Metagenomics is an emerging field of molecular biology that uses high-throughput sequencers to identify genes in complex microbial environment.
Soil characterization (structure of communities) at metagenomic level could provide a predictive tool for crop productivity and soil health based on soil biodiversity (total DNA or RNA) analysis in combination to soil chemical and physical properties (especially under different anthropization gradient)?
How can we make it possible?
This is a quiet interesting question, and scientists are focusing on it in the environmental point of view. Soil meta-genomic is not widely used yet in agriculture due to the huge interactions that could occur into the soil, on the crops and at rhizosphere level.
I found (file attached) this interesting research work done by INRA France to collect soil DNA from all over the country in order to dress a soil bacterial DNA map.
Soil samples can analysed for microbial communities by analyzing phospholipid fatty acids (PLFA) and phospholipid etherlipids (PLEL) to determine bacterial, eucaryotic and archaeal microorganisms (Gattinger et al., 2003; Zelles, 1999). PLFA and PLEL biomarker could be determined by gaschromatography/mass spectrometry-combustion-isotope ratio mass spectrometry (GC/MS-C-IRMS). There is another way by simple ATP analysis (see attached file), but mostly used for compost samples.
There are many tools to assess microbial community int o soil, here attached also more information in the methods part (Soil DNA Isolation Kit and Microarray analysis)
I know one Professor who has experience on Meta Genomics of Soil. I am giving his address, You may contact him to share his experience.
M. Tofazzal Islam
Professor
Dept of Biotechnology, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
E-mail: [email protected]
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