MNBC: a multithreaded Minimizer-based Naïve Bayes Classifier for improved metagenomic sequence classification.

Motivation: State-of-the-art tools for classifying metagenomic sequencing reads provide both rapid and accurate options, although the combination of both in a single tool is a constantly improving area of research. The machine learning-based Naïve Bayes Classifier (NBC) approach provides a theoretical basis for accurate classification of all reads in a sample.

Results: We developed the multithreaded Minimizer-based Naïve Bayes Classifier (MNBC) tool to improve the NBC approach by applying minimizers, as well as plurality voting for closely related classification scores.

A New Multiplex TaqMan qPCR for Precise Detection and Quantification of in Seeds and Plant Tissue.

Bacterial canker of tomato caused by () is one of the most devastating bacterial diseases affecting the tomato industry worldwide. As the result of colonization of the xylem, the susceptible host shows typical symptoms of wilt, marginal leaf necrosis, stem cankers, and ultimately plant death. However, what makes an even more dangerous pathogen is its ability to infect seeds and plants without causing symptoms.

Composition and Dynamics of Plant- and Soil-Associated Microbial Communities in Forest and Agricultural Ecosystems.

Peter Kropotkin (1842-1921) is well known as an anarchist intellectual, an amiable mass of contradictions who loved humanity and was highly regarded in academic and intellectual circles, yet also penned "fiery peans to violence" in , the anarchist journal he established with Elisée Reclus in the 1870s [...

Crop rotation significantly influences the composition of soil, rhizosphere, and root microbiota in canola (Brassica napus L.).

Background: Crop rotation is an agronomic practice that is known to enhance productivity and yield, and decrease pest and disease pressure. Economic and other factors have increased the frequency of certain crops, including canola, with unknown effects on the below ground microbial communities that impact plant health and performance. This study investigated the effect of 12 years of crop rotation including canola-wheat; canola-pea-barley; and unrotated canola across three geographic sites in Western Canada with diverse soil types and environmental conditions.

Modeling the microbial pretreatment of camelina straw and switchgrass by and solid-state fermentation process: A growth kinetic sub-model in the context of biomass-based biorefineries.

Advancing microbial pretreatment of lignocellulose has the potential not only to reduce the carbon footprint and environmental impacts of the pretreatment processes from cradle-to-grave, but also increase biomass valorization, support agricultural growers, and boost the bioeconomy. Mathematical modeling of microbial pretreatment of lignocellulose provides insights into the metabolic activities of the microorganisms as responses to substrate and environment and provides baseline targets for the design, development, and optimization of solid-state-fermentation (SSF) bioreactors, including substrate concentrations, heat and mass transfer. In this study, the growth of 52J (TV52J), m4D (TVm4D), and (PC) on camelina straw (CS) and switchgrass (SG) during an SSF process was examined.