Detection of methanotrophs with highly divergent pmoA genes from Arctic soils

Tundra soil samples from the Canadian Arctic community, Kuujjuaq, were analyzed for the presence of the soluble (sMMO) and particulate (pMMO) methane monooxygenase genes. Total genomic DNA extracted from these soils was used as template for PCR using sMMO- and pMMO-specific primers, mmoX1-mmoX2 and A189-A682, respectively. pMMO and sMMO genes were detected in the Kuujjuaq soil samples. Isolation of sMMO-possessing methanotrophic microorganisms from the three soils, as determined by the colony naphthalene oxidation assay, was carried out using direct plating (5 degrees C) and methane enrichment studies (5 degrees C and 25 degrees C). Direct plating did not yield sMMO-possessing methanotrophic bacteria, whereas methane enrichments yielded isolates possessing and expressing sMMO activity. Analysis of derived amino acid sequences of pmoA genes and partial 16S rRNA genes obtained by PCR, using DNA isolated directly from this environment and from isolates, revealed the presence of highly divergent PmoA/AmoA sequences and 16S rRNA sequences that cluster closely with but are distinct from the genes from the genera Methylosinus and Methylocystis.     

Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas

Most individuals throughout the Americas are admixed descendants of Native American, European, and African ancestors. Complex historical factors have resulted in varying proportions of ancestral contributions between individuals within and among ethnic groups. We developed a panel of 446 ancestry informative markers (AIMs) optimized to estimate ancestral proportions in individuals and populations throughout Latin America. We used genome-wide data from 953 individuals from diverse African, European, and Native American populations to select AIMs optimized for each of the three main continental populations that form the basis of modern Latin American populations. We selected markers on the basis of locus-specific branch length to be informative, well distributed throughout the genome, capable of being genotyped on widely available commercial platforms, and applicable throughout the Americas by minimizing within-continent heterogeneity. We then validated the panel in samples from four admixed populations by comparing ancestry estimates based on the AIMs panel to estimates based on genome-wide association study (GWAS) data. The panel provided balanced discriminatory power among the three ancestral populations and accurate estimates of individual ancestry proportions (R2 > 0.9 for ancestral components with significant between-subject variance). Finally, we genotyped samples from 18 populations from Latin America using the AIMs panel and estimated variability in ancestry within and between these populations. This panel and its reference genotype information will be useful resources to explore population history of admixture in Latin America and to correct for the potential effects of population stratification in admixed samples in the region.     

Associations between primates and other mammals in a central Amazonian forest landscape

Little information exists on mixed-species groups between primates and other mammals in Neotropical forests. In this paper, we describe three such associations observed during an extensive large-vertebrate survey in central Amazonia, Brazil. Mixed-species groups between a primate species and another mammal were observed on seven occasions between squirrel monkeys (Saimiri cf. ustus) and either South American coatis (Nasua nasua) or tayras (Eira barbara) and between brown capuchins (Cebus apella) and coatis. All associations were restricted to floodplain forest during its dry stage. We suggest that the associations involving the coatis are connected to foraging and vigilance but may be induced by a common alternative food resource at a time of food shortage.     

Culture-Free Survey Reveals Diverse and Distinctive Fungal Communities Associated with Developing Figs (Ficus spp.) in Panama

The ancient association of figs (Ficus spp.) and their pollinating wasps (fig wasps; Chalcidoidea, Hymenoptera) is one of the most interdependent plant–insect mutualisms known. In addition to pollinating wasps, a diverse community of organisms develops within the microcosm of the fig inflorescence and fruit. To better understand the multipartite context of the fig–fig wasp association, we used a culture-free approach to examine fungal communities associated with syconia of six species of Ficus and their pollinating wasps in lowland Panama. Diverse fungi were recovered from surface-sterilized flowers of all Ficus species, including gall- and seed flowers at four developmental stages. Fungal communities in syconia and on pollinating wasps were similar, dominated by diverse and previously unknown Saccharomycotina, and distinct from leaf- and stem endophyte communities in the same region. Before pollination, fungal communities were similar between gall- and seed flowers and among Ficus species. However, fungal communities differed significantly in flowers after pollination vs. before pollination, and between anciently diverged lineages of Ficus with active vs. passive pollination syndromes. Within groups of relatively closely related figs, there was little evidence for strict-sense host specificity between figs and particular fungal species. Instead, mixing of fungal communities among related figs, coupled with evidence for possible transfer by pollinating wasps, is consistent with recent suggestions of pollinator mixing within syconia. In turn, changes in fungal communities during fig development and ripening suggest an unexplored role of yeasts in the context of the fig–pollinator wasp mutualism.     

