Culture-Independent Molecular Tools for Soil and Rhizosphere Microbiology

Abstract

Soil microbial communities play an important role in plant health and soil quality. Researchers have developed a wide range of methods for studying the structure, diversity, and activity of microbes to better understand soil biology and plant-microbe interactions. Functional microbiological analyses of the rhizosphere have given new insights into the role of microbial communities in plant nutrition and plant protection against diseases. In this review, we present the most commonly used traditional as well as new culture-independent molecular methods to assess the diversity and function of soil microbial communities. Furthermore, we discuss advantages and disadvantages of these techniques and provide a perspective on emerging technologies for soil microbial community profiling.

Plant and microbe genomics and beyond: potential for developing a novel molecular plant nutrition approach

“…However, to date, none of them has been optimized to make direct specific measurements in the environment (Rincon-Florez et al 2013).…”

“…Improved understanding of plant-microbe interactions and advances in molecular biology applied to soil microbiology have led to the emergence of areas such as molecular microbiology, soil metagenomics and molecular plant nutrition (Rincon-Florez et al 2013).…”

Unravelling the composition of soil belowground microbial community before sowing transgenic cotton

“…The soil is considered to harbour the most diverse bacterial communities on earth providing habitats for them (Roesch et al 2007). Soil microbial communities play an important role in plant health, soil quality and ecosystem sustainability of agricultural systems (Rincon-Florez et al 2013). Bacterial communities are important drivers for all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformations in soil (Roesch et al 2007, Rincon-Florez et al 2013).…”

“…Soil microbial communities play an important role in plant health, soil quality and ecosystem sustainability of agricultural systems (Rincon-Florez et al 2013). Bacterial communities are important drivers for all biogeochemical cycles in terrestrial ecosystems and participate in most nutrient transformations in soil (Roesch et al 2007, Rincon-Florez et al 2013). There are biotic and abiotic factors that are assumed to influence the structural and functional diversity of bacterial communities in the rhizosphere soil, such as climate, season, herbicide application, management practices (Galazka et al 2017a,b), integrated livestock-crop system (Acosta-Martínez et al 2010), soil quality (Galazka et al 2017b), plant developmental stage and plant species (Berg and Smalla 2009).…”

“…However, in another study the bacterial communities were affected only by growth stage, herbicide application or soil type more than genetic modification (Schmalenberger and Tebbe 2002). Although molecular methods have been used to study the structure, diversity, and activity of soil bacterial communities (Rincon-Florez et al 2013), few studies have employed the next generation sequencing (NGS) techniques to study the structure of bacterial communities in soils just before GMO (genetically modified organism) seeds sowing. The aim of the study was to characterize the ecological status of the diversity in soil microbial community before the introduction of transgenic crops to determine the effects of conventional or transgenic plants sown on these unused soils.…”