The SW Atlantic burrowing crab Chasmagnathus granulatus Dana affects the distribution and survival of the fiddler crab Uca uruguayensis Nobili

In this paper, we address the question of whether the presence of the burrowing crab Chasmagnathus granulatus affects the habitat use of the fiddler crab Uca uruguayensis. Field samples showed that the species have a disjoint spatial distribution. Male fiddler crab density decreased in zones with C. granulatus, however, female density increased. Male fiddler crabs avoided feeding on sediment affected by C. granulatus and were more preyed. Predation was higher during the fiddler crab reproductive season and, probably due to predation risk, males showed lower reproductive display in shared zones. Field experiments shows that when C. granulatus were excluded, densities of U. uruguayensis increased mainly due to an increase in density of males. Habitat differentiation of these species may be because C. granulatus affects U. uruguayensis in several ways, including direct predation, disturbance and behavioural changes associated to predation risk. Males and females are affected differentially probably because of the extreme sexual dimorphism of this crab species. Coloration on enlarged claw and waving activities are all factors that increase predation risk for male and the presence of only one feeding claw may increase sediment-mediated effects.     

The relationship between sea surface temperature and population change of Great Cormorants Phalacrocorax carbo breeding near Disko Bay,Greenland

Arctic seas have warmed and sea ice has retreated. This has resulted in range contraction and population declines in some species, but it could potentially be a boon for others. Great Cormorants Phalacrocorax carbo have a partially wettable plumage and seem poorly suited to foraging in Arctic waters. We show that rates of population change of Cormorant colonies around Disko Bay, Greenland, are positively correlated with sea surface temperature, suggesting that they may benefit from a warming Arctic. However, although Cormorant populations may increase in response to Arctic warming, the extent of expansion of their winter range may ultimately be limited by other factors, such as sensory constraints on foraging behaviour during long Arctic nights.     

Compositions of fungal secretomes indicate a greater impact of phylogenetic history than lifestyle adaptation

Background

Since the first fungal genome sequences became available, investigators have been employing comparative genomics to understand how fungi have evolved to occupy diverse ecological niches. The secretome, i.e. the entirety of all proteins secreted by an organism, is of particular importance, as by these proteins fungi acquire nutrients and communicate with their surroundings.

Results

It is generally assumed that fungi with similar nutritional lifestyles have similar secretome compositions. In this study, we test this hypothesis by annotating and comparing the soluble secretomes, defined as the sets of proteins containing classical signal peptides but lacking transmembrane domains of fungi representing a broad diversity of nutritional lifestyles. Secretome size correlates with phylogeny and to a lesser extent with lifestyle. Plant pathogens and saprophytes have larger secretomes than animal pathogens. Small secreted cysteine-rich proteins (SSCPs), which may comprise many effectors important for the interaction of plant pathogens with their hosts, are defined here to have a mature length of ≤ 300 aa residues, at least four cysteines, and a total cysteine content of ≥5%. SSCPs are found enriched in the secretomes of the Pezizomycotina and Basidiomycota in comparison to Saccharomycotina. Relative SSCP content is noticeably higher in plant pathogens than in animal pathogens, while saprophytes were in between and closer to plant pathogens. Expansions and contractions of gene families and in the number of occurrences of functional domains are largely lineage specific, e.g. contraction of glycoside hydrolases in Saccharomycotina, and are only weakly correlated with lifestyle. However, within a given lifestyle a few general trends exist, such as the expansion of secreted family M14 metallopeptidases and chitin-binding proteins in plant pathogenic Pezizomycotina.

Conclusions

While the secretomes of fungi with similar lifestyles share certain characteristics, the expansion and contraction of gene families is largely lineage specific, and not shared among all fungi of a given lifestyle.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-722) contains supplementary material, which is available to authorized users.     

The presence of phospholipids and diglyceride kinase activity in microtubules from different tissues

Microtubular preparations obtained by different procedures from chick embryonic muscles and brains and from HeLa cells have associated, in addition to the protein kinase which can phosphorylate tubulin, an enzymatic activity which has been identified as that of a diglyceride kinase. They have also consistently associated various phospholipids, lecithin being the principal one. The phosphatidic acid formation is greatly stimulated by exogenous diglycerides or pretreatment with phospholipase C, and it is not present in partially purified preparations of cytoplasmic protein kinases of chick muscle. The significance of these findings is discussed.     

Latitudinal patterns of magnitude and interannual variability in net ecosystem exchange regulated by biological and environmental variables

Over the last two and half decades, strong evidence showed that the terrestrial ecosystems are acting as a net sink for atmospheric carbon. However the spatial and temporal patterns of variation in the sink are not well known. In this study, we examined latitudinal patterns of interannual variability (IAV) in net ecosystem exchange (NEE) of CO₂ based on 163 site-years of eddy covariance data, from 39 northern-hemisphere research sites located at latitudes ranging from ∼29°N to ∼64°N. We computed the standard deviation of annual NEE integrals at individual sites to represent absolute interannual variability (AIAV), and the corresponding coefficient of variation as a measure of relative interannual variability (RIAV). Our results showed decreased trends of annual NEE with increasing latitude for both deciduous broadleaf forests and evergreen needleleaf forests. Gross primary production (GPP) explained a significant proportion of the spatial variation of NEE across evergreen needleleaf forests, whereas, across deciduous broadleaf forests, it is ecosystem respiration (Re). In addition, AIAV in GPP and Re increased significantly with latitude in deciduous broadleaf forests, but AIAV in GPP decreased significantly with latitude in evergreen needleleaf forests. Furthermore, RIAV in NEE, GPP, and Re appeared to increase significantly with latitude in deciduous broadleaf forests, but not in evergreen needleleaf forests. Correlation analyses showed air temperature was the primary environmental factor that determined RIAV of NEE in deciduous broadleaf forest across the North American sites, and none of the chosen climatic factors could explain RIAV of NEE in evergreen needleleaf forests. Mean annual NEE significantly increased with latitude in grasslands. Precipitation was dominant environmental factor for the spatial variation of magnitude and IAV in GPP and Re in grasslands.     

