Antimicrobial and antiviral activities of an actinomycete (Streptomyces sp.) isolated from a Brazilian tropical forest soil

A promising producer of bioactive compounds isolated from a Brazilian tropical soil was tested for its range of antimicrobial activities. Strain 606, classified as Streptomyces sp., could not be identified up to species level, suggesting a possible new taxon. The supernatant and 10 extracts and fractions, obtained by extraction and chromatographic techniques, presented antimicrobial activity using antibiograms. The methanolic fraction was highly active against pathogenic bacteria, phytopathogenic fungi and the human pathogenic yeast Candida albicans. It also possessed high antiviral activity inhibiting the propagation of an acyclovir-resistant herpes simplex virus type 1 strain on HEp-2 cells at non-cytotoxic concentration. The strong cytotoxic effect suggests an antitumour action. This revised version was published online in August 2006 with corrections to the Cover Date.     

Multiomic Metabolic Enrichment Network Analysis Reveals Metabolite–Protein Physical Interaction Subnetworks Altered in Cancer

Metabolism is recognized as an important driver of cancer progression and other complex diseases, but global metabolite profiling remains a challenge. Protein expression profiling is often a poor proxy since existing pathway enrichment models provide an incomplete mapping between the proteome and metabolism. To overcome these gaps, we introduce multiomic metabolic enrichment network analysis (MOMENTA), an integrative multiomic data analysis framework for more accurately deducing metabolic pathway changes from proteomics data alone in a gene set analysis context by leveraging protein interaction networks to extend annotated metabolic models. We apply MOMENTA to proteomic data from diverse cancer cell lines and human tumors to demonstrate its utility at revealing variation in metabolic pathway activity across cancer types, which we verify using independent metabolomics measurements. The novel metabolic networks we uncover in breast cancer and other tumors are linked to clinical outcomes, underscoring the pathophysiological relevance of the findings.     

A predictive model for freshwater bioassessment (Mondego River,Portugal)

We sampled macroinvertebrates at 75 locations in the Mondego river catchment, Central Portugal, and developed a predictive model for water quality assessment of this basin, based on the Reference Condition Approach. Sampling was done from June to September 2001. Fifty-five sites were identified as “Reference sites” and 20 sites were used as “Test sites” to test the model. At each site we also measured 40 habitat variables to characterize water physics and chemistry, habitat type, land use, stream hydrology and geographic location. Macroinvertebrates were generally identified to species or genus level; a total of 207 taxa were found. By Unweighted Pair Group Method with Arithmetic mean (UPGMA) clustering and analysis of species contribution to similarities percentage (SIMPER), two groups of reference sites were established. Using Discriminant Analysis (stepwise forward), four variables correctly predicted 78% of the reference sites to the appropriate group: stream order, pool quality, substrate quality and current velocity. Test sites’ environmental quality was established from their relative distance to reference sites, in MDS ordination space, using a series of bands (BEAST methodology). The model performed well at upstream sites, but at downstream sites it was compromised by the lack of reference sites. As with the English RIVPACS predictive model, the Mondego model should be continually improved with the addition of new reference sites. The adaptation of the Mondego model methodology to the Water Framework Directive is possible and would consist mainly of the integration of the WFD typology and increasing the number of ellipses that define quality bands. Handling editor: K. Martens     

Environment versus dispersal in the assembly of western Amazonian palm communities

Aim It is a central issue in ecology and biogeography to understand what governs community assembly and the maintenance of biodiversity in tropical rain forest ecosystems. A key question is the relative importance of environmental species sorting (niche assembly) and dispersal limitation (dispersal assembly), which we investigate using a large dataset from diverse palm communities. Location Lowland rain forest, western Amazon River Basin, Peru. Methods We inventoried palm communities, registering all palm individuals and recording environmental conditions in 149 transects of 5 m × 500 m. We used ordination, Mantel tests and indicator species analysis (ISA) to assess compositional patterns, species responses to geographical location and environmental factors. Mantel tests were used to assess the relative importance of geographical distance (as a proxy for dispersal limitation) and environmental differences as possible drivers of dissimilarity in palm species composition. We repeated the Mantel tests for subsets of species that differ in traits of likely importance for habitat specialization and dispersal (height and range size). Results We found a strong relationship between compositional dissimilarity and environmental distance and a weaker but also significant relationship between compositional dissimilarity and geographical distance. Consistent with expectations, relationships with environmental and geographical distance were stronger for understorey species than for canopy species. Geographical distance had a higher correlation with compositional dissimilarity for small‐ranged species compared with large‐ranged species, whereas the opposite was true for environmental distance. The main environmental correlates were inundation and soil nutrient levels. Main conclusions The assembly of palm communities in the western Amazon appears to be driven primarily by species sorting according to hydrology and soil, but with dispersal limitation also playing an important role. The importance of environmental characteristics and geographical distance varies depending on plant height and geographical range size in agreement with functional predictions, increasing our confidence in the inferred assembly mechanisms.     

