MDQC: a new quality assessment method for microarrays based on quality control reports

Motivation: The process of producing microarray data involves multiple steps, some of which may suffer from technical problems and seriously damage the quality of the data. Thus, it is essential to identify those arrays with low quality. This article addresses two questions: (1) how to assess the quality of a microarray dataset using the measures provided in quality control (QC) reports; (2) how to identify possible sources of the quality problems. Results: We propose a novel multivariate approach to evaluate the quality of an array that examines the ‘Mahalanobis distance' of its quality attributes from those of other arrays. Thus, we call it Mahalanobis Distance Quality Control (MDQC) and examine different approaches of this method. MDQC flags problematic arrays based on the idea of outlier detection, i.e. it flags those arrays whose quality attributes jointly depart from those of the bulk of the data. Using two case studies, we show that a multivariate analysis gives substantially richer information than analyzing each parameter of the QC report in isolation. Moreover, once the QC report is produced, our quality assessment method is computationally inexpensive and the results can be easily visualized and interpreted. Finally, we show that computing these distances on subsets of the quality measures in the report may increase the method's ability to detect unusual arrays and helps to identify possible reasons of the quality problems. Availability: The library to implement MDQC will soon be available from Bioconductor Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics onlin

Dominant Trees in a Subtropical Forest Respond to Drought Mainly via Adjusting Tissue Soluble Sugar and Proline Content

It is well-known that drought has considerable effects on plant traits from leaf to ecosystem scales; however, little is known about the relative contributions of various traits within or between tree species in determining the plant’s sensitivity or the tolerance to drought under field conditions. We conducted a field throughfall exclusion experiment to simulate short-term drought (∼67% throughfall exclusion during the dry season from October to March) and prolonged drought (∼67% throughfall exclusion prolonging the dry season from October to May) and to understand the effects of drought on two dominant tree species (Michelia macclurei and Schima superba) in subtropical forests of southern China. The morphological, physiological, and nutritional responses of the two species to the two types of drought were determined. There were significantly different morphological (leaf max length, max width, leaf mass per area), physiological (leaf proline) and nutritional (P, S, N, K, Ca, Mg) responses by M. macclurei and S. superba to prolonged drought. Comparison between the drought treatments for each species indicated that the trees responded species–specifically to the short-term and prolonged drought, with S. superba exhibiting larger plasticity and higher adaption than M. macclurei. M. macclurei responded more sensitively to prolonged drought in terms of morphology, proline content, and nutritional traits and to short-term drought with regard to soluble sugars content. The differential species-specific responses to drought will allow us to estimate the changes in dominant trees in subtropical forests of China that have experienced a decade’s worth of annual seasonal drought

Seasonal drought may alter N availability but not water use efficiency of dominant trees in a subtropical forest

Drought has had considerable effects on the ecological functions and processes of terrestrial ecosystems. However, little is known about the impacts of seasonal drought on the water use efficiency (WUE) and plant nitrogen (N) availability of dominant trees under field conditions. In this study, a field throughfall exclusion experiment simulating short-term drought (∼67% throughfall exclusion during the dry season from October to March) and prolonged drought (∼67% throughfall exclusion prolonging the dry season from October to May) was designed to understand the effects of seasonal drought on two dominant tree species (Michelia macclurei and Schima superba) in subtropical forest. The C and N content and isotopes in the deeper but not the surface soils in the forest were significantly affected by the seasonal drought. Neither the short-term nor the prolonged drought significantly altered δ13C values in the leaves and fine roots of the two species, but the short-term drought caused significant changes in δ15N values in the leaves and fine roots of S. superba. The WUE of the two dominant trees, indicated by the leaf δ13C values, was not significantly changed by the short-term and the prolonged drought. However, the N availability of S. superba, indicated by the δ15N values, was significantly altered by the seasonal short-term drought. Long-term influence of seasonal drought on the forest hydrological and N cycling and the potential shifts of species dominance induced by the changed N availability in subtropical forests should be assessed in the future research. Keywords: Nitrogen availability, Seasonal drought, Subtropical forest, Throughfall exclusion, Water use efficienc

