Impacts of alien plants and man‐made disturbance on soil‐growing bryophyte and lichen diversity in coastal areas of Sardinia (Italy)

Abstract

Seventy phytosociological relevés were performed in 1 m × 1 m plots at 14 study sites spread along sandy shores in northern and southern Sardinia (Italy). The plots were selected in different habitat types (open dunes, native Juniperus woodlands, maquis, and plantations with Acacia, Eucalyptus and Pinus) according to a stratified sampling method in order to investigate impacts deriving from different levels of Carpobrotus spp. cover, dry litter from exotic trees, and other disturbance types. The quantile regression and logistic regression analyses revealed that the reduction in the amount of bryophyte and lichen cover on sand dunes of the study area is caused either by a high cover of Carpobrotus spp. mats or by a high cover of dry exotic litter in dense, unmanaged or poorly managed forest plantations. Additional detrimental effects are often driven by other kinds of man‐made disturbances. Forest management in the coastal areas of Sardinia should be gradually modified to take into account the conservation of bryophytes and lichens. Some of the biological indicators used are quite widespread in the Mediterranean coastal habitats or are exclusively associated with sand dunes; therefore, they can also be conveniently used as indicators of biological impacts in other countries or islands of the same biogeographical region.     

Experimental and modelling studies of drought‐adaptive root architectural traits in wheat (Triticum aestivum L.)

Abstract

This paper presents an interdisciplinary approach to crop improvement that links physiology with plant breeding and simulation modelling to enhance the selection of high‐yielding, drought‐tolerant varieties. In a series of field experiments in Queensland, Australia, we found that the yield of CIMMYT wheat line SeriM82 ranged from 6% to 28% greater than the current cultivar Hartog. Physiological studies on the adaptive traits revealed that SeriM82 had a narrower root architecture and extracted more soil moisture, particularly deep in the profile. Results of a simulation analysis of these adaptive root traits with the cropping system model APSIM for a range of rain‐fed environments in southern Queensland indicated a mean relative yield benefit of 14.5% in water‐deficit seasons. Furthermore, each additional millimetre of water extracted during grain filling generated an extra 55 kg ha^?1 of grain yield. Further root studies of a large number of wheat genotypes revealed that wheat root architecture is closely linked to the angle of seminal roots at the seedling stage – a trait which is suitable for large‐scale and cost‐effective screening programmes. Overall, our results suggest that an interdisciplinary approach to crop improvement is likely to enhance the rate of yield improvement in rain‐fed crops.     

Geometric morphometric analyses of leaf variation in four oak species of the subgenus Quercus (Fagaceae)

Abstract

This paper defines a protocol for the study of leaf morphology and morphometric relationships among Quercus frainetto, Quercus robur, Quercus petraea and Quercus pubescens. Leaf shapes were investigated in an attempt to characterize and discriminate among these four species. Landmark and outline data were compared in order to ascertain their relative efficacy for describing variation in leaf morphology. MANOVA was performed to assess intra‐specific differentiation and to compare the distribution of variance in individuals, populations and species. A strong correlation was found between landmark and outline datasets of the four species: both methods proved capable of discriminating among the four species. Finally, a Two‐Block Partial Least‐Squares analysis was performed for each species in order to assess the correlation between intra‐specific shape variation and environmental factors.     

Stand characteristics and biodiversity indicators along the productivity gradient in boreal forests: Defining a critical set of indicators for the monitoring of habitat nature quality

Abstract

We quantified the effects of anthropogenic disturbances on the structure and biodiversity of boreal forests on acidic soils and created a statistically supported rational set of indicators to monitor the stand “naturalness”. For that, we surveyed various traits of tree layer, understory, herb layer, forest floor and several widely accepted biodiversity epiphytic indicators in 252 old‐aged boreal stands in Estonia, mostly dominated by Scots pine or Norway spruce. Multifactorial general linear model analyses showed that many forest characteristics and potential indicators were confounded by the gradient of soil productivity (reflected by the forest site type), local biogeographic gradients and also by stand age. Considering confounding effects, boreal forests in a near‐natural state have more large‐diameter trees (diameter at breast height >40 cm) and larger variety of diameter classes, higher proportion of spruce or deciduous trees, a larger amount of coarse woody debris in various stages, a more closed tree canopy and denser understory than managed mature forests. By increasing light availability above the field layer, forest management indirectly increases the coverage of herbs and lichens on the forest floor but reduces the alpha‐ and beta‐diversity of herbs and the proportion of graminoids. Human disturbances reduce the relative incidence of many commonly accepted biodiversity indicators such as indicator lichens, woodpeckers, wood‐dwelling insects or fungi on trees. The test for the predictive power of characteristics reacting on disturbance revealed that only a fraction of them appeared to be included in a diagnostic easy‐to‐apply set of indicators to assess the nature quality of boreal forest: the amount of dead wood, the proportion of deciduous trees, the presence of specially shaped trees and woodpeckers and, as an indicator of disturbances, the forest herb Melampyrum pratensis. Many of these indicators have already been implemented in practice.     

ATPase‐driven oligomerization of RIG‐I on RNA allows optimal activation of type‐I interferon

The cytosolic pathogen sensor RIG‐I is activated by RNAs with exposed 5′‐triphosphate (5′‐ppp) and terminal double‐stranded structures, such as those that are generated during viral infection. RIG‐I has been shown to translocate on dsRNA in an ATP‐dependent manner. However, the precise role of the ATPase activity in RIG‐I activation remains unclear. Using in vitro‐transcribed Sendai virus defective interfering RNA as a model ligand, we show that RIG‐I oligomerizes on 5′‐ppp dsRNA in an ATP hydrolysis‐dependent and dsRNA length‐dependent manner, which correlates with the strength of type‐I interferon (IFN‐I) activation. These results establish a clear role for the ligand‐induced ATPase activity of RIG‐I in the stimulation of the IFN response.     

Discovery and development of exome‐based,co‐dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.)

Globally, wheat is the most widely grown crop and one of the three most important crops for human and livestock feed. However, the complex nature of the wheat genome has, until recently, resulted in a lack of single nucleotide polymorphism (SNP)‐based molecular markers of practical use to wheat breeders. Recently, large numbers of SNP‐based wheat markers have been made available via the use of next‐generation sequencing combined with a variety of genotyping platforms. However, many of these markers and platforms have difficulty distinguishing between heterozygote and homozygote individuals and are therefore of limited use to wheat breeders carrying out commercial‐scale breeding programmes. To identify exome‐based co‐dominant SNP‐based assays, which are capable of distinguishing between heterozygotes and homozygotes, we have used targeted re‐sequencing of the wheat exome to generate large amounts of genomic sequences from eight varieties. Using a bioinformatics approach, these sequences have been used to identify 95 266 putative single nucleotide polymorphisms, of which 10 251 were classified as being putatively co‐dominant. Validation of a subset of these putative co‐dominant markers confirmed that 96% were true polymorphisms and 65% were co‐dominant SNP assays. The new co‐dominant markers described here are capable of genotypic classification of a segregating locus in polyploid wheat and can be used on a variety of genotyping platforms; as such, they represent a powerful tool for wheat breeders. These markers and related information have been made publically available on an interactive web‐based database to facilitate their use on genotyping programmes worldwide.