A single‐stranded conformational polymorphism (SSCP)‐derived quantitative variable to monitor the virulence of a Barley yellow dwarf virus‐PAV (BYDV‐PAV) isolate during adaptation to the TC14 resistant wheat line

A standardized single‐stranded conformational polymorphism (SSCP) procedure is proposed as an alternative to the time‐consuming biological characterization of Barley yellow dwarf virus‐PAV (BYDV‐PAV) isolates. Using this procedure, six of 21 overlapping regions used to scan the viral genome gave patterns specific to ‘4E’ (avirulent) or ‘4T’ (‘4E’‐derived virulent) isolates. The calibration of samples and integration of SSCP patterns corresponding to the nucleotide region 1482–2023 allowed the estimation of P_T values that reflect the proportions of a ‘4T’‐specific band. Analysis of the biological (area under the pathogen progress curve) and molecular (P_T) data suggested a positive linear relation between these variables. Moreover, sequence analysis of the nucleotide region 1482–2023 highlighted the presence of a nucleotide polymorphism (C/A₁₈₃₅) which can be considered as a candidate for virus–host interactions linked to the monitored virulence. According to these parameters, P_T values associated with ‘4E’‐ and ‘4T’‐derived populations show that: (i) long‐term infection of a BYDV‐PAV isolate on the ‘TC14’ resistant host leads to the fixation of virulent individuals in viral populations; and (ii) the introduction of susceptible hosts in successive ‘TC14’ infections results in the maintenance of low virulence of the populations. Thus, the presented study demonstrates that SSCP is a useful tool for monitoring viral populations during the host adaptation process. The described impact of host alternation provides new opportunities for the use of the ‘TC14’ resistance source in BYDV‐resistant breeding programmes. This study is part of the global effort made by the scientific community to propose sustainable alternatives to the chemical control of this viral disease.     

Relative influences of submersed macrophytes and bioturbating fauna on biogeochemical processes and microbial activities in freshwater sediments

1. Invertebrates and aquatic plants often play a key role in biogeochemical processes occurring at the water–sediment interface of aquatic ecosystems. However, few studies have investigated the respective influences of plants and bioturbating animals on ecological processes (nutrient fluxes, benthic oxygen uptake, microbial activities) occurring in freshwater sediments. 2. We developed a laboratory experiment in aquaria to quantify the effects of (i) one invertebrate acting as a bioturbator (Tubifex tubifex); (ii) one submersed plant with a high sediment‐oxygenating potential (Myriophyllum spicatum) and (iii) one submersed plant with a low sediment‐oxygenating potential (Elodea canadensis). 3. The tubificid worms significantly increased the fluxes of nitrogen at the water–sediment interface (influx of nitrate, efflux of ammonium), whereas the two plant species did not have significant influences on these nitrogen fluxes. The differences in nitrogen fluxes between tubificid worms and plants were probably due to the bioirrigation process caused by T. tubifex, which increased water exchanges at the water–sediment interface. Tubifex tubifex and M. spicatum produced comparable reductions of nutrient concentrations in pore water and comparable stimulations of benthic oxygen uptake and microbial communities (percentages of active eubacteria and hydrolytic activity) whereas E. canadensis had a very weak influence on these variables. These differences between the two plants were due to their contrasting abilities to increase oxygen in sediments by radial oxygen losses (release of oxygen from roots). 4. Our study suggests that the bioirrigation process and radial oxygen loss are major functional traits affecting biogeochemical functioning at the water–sediment interface of wetlands.     

Land cover change 2002–2005 in Borneo and the role of fire derived from MODIS imagery

Borneo has experienced heavy deforestation and forest degradation during the past two decades. In this study the Moderate Resolution Imaging Spectroradiometer was used to monitor land cover change in Borneo between 2002 and 2005 in order to assess the current extent of the forest cover, the deforestation rate and the role of fire. Using Landsat and ground observation for validation it was possible to discriminate 11 land cover classes. In 2002 57% of the land surface of Borneo was covered with forest of which 74% was dipterocarp and more than 23% peat swamp forest. The average deforestation rate between 2002 and 2005 was 1.7% yr^{− 1}. The carbon-rich ecosystem of peat swamp forests showed a deforestation rate of 2.2%. Almost 98% of all deforestation occurred within a range of 5 km to the forest edge. Fire is highly correlated with land cover changes. Most fires were detected in degraded forests. Ninety-eight per cent of all forest fires were detected in the 5 km buffer zone, underlining that fire is the major driver for forest degradation and deforestation.     

