to the west may be related to a recolonization wave originating in the eastern-most parts of the chain, where the main glacial refugium was likely located. The Pyrenean populations are nested within the western Alps group and show a low level of genetic diversity, probably due to recent long-distance colonization. In contrast to the Alps, we found no phylogeographical structure in the Carpathians. The combination of reduced ice extension during the Würm period and the presence of large areas of siliceous substrate at suitable elevation suggest that in contrast to populations in the Alps, the species in the Carpathians underwent a local vertical migration rather than extinction and recolonization over long distance.

White pine weevil (Pissodes strobi) biological performance is unaffected by the jasmonic acid or wound-induced defense response in Norway spruce (Picea abies).

In eastern Canada, the white pine weevil (Pissodes strobi Peck) is a pest of several native pine and spruce species and of the introduced species, Norway spruce (Picea abies Karst). We evaluated the feeding activities, oviposition and rate of adult emergence of white pine weevil on field-grown Norway spruce subjected to jasmonic acid or wounding pretreatments. We also monitored the host-plant reaction to white pine weevil attack, jasmonic acid and wounding treatments by quantifying several mono- and sesquiterpenes in bark and characterizing some molecular aspects of the terpenoid response. Two cDNA sequences were identified that had a high percentage of identity with genes encoding monoterpene or sesquiterpene synthases. Both putative terpene synthase genes showed distinctive profiles in Norway spruce bark and needles following all treatments. Although the Norway spruce trees showed different physiological responses to mechanical wounding and white pine weevil attack, transcript activity of the gene encoding terpenoid synthase and consequent accumulation of terpenoid resin did not significantly affect the weevils' feeding activities, oviposition or rate of adult emergence.

Cytochemical labeling for fungal and host components in plant tissues inoculated with fungal wilt pathogens.

Antibodies to detect pectin in present investigations attached to distinct fibrils in vessel lumina. In carnation infected with an isolate of Fusarium oxysporum f.sp., labeling of pathogen cells also occurred; in a resistant cultivar (cv.), it was coincident with proximate pectin fibrils and linked to altered fungal walls, which was the opposite in the susceptible cv., indicating that hindrance of pathogen ability to degrade pectin may be related to resistance. Labeling of the fungus in culture was nil, except in media containing pectin, showing that pectin is not native to the pathogen. Labeling of fungal walls for cellulose in elm (inoculated with Ophiostoma novo-ulmi) and carnation also occurred, linked to adsorbed host wall components. The chitin probe often attached to dispersed matter, in vessel lumina, traceable to irregularly labeled fungal cells and host wall degradation products. With an anti-horseradish peroxidase probe, host and fungal walls were equally labeled, and with a glucosidase, differences of labeling between these walls were observed, depending on pH of the test solution. Fungal extracellular matter and filamentous structures, present in fungal walls, predominantly in another elm isolate (Phaeotheca dimorphospora), did not label with any of the probes used. However, in cultures of this fungus, extracellular material labeled, even at a distance from the colony margin, with an anti-fimbriae probe.

Somatic stability of microsatellite loci in Eastern white pine, Pinus strobus L.

Variation at nuclear- and chloroplast-encoded microsatellite loci was studied among and within clonally propagated individuals of Eastern white pine. Total DNA was extracted and assayed from gamete-bearing tissue (megagametophytes) located on six different branch positions on each of 12 individual genets. No within-individual variation was observed among 12 loci studied. Estimates of numbers of mitotic cell divisions required to produce the tissue used as the source of genomic DNA were obtained by combining tree growth and anatomical data. This allowed for the calculation of upper bound estimates of numbers of mutations per locus per somatic cell division. The estimated somatic mutation rate was found to be substantially lower than those published for genomic microsatellite mutation rates in other plant species.

Formation of Ligno-Suberized Tissues in Jack Pine Resistant to the European Race of Gremmeniella abietina.

