Soil Functional Gene Microarrays and Applications in Plant-Microbe Interactions
Lilia C. Carvalhais, Vivian Rincon and Peer M. Schenk
from: Microarrays: Current Technology, Innovations and Applications (Edited by: Zhili He). Caister Academic Press, U.K. (2014)
Undoubtedly, soil is one of the most complex microbial environments that harbours thousands of species of bacteria, fungi, archaea and protists. This diversity can be functionally characterized by soil microarrays that either contain 16S rDNA sequences (microbial community analyses) or other genomic or cDNA sequences from functional genes (functional gene arrays). Microorganisms play essential roles for nutrient acquisition, nutrient conversion and mineralization in soil. These processes are also critical for plant growth, nutrient uptake, plant health and the recycling of organic matter, but some soil microorganisms also act as plant pathogens. Recent technological advances have led to simultaneous time-course analyses of plant hosts and their interacting microorganism(s). Apart from the use of functional gene arrays, this "interaction transcriptome" profiling can also be achieved by quantitative real-time PCR (qRT-PCR), as well as next generation sequencing, especially if at least one genome sequence of the interacting organisms (host or colonizing microorganism) is known. Furthermore, several laboratories are currently pursuing a metatranscriptomics approach to analyse interactions of plants with soil microbial communities. This chapter compares available techniques for gene expression profiling in soil and plants with a focus on soil functional gene microarrays and their applications to study plant-microbe interactions in the rhizosphere read more ...