Vertical Distribution of Soil Denitrifying Communities in a Wet Sclerophyll Forest under Long-Term Repeated Burning

Soil biogeochemical cycles are largely mediated by microorganisms, while fire significantly modifies biogeochemical cycles mainly via altering microbial community and substrate availability. Majority of studies on fire effects have focused on the surface soil; therefore, our understanding of the vertical distribution of microbial communities and the impacts of fire on nitrogen (N) dynamics in the soil profile is limited. Here, we examined the changes of soil denitrification capacity (DNC) and denitrifying communities with depth under different burning regimes, and their interaction with environmental gradients along the soil profile. Results showed that soil depth had a more pronounced impact than the burning treatment on the bacterial community size. The abundance of 16S rRNA and denitrification genes (narG, nirK, and nirS) declined exponentially with soil depth. Surprisingly, the nosZ-harboring denitrifiers were enriched in the deeper soil layers, which was likely to indicate that the nosZ-harboring denitrifiers could better adapt to the stress conditions (i.e., oxygen deficiency, nutrient limitation, etc.) than other denitrifiers. Soil nutrients, including dissolved organic carbon (DOC), total soluble N (TSN), ammonium (NH4 +), and nitrate (NO3 −), declined significantly with soil depth, which probably contributed to the vertical distribution of denitrifying communities. Soil DNC decreased significantly with soil depth, which was negligible in the depths below 20 cm. These findings have provided new insights into niche separation of the N-cycling functional guilds along the soil profile, under a varied fire disturbance regime

Vertical Distribution of Soil Denitrifying Communities in a Wet Sclerophyll Forest under Long-Term Repeated Burning

Soil biogeochemical cycles are largely mediated by microorganisms, while fire significantly modifies biogeochemical cycles mainly via altering microbial community and substrate availability. Majority of studies on fire effects have focused on the surface soil; therefore, our understanding of the vertical distribution of microbial communities and the impacts of fire on nitrogen (N) dynamics in the soil profile is limited. Here, we examined the changes of soil denitrification capacity (DNC) and denitrifying communities with depth under different burning regimes, and their interaction with environmental gradients along the soil profile. Results showed that soil depth had a more pronounced impact than the burning treatment on the bacterial community size. The abundance of 16S rRNA and denitrification genes (narG, nirK, and nirS) declined exponentially with soil depth. Surprisingly, the nosZ-harboring denitrifiers were enriched in the deeper soil layers, which was likely to indicate that the nosZ-harboring denitrifiers could better adapt to the stress conditions (i.e., oxygen deficiency, nutrient limitation, etc.) than other denitrifiers. Soil nutrients, including dissolved organic carbon (DOC), total soluble N (TSN), ammonium (NH4 +), and nitrate (NO3 −), declined significantly with soil depth, which probably contributed to the vertical distribution of denitrifying communities. Soil DNC decreased significantly with soil depth, which was negligible in the depths below 20 cm. These findings have provided new insights into niche separation of the N-cycling functional guilds along the soil profile, under a varied fire disturbance regime

The origin of suspended particulate matter in the Great Barrier Reef

Abstract River run-off has long been regarded as the largest source of organic-rich suspended particulate matter (SPM) in the Great Barrier Reef (GBR), contributing to high turbidity, pollutant exposure and increasing vulnerability of coral reef to climate change. However, the terrestrial versus marine origin of the SPM in the GBR is uncertain. Here we provide multiple lines of evidence (13C NMR, isotopic and genetic fingerprints) to unravel that a considerable proportion of the terrestrially-derived SPM is degraded in the riverine and estuarine mixing zones before it is transported further offshore. The fingerprints of SPM in the marine environment were completely different from those of terrestrial origin but more consistent with that formed by marine phytoplankton. This result indicates that the SPM in the GBR may not have terrestrial origin but produced locally in the marine environment, which has significant implications on developing better-targeted management practices for improving water quality in the GBR