Identification of the selected soil bacteria genera based on their geometric and dispersion features.

The visual analysis of microscopic images is often used for soil bacteria recognition in microbiology. Such task can be automated with the aid of machine learning and digital image processing techniques. The best results for soil microorganism identification usually rely on extracting features based on color. However, accommodating in the latter an extra impact of lighting conditions or sample's preparation on classification accuracy is often omitted. In contrast, this research examines features which are insensitive to the above two factors by focusing rather on bacteria shape and their specific group dispersion. In doing so, the calculation of layout features resorts to k-means and mean shift methods. Additionally, the dependencies between specific distances determined from bacteria cells and the curvature of interpolated bacteria boundary are computed to extract vital geometric shape information. The proposed bacteria recognition tool involves testing four different classification methods for which the parameters are iteratively adjusted. The results obtained here for five selected soil bacteria genera: Enterobacter, Rhizobium, Pantoea, Bradyrhizobium and Pseudomonas reach 85.14% classification accuracy upon combining both geometric and dispersion features. The latter forms a promising result as a substitutive tool for color-based feature classification.

Integrated multi-channel optical system for bacteria characterization and its potential use for monitoring of environmental bacteria.

The potential use of a novel multichannel optical system towards fast and non-destructive bacteria identification and its application for environmental bacteria characterisation on the strain level is presented. It is the first attempt to use the proposed optical method to study various bacteria species (Gram-negative, Gram-positive) commonly present in the environment. The novel configuration of the optical system enables multichannel examination of bacterial colonies and provides additional functionality such as registration of two-dimensional (2D) distribution of monochromatic transmission coefficient of examined colonies, what can be used as a novel optical signature for bacteria characterization. Performed statistical analysis indicates that it is possible to identify representatives of environmental soil bacteria on the species level with the 98.51% accuracy and in case of two strains of Rahnella aquatilis bacteria on the strain level with the 98.8% accuracy. The proposed method is an alternative to the currently used preliminary bacteria examination in environment safety control with the advantage of being fast, reliable, non-destructive and requiring minimal sample preparation.

Biochar-rhizosphere interactions - A review.

Biochar is a solid material of biological origin obtained from the biomass carbonization, designed as a mean to reduce greenhouse gases emission and carbon sequestration in soils for a long time. Biochar has a wide spectrum of practical utilization and is applied as a promising soil improver or fertilizer in agriculture, or as a medium for soil or water remediation. Preparations of biochar increase plant growth and yielding when applied into soil and also improve plant growth conditions, mainly bio, physical and chemical properties of soil. Its physical and chemical properties have influence on bacteria, fungi and invertebrates, both in field and laboratory conditions. Such effects on rhizosphere organisms are positive or negative depending on biochar raw material origin, charring conditions, frequency of applications, applications method and doses, but long terms effects are generally positive and are associated mainly with increased soil biota activity. However, a risk assessment of biochar applications is necessary to protect the food production and soil environment. This should be accomplished by biochar production and characterization, land use implementation, economic analysis, including life cycle assessment, and environmental impact assessment.