THE POSTCRANIUM OF ARCHEGOSAURUS DECHENI, AND A PHYLOGENETIC ANALYSIS OF TEMNOSPONDYL POSTCRANIA

Abstract:  The gharial-like Archegosaurus decheni from the Permian/Carboniferous boundary of south-west Germany is one of the best known temnospondyls. Based largely on new material, we restudied the postcranial anatomy of this species, including ontogenetic aspects. A. decheni has 24 presacral vertebrae, and the length of the deep tail exceeds the length of the rest of the body. Neural spines are moderately high and slowly become differentiated during ontogeny. The intercentra start to ossify very late. Distal uncinate processes are developed on the anterior ribs in adult specimens. Only the ventral portion of the scapula is ossified. The slender ilium and the ischium are not co-ossified, and the pubis remained cartilaginous. Among stereospondylomorph temnospondyls, the very short and rudimentarily developed humerus exhibits a unique morphology. Carpals and tarsals start to ossify only in the largest specimens. The poorly ossified postcranium indicates that A. decheni was primarily an aquatic temnospondyl. We undertook a phylogenetic study of A. decheni and 16 other temnospondyls, based exclusively on postcranial characters. We analysed 52 characters, obtaining a single most parsimonious tree that agrees in many aspects with cranium-based analyses: Trimerorhachis and Dvinosaurus form a basal clade (Dvinosauria), followed by monophyletic euskelians (dissorophoids plus eryopids) and finally the stereospondylomorphs, within which A. decheni is nested above Sclerocephalus . Among stereospondyls, trematosaurids and metoposaurids form a clade, whereas the chigutisaurid Siderops is nested with capitosauroids. The primitive condition of Temnospondyli is still not adequately understood, especially the degree of terrestriality of the earliest temnospondyls.     

Chloroplast DNA‐based studies in molecular ecology may be compromised by nuclear‐encoded plastid sequence

Ongoing genetic transfer from mitochondria and plastids into the nucleus is a well‐documented fact. While in metazoan molecular ecology the need for surveillance against pseudogene‐mediated artefacts when analysing mtDNA sequences is commonly accepted, no comparable measurements have been established for plastid‐based studies. We highlight the impact and management of nuclear mitochondrial insertions, argue that nuclear plastid sequences represent an underestimated but major factor in plant molecular ecology, and discuss potential avenues of remedy in chloroplast studies.     

Interactions between fauna and sediment control the breakdown of plant matter in river sediments

1. A substantial portion of particulate organic matter (POM) is stored in the sediment of rivers and streams. Leaf litter breakdown as an ecosystem process mediated by microorganisms and invertebrates is well documented in surface waters. In contrast, this process and especially the implication for invertebrates in subsurface environments remain poorly studied. 2. In the hyporheic zone, sediment grain size distribution exerts a strong influence on hydrodynamics and habitability for invertebrates. We expected that the influence of shredders on organic matter breakdown in river sediments would be influenced strongly by the physical structure of the interstitial habitat. 3. To test this hypothesis, the influence of gammarids (shredders commonly encountered in the hyporheos) on degradation of buried leaf litter was measured in experimental systems (slow filtration columns). We manipulated the structure of the sedimentary habitat by addition of sand to a gravel‐based sediment column to reproduce three conditions of accessible pore volume. Ten gammarids were introduced in columns together with litter bags containing alder leaves at a depth of 8 cm in sediment. Leaves were collected after 28 days to determine leaf mass loss and associated microbial activity (fungal biomass, bacterial abundance and glucosidase, xylosidase and aminopeptidase activities). 4. As predicted, the consumption of buried leaf litter by shredders was strongly influenced by the sediment structure. Effective porosity of 35% and 25% allowed the access to buried leaf litter for gammarids, whereas a lower porosity (12%) did not. As a consequence, leaf litter breakdown rates in columns with 35% and 25% effective porosity were twice as high as in the 12% condition. Microbial activity was poorly stimulated by gammarids, suggesting a low microbial contribution to leaf mass loss and a direct effect of gammarids through feeding activity. 5. Our results show that breakdown of POM in subsurface waters depends on the accessibility of food patches to shredders.     

