Edge effects on moisture reduce wood decomposition rate in a temperate forest

Forests around the world are increasingly fragmented, and edge effects on forest microclimates have the potential to affect ecosystem functions such as carbon and nutrient cycling. Edges tend to be drier and warmer due to the effects of insolation, wind, and evapotranspiration and these gradients can penetrate hundreds of metres into the forest. Litter decomposition is a key component of the carbon cycle, which is largely controlled by saprotrophic fungi that respond to variation in temperature and moisture. However, the impact of forest fragmentation on litter decay is poorly understood. Here, we investigate edge effects on the decay of wood in a temperate forest using an experimental approach, whereby mass loss in wood blocks placed along 100 m transects from the forest edge to core was monitored over 2 years. Decomposition rate increased with distance from the edge, and was correlated with increasing humidity and moisture content of the decaying wood, such that the decay constant at 100 m was nearly twice that at the edge. Mean air temperature decreased slightly with distance from the edge. The variation in decay constant due to edge effects was larger than that expected from any reasonable estimates of climatic variation, based on a published regional model. We modelled the influence of edge effects on the decay constant at the landscape scale using functions for forest area within different distances from edge across the UK. We found that taking edge effects into account would decrease the decay rate by nearly one quarter, compared with estimates that assumed no edge effect.     

Blistering1 Modulates Penicillium expansum Virulence Via Vesicle-mediated Protein Secretion

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Highlights

• •The Blistering1 locus in Penicillium expansum encodes a novel protein with a DnaJ domain.
• •A single T-DNA insertion was generated in the blistering1 gene which manifested in reduced decay in apple and nearly undetectable levels of the mycotoxin patulin in the T625 mutant.
• •T625 failed to secrete a set of enzymes that degrade plant cell walls and the three final biosynthetic enzymes of patulin synthesis.
• •Quantitative mass spectrometry of mycelial proteins revealed that the mutant had altered cellular networks controlling protein processing in the endoplasmic reticulum, protein export, vesicle-mediated transport, and endocytosis.
• •Transmission electron microscopy of hyphal cross sections confirmed that the mutant formed abnormally enlarged endosomes or vacuoles.
• •These data reveal that Blistering1 affects internal and external protein processing involving vesicle-mediated transport in a family of fungi with medical, commercial, and agricultural importance.

     

Different biogeographic patterns of prokaryotes and microbial eukaryotes in epilithic biofilms

Microbial biogeography studies expend much effort in determining whether environmental selection or stochastic processes related to dispersal are more important in shaping community composition. While both types of factors are possibly influential, it is tacitly assumed that protists, or microbial eukaryotes in general, behave biogeographically as prokaryotes because of their small physical size. However, direct evidence for this in exactly the same environment and at the same phylogenetic depth is lacking. In this study, we compared the structure of both prokaryotic and eukaryotic components of microbial communities forming biofilms on mineral substrates in different geographic locations at the level of small-subunit (SSU) rRNA-based operational taxonomic units (OTUs). These microbial communities are subjected to strong environmental selection and contain significant proportions of extremophilic microorganisms adapted to desiccation and UV radiation. We find that the nature of the substrate as well as climatic variables and geography influences microbial community structure. However, constrained correspondence analyses and distance-decay curves showed that, whereas the substrate type was the most significant factor structuring bacterial communities, geographic location was the most influential factor for microbial eukaryote communities. Biological explanations implying a higher dispersal success for bacteria combined with more mobile lifestyles for predatory protists may underlie these different prokaryote versus microbial eukaryote biogeographic patterns.     

Dispersal, environmental niches and oceanic-scale turnover in deep-sea bivalves

Patterns of beta-diversity or distance decay at oceanic scales are completely unknown for deep-sea communities. Even when appropriate data exist, methodological problems have made it difficult to discern the relative roles of environmental filtering and dispersal limitation for generating faunal turnover patterns. Here, we combine a spatially extensive dataset on deep-sea bivalves with a model incorporating ecological dynamics and shared evolutionary history to quantify the effects of environmental filtering and dispersal limitation. Both the model and empirical data are used to relate functional, taxonomic and phylogenetic similarity between communities to environmental and spatial distances separating them for 270 sites across the Atlantic Ocean. This study represents the first ocean-wide analysis examining distance decay as a function of a broad suite of explanatory variables. We find that both strong environmental filtering and dispersal limitation drive turnover in taxonomic, functional and phylogenetic composition in deep-sea bivalves, explaining 26 per cent, 34 per cent and 9 per cent of the variation, respectively. This contrasts with previous suggestions that dispersal is not limiting in broad-scale biogeographic and biodiversity patterning in marine systems. However, rates of decay in similarity with environmental distance were eightfold to 44-fold steeper than with spatial distance. Energy availability is the most influential environmental variable evaluated, accounting for 3.9 per cent, 9.4 per cent and 22.3 per cent of the variation in functional, phylogenetic and taxonomic similarity, respectively. Comparing empirical patterns with process-based theoretical predictions provided quantitative estimates of dispersal limitation and niche breadth, indicating that 95 per cent of deep-sea bivalve propagules will be able to persist in environments that deviate from their optimum by up to 2.1 g m(-2) yr(-1) and typically disperse 749 km from their natal site.     