Forest refugia revisited: nSSRs and cpDNA sequences support historical isolation in a wide‐spread African tree with high colonization capacity,Milicia excelsa (Moraceae)

The impact of the Pleistocene climate oscillations on the structure of biodiversity in tropical regions remains poorly understood. In this study, the forest refuge theory is examined at the molecular level in Milicia excelsa, a dioecious tree with a continuous range throughout tropical Africa. Eight nuclear microsatellites (nSSRs) and two sequences and one microsatellite from chloroplast DNA (cpDNA) showed a deep divide between samples from Benin and those from Lower Guinea. This suggests that these populations were isolated in separate geographical regions, probably for several glacial cycles of the Pleistocene, and that the nuclear gene pools were not homogenized despite M. excelsa’s wind‐pollination syndrome. The divide could also be related to seed dispersal patterns, which should be largely determined by the migration behaviour of M. excelsa’s main seed disperser, the frugivorous bat Eidolon helvum. Within Lower Guinea, a north–south divide, observed with both marker types despite weak genetic structure (nSSRs: F_ST = 0.035, cpDNA: G_ST = 0.506), suggested the existence of separate Pleistocene refugia in Cameroon and the Gabon/Congo region. We inferred a pollen‐to‐seed dispersal distance ratio of c. 1.8, consistent with wide‐ranging gene dispersal by both wind and bats. Simulations in an Approximate Bayesian Computation framework suggested low nSSR and cpDNA mutation rates, but imprecise estimates of other demographic parameters, probably due to a substantial gene flow between the Lower Guinean gene pools. The decline of genetic diversity detected in some Gabonese populations could be a consequence of the relatively recent establishment of a closed canopy forest, which could negatively affect M. excelsa’s reproductive system.     

Purification and properties of an aspartic protease from potato tuber that is inhibited by a basic chitinase

A protease was isolated from potato ( Solanum tuberosum L. cv. Huinkul) tuber disks after 24 h of aeration when proteolysis is markedly increased. Purification was performed by ammonium sulfate precipitation, ion exchange chromatography, and affinity chromatography. A size of 40 kDa was estimated by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and gel filtration, it is monomeric and its properties are consistent with those of aspartic proteinases (EC 3.4.23): it had a pH optimum between 4 and 5 and it was inhibited by pepstatin. Partial homology with other plant aspartic proteinases was observed in two sequenced tryptic fragments. It binds to Sepharose-concanavalin A and can be eluted with α -methyl mannoside, indicating that it is possibly glycosylated. Unlike other aspartic proteinases from Solanaceae that degrade pathogenesis-related proteins, it is unable to cleave a basic chitinase from potato. Moreover, this aspartic protease is strongly inhibited by the basic chitinase; the 50% inhibition is obtained when the molar ratio approaches 1, the same as with pepstatin. The interaction between this aspartic protease and a new type of endogenous inhibitor may be an interesting starting point to study the regulation of these aspartic proteases during stress.     

Diglyceride kinase activity of microtubules. Characterization and comparison with the protein kinase and ATPase activities associated with vinblastine-isolated tubulin of chick embryonic muscles.

Vinblastine-isolated microtubule protein from chick embryonic muscles has an enzymatic activity which catalyzes the formation of phosphatidic acid from diglycerides and ATP. The pH optimum (6.4), sedimentation on sucrose gradients (Mr = 85 000), and sensitivity to ions of this diglyceride kinase activity are different to those of a similar enzymatic activity present in 150 000 X g supernatants of chick embryonic muscle homogenates, suggesting that it is a different species which is associated specifically with the microtubules. The reaction requires a divalent ion (e.g. 0.4 mM Mg2+ gives half-maximal stimulation), and GTP can replace ATP rather effectively, especially at nucleotide concentrations lower than 50 muM. The sedimentation of the diglyceride kinase on sucrose gradients coincides with that of the microtubules-associated protein kinase (Mr = 75 000); the heat-stability and sensivitity to proteolysis of both activities are also very similar. Stimulation of one reaction by the addition of the corresponding exogenous substrate does not impair the phosphorylation of the other, and no radioactivity is lost from phosphatidic acid or the protein moiety upon incubation of pre-labelled microtubules with a large excess of unlabelled ATP or GTP. In addition to diglyceride and protein kinase activities (0.2 and 0.3 nmol 32P-transferred X min-1 X mg-1 microtubular protein, respectively), microtubules also contain an associated ATPase (2.8 nmol X min-1 X mg-1), which requires either Mg2+ or Ca2+, can hydrolyze GTP quite effectively, and sediments with a molecular weight of 95000. The results obtained are discussed in connection with the possible relationships existing among these enzymatic activities, as well as their probable role in microtubular functions.