Effects of grazing intensity and grazing exclusion on litter decomposition in the temperate steppe of Nei Mongol,China

Aims Grazing intensity and grazing exclusion affect ecosystem carbon cycling by changing the plant community and soil micro-environment in grassland ecosystems. The aims of this study were: 1) to determine the effects of grazing intensity and grazing exclusion on litter decomposition in the temperate grasslands of Nei Mongol; 2) to compare the difference between above-ground and below-ground litter decomposition; 3) to identify the effects of precipitation on litter production and decomposition. Methods We measured litter production, quality, decomposition rates and soil nutrient contents during the growing season in 2011 and 2012 in four plots, i.e. light grazing, heavy grazing, light grazing exclusion and heavy grazing exclusion. Quadrate surveys and litter bags were used to measure litter production and decomposition rates. All data were analyzed with ANOVA and Pearson’s correlation procedures in SPSS. Important findings Litter production and decomposition rates differed greatly among four plots. During the two years of our study, above-ground litter production and decomposition in heavy-grazing plots were faster than those in light-grazing plots. In the dry year, below-ground litter production and decomposition in light-grazing plots were faster than those in heavy-grazing plots, which is opposite to the findings in the wet year. Short-term grazing exclusion could promote litter production, and the exclusion of light-grazing could increase litter decomposition and nutrient cycling. In contrast, heavy-grazing exclusion decreased litter decomposition. Thus, grazing exclusion is beneficial to the restoration of the light-grazing grasslands, and more human management measures are needed during the restoration of heavy-grazing grasslands. Precipitation increased litter production and decomposition, and below-ground litter was more vulnerable to the inter-annual change of precipitation than above-ground litter. Compared to the light-grazing grasslands, heavy-grazing grasslands had higher sensitivity to precipitation. The above-ground litter decomposition was strongly positively correlated with the litter N content (R² = 0.489, p < 0.01) and strongly negatively correlated with the soil total N content (R² = 0.450, p < 0.01), but it was not significantly correlated with C:N and lignin:N. Below-ground litter decomposition was negatively correlated with the litter C (R² = 0.263, p < 0.01), C:N (R² = 0.349, p < 0.01) and cellulose content (R² = 0.460, p < 0.01). Our results will provide a theoretical basis for ecosystem restoration and the research of carbon cycling.     

Biotic and abiotic determinants of the formation of ant mosaics in primary Neotropical rainforests

1. Ants are widespread in tropical rainforests, including in the canopy where territorially dominant arboreal species represent the main part of the arthropod biomass. 2. By mapping the territories of dominant arboreal ant species and using a null model analysis and a pairwise approach this study was able to show the presence of an ant mosaic on the upper canopy of a primary Neotropical rainforest (c. 1 ha sampled; 157 tall trees from 28 families). Although Neotropical rainforest canopies are frequently irregular, with tree crowns at different heights breaking the continuity of the territories of dominant ants, the latter are preserved via underground galleries or trails laid on the ground. 3. The distribution of the trees influences the structure of the ant mosaic, something related to the attractiveness of tree taxa for certain arboreal ant species rather than others. 4. Small‐scale natural disturbances, most likely strong winds in the area studied (presence of canopy gaps), play a role by favouring the presence of two ant species typical of secondary formations: Camponotus femoratus and Crematogaster levior, which live in parabiosis (i.e. share territories and nests but lodge in different cavities) and build conspicuous ant gardens. In addition, pioneer Cecropia myrmecophytic trees were recorded.