ABSTRACT A histological study was conducted to provide insights into the defense mechanisms of Pinus banksiana resistant to the European (EU) race of Gremmeniella abietina in naturally infected sites. At the time of sampling, the only apparent symptom was a blight induced at the tip of the shoots. The identity of G. abietina during microscopic examinations was confirmed by an immunogold labeling method. Once the fungus had succeeded in penetrating the bracts through stomata, it invaded the stem cortex and the phloem cells and attained the vascular cambium. The progression of the pathogen to the pith was possible principally through intense colonization of needle traces but also by the invasion of the rays. Ligno-suberized tissues confining the pathogen within the necrotic area were revealed by histochemical tests. Well-defined boundaries were initiated at the base of healthy needles and at the vascular cambium level. They regularly formed one continuous suberized barrier completely crossing the shoot from one needle to the other. A nonlamellar form of suberin was observed in transmission electron microscopy. Restoration of cambial activities and tissue regeneration following necrophylactic periderm formation were suggested as essential factors in the defense system of P. banksiana against the EU race of G. abietina. To our knowledge, this is the first demonstration of an anatomical defense mechanism of a conifer against Scleroderris canker.

Immunocytochemical Evidence that Secretion of Pectin Occurs During Gel (Gum) and Tylosis Formation in Trees.

ABSTRACT During gel (gum) formation in angiosperm trees, fibrillar material accumulated in protective layers of xylem parenchyma cells before being secreted across half-bordered pit membranes into vessel elements. Immunogold labeling demonstrated that this fibrillar material was mainly composed of partially esterified pectic polysaccharides. The primary wall of expanding tyloses, an extension of the parenchyma protective layer, secreted similar pectic substances to completely block vessel elements. In most studies, these occluding structures were reported to be formed in response to causative factors such as aging processes, injuries, or infections. Current observations support the view that partial to complete embolism, which almost always accompanies these factors, might be the main cause triggering the formation of vessel occlusions. Whereas pectin seems to be the basic component of gels (gums) and of the external layer of tyloses, other substances, such as phenols, were also detected either as a part of these plugs or as accumulations beside them in vessels. Finally, it is proposed that the term 'gel' instead of 'gum' be used in future studies to describe the occluding material secreted by ray and paratracheal parenchyma cells.

A Cytochemical Study of Extracellular Sheaths Associated with Rigidoporus lignosus during Wood Decay.

An ultrastructural and cytochemical investigation of the development of Rigidoporus lignosus, a white-rot fungus inoculated into wood blocks, was carried out to gain better insight into the structure and role of the extracellular sheaths produced by this fungus during wood degradation. Fungal sheaths had a dense or loose fibrillar appearance and were differentiated from the fungal cell wall early after wood inoculation. Close association between extracellular fibrils and wood cell walls was observed at both early and advanced stages of wood alteration. Fungal sheaths were often seen deep in host cell walls, sometimes enclosing residual wood fragments. Specific gold probes were used to investigate the chemical nature of R. lignosus sheaths. While labeling of chitin, pectin, beta-1,4- and beta-1,3-glucans, beta-glucosides, galactosamine, mannose, sialic acid, RNA, fucose, and fimbrial proteins over fungal sheaths did not succeed, galactose residues and laccase (a fungal phenoloxidase) were found to be present. The positive reaction of sheaths with the PATAg test indicates that polysaccharides such as beta-1,6-glucans are important components. Our data suggest that extracellular sheaths produced by R. lignosus during host cell colonization play an important role in wood degradation. Transportation of lignin-degrading enzymes by extracellular fibrils indicates that alteration of plant polymers may occur within fungal sheaths. It is also proposed that R. lignosus sheaths may be involved in recognition mechanisms in fungal cell-wood surface interactions.

Long-term use of intramuscular insulin therapy in a type I diabetic patient with subcutaneous insulin resistance.

We studied a 26-year-old Type 1 diabetic patient who experienced recurrent episodes of ketoacidosis and who was unresponsive to subcutaneous insulin, but normally responsive to intravenous insulin as demonstrated by insulin challenge test. Attempts at intravenous and intraperitoneal insulin administration were complicated by recurrent septicaemia. We therefore investigated the hypoglycaemic effect of intramuscular insulin administration in this patient. After intramuscular injection of NPH and Ultralente human insulin (0.1 U kg-1), the lowest plasma glucose levels occurred 1 and 7 h later, respectively; the hypoglycaemic effect lasted approximately 2 and 12 h, respectively. We based insulin therapy on intramuscular NPH as a fast-acting insulin and Ultralente as an intermediate-acting insulin using four injections a day. During the next 24 months, the patient was hospitalized for 4 weeks versus 56 weeks in the 20 months preceding intramuscular insulin administration, and was able to resume full-time work. HbAlC decreased from 11.7% to 8.7% (normal range: 4.2-5.9%). Thus, long-term intramuscular insulin therapy is a feasible alternative to intravenous or intraperitoneal insulin in patients with well-demonstrated resistance to subcutaneous insulin.