Evaluating different methods of microarray data normalization

Background  

With the development of DNA hybridization microarray technologies, nowadays it is possible to simultaneously assess the expression levels of thousands to tens of thousands of genes. Quantitative comparison of microarrays uncovers distinct patterns of gene expression, which define different cellular phenotypes or cellular responses to drugs. Due to technical biases, normalization of the intensity levels is a pre-requisite to performing further statistical analyses. Therefore, choosing a suitable approach for normalization can be critical, deserving judicious consideration.     

Soil Carbon Turnover Measurement by Physical Fractionation at a Forest-to-Pasture Chronosequence in the Brazilian Amazon

The effect of conversion from forest-to-pasture upon soil carbon stocks has been intensively discussed, but few studies focus on how this land-use change affects carbon (C) distribution across soil fractions in the Amazon basin. We investigated this in the 20 cm depth along a chronosequence of sites from native forest to three successively older pastures. We performed a physicochemical fractionation of bulk soil samples to better understand the mechanisms by which soil C is stabilized and evaluate the contribution of each C fraction to total soil C. Additionally, we used a two-pool model to estimate the mean residence time (MRT) for the slow and active pool C in each fraction. Soil C increased with conversion from forest-to-pasture in the particulate organic matter (>250 μm), microaggregate (53–250 μm), and d-clay (<2 μm) fractions. The microaggregate comprised the highest soil C content after the conversion from forest-to-pasture. The C content of the d-silt fraction decreased with time since conversion to pasture. Forest-derived C remained in all fractions with the highest concentration in the finest fractions, with the largest proportion of forest-derived soil C associated with clay minerals. Results from this work indicate that microaggregate formation is sensitive to changes in management and might serve as an indicator for management-induced soil carbon changes, and the soil C changes in the fractions are dependent on soil texture.     

Ecological thresholds and regime shifts: approaches to identification

There is an apparent gap between the prominence of present theoretical frameworks involving ecological thresholds and regime shifts, and the paucity of efforts to conduct simple tests and quantitative inferences on the actual appearance of such phenomena in ecological data. A wide range of statistical methods and analytical techniques are now available that render these questions tractable, some of them even dating back half a century. Yet, their application has been sparse and confined within a narrow subset of cases of ecological regime shifts. Our objective is to raise awareness on the range of techniques available, and to their principles and limitations, to promote a more operational approach to the identification of ecological thresholds and regime shifts.     

Vegetation composition,structure, and biomass of two unpolluted watersheds in the Cordillera de Piuchué, Chiloé Island,Chile

Research in pristine forests provides a necessary reference of energy and nutrient cycling in absence of anthropogenic influence. Therefore two unpolluted watersheds in the Cordillera de Piuchué of southern Chile (42 °30 S) were chosen for detailed ecosystem analysis. The goals of this study were to quantify the distribution of the living biomass in the research watershed and to document topographic gradients in the vegetation. Across a small spatial gradient from ravine bottom to ridgetop (approximately 60 m in elevation and < 300 m in length) in the Cordillera de Piuchué watersheds, there were significant shifts in vegetation composition, structure, and biomass. Based on sampling in 18, 100 m² plots, we identified three distinct community associations: a Fitzroya forest at the bottom of the watershed, a mid-slope Pilgerodendron-Tepualia transition zone, and a ridgetop moorland community. The Fitzroya forest was dominated by a cohort of approximately 400 year-old Fitzroya cupressoides trees. Both tree basal area (138 m²/ha) and total live biomass (656 Mg ha^–1) reached a maximum in this vegetation type. The Pilgerodendron-Tepualia forest consisted of smaller, shorter, and younger trees with dominance shared by Pilgerodendron uviferum, Tepualia stipularis, and to a lesser extent, F. cupressoides. Basal area and biomass were half that of the Fitzroya forest (69.5 m² ha^–1; 350 Mg ha^–1) but tree density was 65% greater. The moorland can best be described as an open community of mosses and cushion plants that included low stature individuals of P. uviferum, F. cupressoides, and T. stipularis. The size and age structure of F. cupressoides in the bottomland forest suggest that the current cohort of adult trees was established following a catastrophic disturbance and that F. cupressoides is unable to regenerate under its own canopy. In contrast, the size structure of the tree populations in the Pilgerodendron-Tepualia zone indicates that all the constituent tree species, except F. cupressoides, are able to reproduce at least at some microsites in the understory. The watershed-level means for live biomass were 306 Mg ha^–1 of aboveground tree biomass, 25 Mg ha^–1 of large root biomass (diameter ge 1 cm), and 46 Mg ha^–1 of small root biomass (diameter < 1 cm).