Saproxylic species are linked to the amount and isolation of dead wood across spatial scales in a beech forest

Context

Dead wood is a key habitat for saproxylic species, which are often used as indicators of habitat quality in forests. Understanding how the amount and spatial distribution of dead wood in the landscape affects saproxylic communities is therefore important for maintaining high forest biodiversity.

Objectives

We investigated effects of the amount and isolation of dead wood on the alpha and beta diversity of four saproxylic species groups, with a focus on how the spatial scale influences results.

Methods

We inventoried saproxylic beetles, wood-inhabiting fungi, and epixylic bryophytes and lichens on 62 plots in the Sihlwald forest reserve in Switzerland. We used GLMs to relate plot-level species richness to dead wood amount and isolation on spatial scales of 20–200 m radius. Further, we used GDMs to determine how dead wood amount and isolation affected beta diversity.

Results

A larger amount of dead wood increased beetle richness on all spatial scales, while isolation had no effect. For fungi, bryophytes and lichens this was only true on small spatial scales. On larger scales of our study, dead wood amount had no effect, while greater isolation decreased species richness. Further, we found no strong consistent patterns explaining beta diversity.

Conclusions

Our multi-taxon study shows that habitat amount and isolation can strongly differ in the spatial scale on which they influence local species richness. To generally support the species richness of different saproxylic groups, dead wood must primarily be available in large amounts but should also be evenly distributed because negative effects of isolation already showed at scales under 100 m.

     

Vegetation-mediated feedback in water, carbon, nitrogen and phosphorus cycles

Since the industrial revolution, industry, traffic and the manufacture and application of nitrogenous fertilizers have increased carbon dioxide emissions and accelerated the nitrogen (N) cycle. The combined effects of a warming climate, CO₂ fertilization, land-use change and increased N availability may be responsible for primary productivity increases in many parts of the world. Enhanced productivity may lead to shifts in albedo and transpiration, which feed back to the water cycle through heat fluxes and precipitation. Plants may also respond to elevated CO₂ by closing their stomata or by structurally adapting their stomatal density and size, which potentially diminishes transpiration. Intensification of agriculture has also led to an increase in both nitrogenous (N) and phosphorus (P) fertilization. The combined effect of atmospheric N deposition and P fertilization has distorted the balance between N and P availability in many ecosystems. The active role of plants in accessing nutrients from the soil may trigger switches in nutrient availability, triggering shifts in plant productivity and species composition in these ecosystems and therefore also in the carbon (C) cycle. In response to global change, the above plant responses may influence each other positively or negatively and may impact on the elemental cycles of C, N and P and the water cycle. We are only beginning to understand how these four cycles interact, the role of plant processes and vegetation in these interactions, and the net outcome for plant competition, vegetation distribution, landscape development and directions of global change. In this paper we have integrated a number of recent research findings into known relationships that together elucidate interactions between these cycles through vegetation, and could potentially have unexpected effects on landscapes and larger-scale systems (continental, global). These interactions include processes operating at very distinct temporal and spatial scales, in which terrestrial ecosystems and their spatial organization in the landscape are key. We argue that to better understand the effects of changes in land cover and land use on biogeochemical and biogeophysical fluxes, it is necessary to account for feedbacks via vegetation and how these interfere with elemental cycles. Finally, we suggest directions for further research to fill the current knowledge gaps.     

Essential cytoplasmic translocation of a cytokine receptor-assembled signaling complex

Cytokine signaling is thought to require assembly of multicomponent signaling complexes at cytoplasmic segments of membrane-embedded receptors, in which receptor-proximal protein kinases are activated. Indeed, CD40, a tumor necrosis factor receptor (TNFR) family member, forms a complex containing adaptor molecules TRAF2 and TRAF3, ubiquitin-conjugating enzyme Ubc13, cellular inhibitor of apoptosis proteins 1 and 2 (c-IAP1/2), IkappaB kinase regulatory subunit IKKgamma (also called NEMO), and mitogen-activated protein kinase (MAPK) kinase kinase MEKK1 upon ligation. TRAF2, Ubc13, and IKKgamma were required for complex assembly and activation of MEKK1 and MAPK cascades. However, these kinases were not activated unless the multicomponent signaling complex translocated from CD40 to the cytosol upon c-IAP1/2-induced degradation of TRAF3. This two-stage signaling mechanism may apply to other innate immune receptors, accounting for spatial and temporal separation of MAPK and IKK signaling.     

