I need a precise detection technique to detect bacteria, fungi, plants in soil.
You can use amplicon Taq pyrosequencing to determine the actual count of bacteria, fungi and plant in soil. it check compare to other NGS platform.
It might be hard to design an amplicon sequencing study since you need different primers for the different groups, and the primers will have different amplification efficiencies. If you would do a full shot gun sequencing study (sequencing all DNA) you can later on extract the 16S and 18S reads using the Metaxa software:
Bengtsson et al. 2011, Antonie van Leeuwenhoek 100:471–475. Metaxa: a software tool for automated detection and discrimination among ribosomal small subunit (12S/16S/18S) sequences of archaea, bacteria, eukaryotes, mitochondria, and chloroplasts in metagenomes and environmental sequencing datasets.
Such an approach would have less biases compared to amplicon studies.
Good luck!
Martin
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