Proficiency Testing of Metagenomics-Based Detection of Food-Borne Pathogens Using a Complex Artificial Sequencing Dataset

Metagenomics-based high-throughput sequencing (HTS) enables comprehensive detection of all species comprised in a sample with a single assay and is becoming a standard method for outbreak investigation. However, unlike real-time PCR or serological assays, HTS datasets generated for pathogen detection do not easily provide yes/no answers. Rather, results of the taxonomic read assignment need to be assessed by trained personnel to gain information thereof. Proficiency tests are important instruments of validation, harmonization, and standardization. Within the European Union funded project COMPARE [COllaborative Management Platform for detection and Analyses of (Re-) emerging and foodborne outbreaks in Europe], we conducted a proficiency test to scrutinize the ability to assess diagnostic metagenomics data. An artificial dataset resembling shotgun sequencing of RNA from a sample of contaminated trout was provided to 12 participants with the request to provide a table with per-read taxonomic assignments at species level and a report with a summary and assessment of their findings, considering different categories like pathogen, background, or contaminations. Analysis of the read assignment tables showed that the software used reliably classified the reads taxonomically overall. However, usage of incomplete reference databases or inappropriate data pre-processing caused difficulties. From the combination of the participants\u2019 reports with their read assignments, we conclude that, although most species were detected, a number of important taxa were not or not correctly categorized. This implies that knowledge of and awareness for potentially dangerous species and contaminations need to be improved, hence, capacity building for the interpretation of diagnostic metagenomics datasets is necessary

Geographical and climatic limits of needle types of one- and two-needled pinyon pines

Aim The geographical extent and climatic tolerances of one- and two-needled pinyon pines (Pinus subsect. Cembroides) are the focus of questions in taxonomy, palaeoclimatology and modelling of future distributions. The identification of these pines, traditionally classified by one- versus two-needled fascicles, is complicated by populations with both one- and two-needled fascicles on the same tree, and the description of two more recently described one-needled varieties: the fallax-type and californiarum-type. Because previous studies have suggested correlations between needle anatomy and climate, including anatomical plasticity reflecting annual precipitation, we approached this study at the level of the anatomy of individual pine needles rather than species. Location Western North America. Methods We synthesized available and new data from field and herbarium collections of needles to compile maps of their current distributions across western North America. Annual frequencies of needle types were compared with local precipitation histories for some stands. Historical North American climates were modeled on a c. 1-km grid using monthly temperature and precipitation values. A geospatial model (ClimLim), which analyses the effect of climate modulated physiological and ecosystem processes, was used to rank the importance of seasonal climate variables in limiting the distributions of anatomical needle types. Results The pinyon needles were classified into four distinct types based upon the number of needles per fascicle, needle thickness and the number of stomatal rows and resin canals. The individual needles fit well into four categories of needle types, whereas some trees exhibit a mixture of two needle types. Trees from central Arizona containing a mixture of Pinus edulis and fallax-type needles increased their percentage of fallax-type needles following dry years. All four needle types occupy broader geographical regions with distinctive precipitation regimes. Pinus monophylla and californiarum-type needles occur in regions with high winter precipitation. Pinus edulis and fallax-type needles are found in regions with high monsoon precipitation. Areas supporting californiarum-type and fallax-type needle distributions are additionally characterized by a more extreme May–June drought. Main conclusions These pinyon needle types seem to reflect the amount and seasonality of precipitation. The single needle fascicle characterizing the fallax type may be an adaptation to early summer or periodic drought, while the single needle of Pinus monophylla may be an adaptation to summer–autumn drought. Although the needles fit into four distinct categories, the parent trees are sometimes less easily classified, especially near their ancestral Pleistocene ranges in the Mojave and northern Sonoran deserts. The abundance of trees with both one- and two-needled fascicles in the zones between P. monophylla, P. edulis and fallax-type populations suggest that needle fascicle number is an unreliable characteristic for species classification. Disregarding needle fascicle number, the fallax-type needles are nearly identical to P. edulis, supporting Little’s (1968) initial classification of these trees as P. edulis var. fallax, while the californiarum-type needles have a distinctive morphology supporting Bailey’s (1987) classification of this tree as Pinus californiarum

Pretreatment Tree Dominance and Conifer Removal Treatments Affect Plant Succession in Sagebrush Communities

In sagebrush (Artemisia tridentata Nutt.) ecosystems, expansion and infilling of conifers decreases the abundance of understory perennial vegetation and lowers ecosystem resilience and resistance of the once shrub grass-dominated state. We prescribed burned or cut juniper (Juniperus spp. L.) and pinyon (Pinus spp. L.) trees at 10 sites across the western United States. We measured vegetation cover and density on untreated and treated plots 3 and 6 yr after treatment across a gradient of pretreatment tree dominance as quantified by the tree dominance index (TDI); (tree cover)/(tree + shrub + tall grass cover). We analyzed plant responses by functional group using mixed-model analysis of covariance, with TDI treated as a covariate. As tree cover increased and TDI exceeded 0.5, shrub cover declined to < 25% of the maximum on untreated plots. Although total shrub cover recovered on burned plots to untreated percentages 6 yr after treatment, sagebrush cover was still 1.1-0.6% on burned plots compared with 13.9-0.5% on untreated plots across the range of 0-1 TDI. Tall grass cover increased to 25.4-9.4% for burn plots and 24.3-22.4% on cut plots from 0-1 TDI 6 yr after treatment. Cheatgrass (Bromus tectorum L.) increased on prescribed fire and on cut treatments, especially at higher pretreatment TDI. However, ratios of cheatgrass to tall grass cover were much lower on cut than burn plots. To retain the shrub, especially sagebrush, components on a site and increase ecosystem resilience and resistance through increases in tall grasses, we recommend treating at low to mid TDI using mechanical methods, such as cutting or mastication. Effects of fire and mechanical treatments implemented at different phases of tree dominance create different successional trajectories that could be incorporated into state-and-transition-models to guide management decisions. © 2017 The Society for Range Management. Published by Elsevier Inc. All rights reserved.The Rangeland Ecology & Management archives are made available by the Society for Range Management and the University of Arizona Libraries. Contact [email protected] for further information