Glycosylation restores survival of chilled blood platelets

Cooling of blood platelets clusters the von Willebrand factor receptor complex. Macrophage alphaMbeta2 integrins bind to the GPIbalpha subunit of the clustered complex, resulting in rapid clearance of transfused, cooled platelets. This precludes refrigeration of platelets for transfusion, but the current practice of room temperature storage has major drawbacks. We document that alphaMbeta2 is a lectin that recognizes exposed beta-N-acetylglucosamine residues of N-linked glycans on GPIbalpha. Enzymatic galactosylation of chilled platelets blocks alphaMbeta2 recognition, prolonging the circulation of functional cooled platelets. Platelet-associated galactosyltransferase produces efficient galactosylation when uridine diphosphate-galactose is added, affording a potentially simple method for storing platelets in the cold.     

The dog genome: survey sequencing and comparative analysis

A survey of the dog genome sequence (6.22 million sequence reads; 1.5x coverage) demonstrates the power of sample sequencing for comparative analysis of mammalian genomes and the generation of species-specific resources. More than 650 million base pairs (>25%) of dog sequence align uniquely to the human genome, including fragments of putative orthologs for 18,473 of 24,567 annotated human genes. Mutation rates, conserved synteny, repeat content, and phylogeny can be compared among human, mouse, and dog. A variety of polymorphic elements are identified that will be valuable for mapping the genetic basis of diseases and traits in the dog.     

Whole-genome shotgun sequencing of mitochondria from ancient hair shafts

Although the application of sequencing-by-synthesis techniques to DNA extracted from bones has revolutionized the study of ancient DNA, it has been plagued by large fractions of contaminating environmental DNA. The genetic analyses of hair shafts could be a solution: We present 10 previously unexamined Siberian mammoth (Mammuthus primigenius) mitochondrial genomes, sequenced with up to 48-fold coverage. The observed levels of damage-derived sequencing errors were lower than those observed in previously published frozen bone samples, even though one of the specimens was >50,000 14C years old and another had been stored for 200 years at room temperature. The method therefore sets the stage for molecular-genetic analysis of museum collections.     

Genome sequence of Aedes aegypti, a major arbovirus vector

We present a draft sequence of the genome of Aedes aegypti, the primary vector for yellow fever and dengue fever, which at approximately 1376 million base pairs is about 5 times the size of the genome of the malaria vector Anopheles gambiae. Nearly 50% of the Ae. aegypti genome consists of transposable elements. These contribute to a factor of approximately 4 to 6 increase in average gene length and in sizes of intergenic regions relative to An. gambiae and Drosophila melanogaster. Nonetheless, chromosomal synteny is generally maintained among all three insects, although conservation of orthologous gene order is higher (by a factor of approximately 2) between the mosquito species than between either of them and the fruit fly. An increase in genes encoding odorant binding, cytochrome P450, and cuticle domains relative to An. gambiae suggests that members of these protein families underpin some of the biological differences between the two mosquito species.     

A PINOID-dependent binary switch in apical-basal PIN polar targeting directs auxin efflux

Polar transport-dependent local accumulation of auxin provides positional cues for multiple plant patterning processes. This directional auxin flow depends on the polar subcellular localization of the PIN auxin efflux regulators. Overexpression of the PINOID protein kinase induces a basal-to-apical shift in PIN localization, resulting in the loss of auxin gradients and strong defects in embryo and seedling roots. Conversely, pid loss of function induces an apical-to-basal shift in PIN1 polar targeting at the inflorescence apex, accompanied by defective organogenesis. Our results show that a PINOID-dependent binary switch controls PIN polarity and mediates changes in auxin flow to create local gradients for patterning processes.     

A cryptic subgroup of Anopheles gambiae is highly susceptible to human malaria parasites

Population subgroups of the African malaria vector Anopheles gambiae have not been comprehensively characterized owing to the lack of unbiased sampling methods. In the arid savanna zone of West Africa, where potential oviposition sites are scarce, widespread collection from larval pools in the peridomestic human habitat yielded a comprehensive genetic survey of local A. gambiae population subgroups, independent of adult resting behavior and ecological preference. A previously unknown subgroup of exophilic A. gambiae is sympatric with the known endophilic A. gambiae in this region. The exophilic subgroup is abundant, lacks differentiation into M and S molecular forms, and is highly susceptible to infection with wild Plasmodium falciparum. These findings might have implications for the epidemiology of malaria transmission and control.