plant surface microbiology.pdf

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Ajit Varma et al.
mative, quantitative data of in vitro microbial ecology from them at spatial
scales relevant to the microbes themselves. New computer-assisted imaging
technology has been successfully applied to the fascinating field of plant surface
microbiology (Chap. 27). CMEIAS software can “count what really
counts” to enhance the quantitative analysis of microbial communities and
populations in situ without cultivation.
Knowledge of genetic diversity in the bacterial population has increased
considerably over the last 15 years, due to the application of molecular techniques
to microbial ecological studies. Among the molecular methods, the
PCR-based techniques provide a powerful and high throughput approach for
the study of genetic diversity in bacterial populations. Some of the most commons
are the PCR-RFLP of specific sequences (16S rDNA, intergenic transcribed
spacer, ITS), the repetitive extragenic palindromic-PCR and the BOX-
PCR based on the presence of repetitive elements within the bacterial
genome, the DNA amplification fingerprintings, RAPDs (random amplified
polymorphic DNA, and AFLPs (amplified fragment length polymorphism).
ITS, RAPD and AFLP have been shown to be particularly relevant for the
study of genetic diversity within populations of bacteria belonging to the
same or closely related species (Chap. 28). AFLP shows some advantages over
the other methods due to high stringency PCR conditions which give reproducibility
and easy application to plant, animal and bacterial genomic DNA.
AFLP has a high informational content per single reaction, in fact, up to 100
different bands can be displayed in a single lane and the scoring can be done
with an automatic sequencer.
While there is a considerable amount of knowledge based on the ecology
and physiology of mycorrhizal fungi and their uses, the knowledge about cellular
and molecular aspects leading to the growth and development of the
mycorrhizal fungus, as well as the establishment of a functioning symbiosis is
still limited. An appropriate approach to the study of these special fungi is to
understand the molecular process leading to the host recognition, development
and functioning of mycorrhiza through the analysis of expressed
sequences.With the advent of many highly sophisticated techniques that have
been successfully applied to the functional analysis of genes from many
organisms, it is now possible to apply similar strategies to study the various
aspects of the mycorrhizal symbiosis (Chap. 29). The protocol describes
expressed sequence tags (EST) and macroarray techniques. These approaches
provide efficient tools for mycorrhizal symbiosis research. They have the resolution
and ability to obtain a more comprehensive view of various stages of
mycorrhiza development or treatment effects due to nutritional changes or
differences due to host responses. Data can be exchanged and compared
between different laboratories and eventually will provide a platform to
understand the key players (genes) that are markers for ectomycorrhizal and
AM fungal symbiosis. A large number of media compositions are available in
the literature for the cultivation of various groups of fungi, but almost no lit-