Expression and biochemical characterization of two novel feruloyl esterases derived from fecal samples of Rusa unicolor and Equus burchelli

Two novel genes (tvms10a, tvmz2a) were identified in the metagenomic DNA of Rusa unicolor and Equus burchelli fecal samples. The amplified PCR product of tvms10a is composed of 917bp and the gene was found to encode a protein containing 165 amino acids, while the tvmz2a PCR product was 1053bp long encoding 298 amino acid proteins. The gene has 72% primary sequence identity with Clostridiales sp. These amplified PCR products which can encode FAE were cloned into pGEMT Easy TA cloning vector and then sub-cloned into the EcoRI site of pET32a expression vector to generate pET32-tvms10a and pET32-tvmz2a, which was then transformed into Escherichia coli BL21. The recombinants were grown in LB medium and gene expression was induced with IPTG for 6h. Purified recombinant Tvms10a and Tvmz2a proteins showed molecular masses of 18.6 and 31.2kDa respectively, and displayed hydrolytic activity towards substrate ethyl ferulate. The activities of Tvms10a and Tvmz2a produced in E. coli were 15 and 9U/min respectively, and their specific activities 16.6 and 10.4U/mg protein respectively. The optimal pH is between 5.0 and 8.0 and the optimal temperature is 37°C for enzyme reaction. Unusually, these proteins were found to be capable of releasing ferulic acid (FA) and diferulic acid (diFA) from untreated crude plant cell wall materials. The substrate utilization preferences and sequence similarity of these clones place it in the type-D sub-class of FAE.     

The regulation of mRNA stability in mammalian cells: 2.0

Messenger RNA decay is an essential step in gene expression to set mRNA abundance in the cytoplasm. The binding of proteins and/or noncoding RNAs to specific recognition sequences or secondary structures within mRNAs dictates mRNA decay rates by recruiting specific enzyme complexes that perform the destruction processes. Often, the cell coordinates the degradation or stabilization of functional subsets of mRNAs encoding proteins collectively required for a biological process. As well, extrinsic or intrinsic stimuli activate signal transduction pathways that modify the mRNA decay machinery with consequent effects on decay rates and mRNA abundance. This review is an update to our 2001 Gene review on mRNA stability in mammalian cells, and we survey the enormous progress made over the past decade.     

Characterization of the chloroplast genome sequence of oil palm (Elaeis guineensis Jacq.)

Oil palm (Elaeis guineensis Jacq.) is an economically important crop, which is grown for oil production. To better understand the molecular basis of oil palm chloroplasts, we characterized the complete chloroplast (cp) genome sequence obtained from 454 pyrosequencing. The oil palm cp genome is 156,973 bp in length consisting of a large single-copy region of?85,192 bp flanked on each side by inverted repeats of 27,071 bp with a small single-copy region of 17,639 bp joining the?repeats. The genome contains 112 unique genes: 79 protein-coding genes, 4 ribosomal RNA genes and 29 tRNA genes. By aligning the cp?genome sequence with oil palm cDNA sequences, we observed 18 non-silent and 10 silent RNA editing events among 19 cp protein-coding genes. Creation of an initiation codon by RNA editing in rpl2 has been reported in several monocots and was also found in the oil palm cp genome. Fifty common chloroplast protein-coding genes from 33 plant taxa were used to construct ML and MP?phylogenetic trees. Their topologies are similar and strongly support for the position of E. guineensis as the sister of closely related species Phoenix dactylifera in Arecaceae (palm families) of monocot subtrees.     

Disentangling the effects of geographic distance and environmental dissimilarity on global patterns of species turnover

Aim To distinguish the effects of geographic distance and environmental dissimilarity on global patterns of species turnover in four classes of terrestrial vertebrates (mammals, birds, reptiles and amphibians). Location Six hundred and sixty terrestrial ecoregions across the globe. Methods We calculated species turnover between each pair of ecoregions, using the Jaccard index (J). We selected seven variables to quantify environment in each ecoregion, and subjected the environmental values to a principal components analysis. For each realm, we applied multiple regression analysis relating the natural logarithm of the Jaccard index (lnJ) to geographic distance alone and in combination with differences in the environment variables measured as principal components (PC). We used partial correlations to partition variance in lnJ between unique contributions of distance and environmental PC scores, the covariation between distance and environment, and unexplained variance. To examine the latitude and species turnover relationship, we regressed lnJ on latitude with distance between ecoregions being included as a covariate. Results The natural logarithm of the Jaccard index (lnJ) decreased significantly with increasing geographic distance for all vertebrate classes in each zoogeographic realm, and the slopes of the relationships per 1000 km ranged from ?0.251 to ?1.043. With environmental differences included in the analysis, both geographic distance and environmental differences were substantial predictors of lnJ for every combination of taxon and realm. On average, the unique contribution of geographic distance to variation in species turnover between ecoregions was about 1.4 times that of the environmental differences between ecoregions. Species turnover generally decreased with increasing latitude when controlling for geographic distance. The value of lnJ for each vertebrate class was highly and positively correlated with those of the other vertebrate classes. Main conclusions Our analyses suggest that both dispersal‐based and niche‐based processes have played important roles in determining faunal similarities among vertebrate assemblages at the spatial scale examined. Furthermore, reptiles and amphibians exhibited greater distance‐independent faunal heterogeneity among ecoregions and greater turnover among ecoregions with respect to geographic and environmental distance than birds and mammals.