Over‐expression of bacterial γ‐glutamylcysteine synthetase (GSH1) in plastids affects photosynthesis,growth and sulphur metabolism in poplar (Populus tremula × Populus alba) dependent on the resulting γ‐glutamylcysteine and glutathione levels

We compared three transgenic poplar lines over‐expressing the bacterial γ‐glutamylcysteine synthetase (GSH1) targeted to plastids. Lines Lggs6 and Lggs12 have two copies, while line Lggs20 has three copies of the transgene. The three lines differ in their expression levels of the transgene and in the accumulation of γ‐glutamylcysteine (γ‐EC) and glutathione (GSH) in leaves, roots and phloem exudates. The lowest transgene expression level was observed in line Lggs6 which showed an increased growth, an enhanced rate of photosynthesis and a decreased excitation pressure (1‐qP). The latter typically represents a lower reduction state of the plastoquinone pool, and thereby facilitates electron flow along the electron transport chain. Line Lggs12 showed the highest transgene expression level, highest γ‐EC accumulation in leaves and highest GSH enrichment in phloem exudates and roots. This line also exhibited a reduced growth, and after a prolonged growth of 4.5 months, symptoms of leaf injury. Decreased maximum quantum yield (F_v/F_m) indicated down‐regulation of photosystem II reaction centre (PSII RC), which correlates with decreased PSII RC protein D1 (PsbA) and diminished light‐harvesting complex (Lhcb1). Potential effects of changes in chloroplastic and cytosolic GSH contents on photosynthesis, growth and the whole‐plant sulphur nutrition are discussed for each line.     

Natural variation in ozone sensitivity among Arabidopsis thaliana accessions and its relation to stomatal conductance

Genetic variation between naturally occurring populations provides a unique source to unravel the complex mechanisms of stress tolerance. Here, we have analysed O₃ sensitivity of 93 natural Arabidopsis thaliana accessions together with five O₃‐sensitive mutants to acute O₃ exposure. The variation in O₃ sensitivity among the natural accessions was much higher than among the O₃‐sensitive mutants and corresponding wild types. A subset of nine accessions with major variation in their O₃ responses was studied in more detail. Among the traits assayed, stomatal conductance (g_st) was an important factor determining O₃ sensitivity of the selected accessions. The most O₃‐sensitive accession, Cvi‐0, had constitutively high g_st, leading to high initial O₃ uptake rate and dose received during the first 30 min of exposure. Analyzing O₃‐induced changes in stress hormone concentrations indicated that jasmonate (JA) concentration was also positively correlated with leaf damage. Quantitative trait loci (QTL) mapping in a Col‐0 × Cvi‐0 recombinant inbred line (RIL) population identified three QTLs for O₃ sensitivity, and one for high water loss of Cvi‐0. The major O₃ QTL mapped to the same position as the water loss QTL further supporting the role of stomata in regulating O₃ entry and damage.     

Climate change affects colonization dynamics in a metacommunity of three Daphnia species

Climate change is expected to alter the range and abundance of many species by influencing habitat qualities. For species living in fragmented populations, not only the quality of the present patches but also access to new habitat patches may be affected. Here, we show that colonization in a metacommunity can be directly influenced by weather changes, and that these observed weather changes are consistent with global climate change models. Using a long‐term dataset from a rock pool metacommunity of the three species Daphnia magna, Daphnia longispina and Daphnia pulex with 507 monitored habitat patches, we correlated a four‐fold increase in colonization rate with warmer, drier weather for the period from 1982 to 2006. The higher colonization rate after warm and dry summers led to an increase in metacommunity dynamics over time. A mechanistic explanation for the increased colonization rate is that the resting stages have a higher exposure to animal and wind dispersal in desiccated rock pools. Although colonization rates reacted in the same direction in all three species, there were significant species‐specific effects that resulted in an overall change in the metacommunity composition. Increased local instability and colonization dynamics may even lead to higher global stability of the metacommunity. Thus, whereas climate change has been reported to cause a unidirectional change in species range for many other species, it changes the dynamics and composition of an entire community in this metacommunity, with winners and losers difficult to predict.