The one method that I know is the DGGE (Denaturing Grading Gel Electrophoresis), that is used to determine the type of bacterial or fungal diversity in soil/water by isolating the community DNA then perform DGGE.
Are there other methods which are efficient, easy, less time consuming and economical?
You can do sequence-based metagenomic analysis. It is the most efficient, easy and less time consuming but not so economical.
Most simple method of determining the microbial load by total aerobic and viable count method by using pour plate method (serial dilution of soil sample 1:10 dilution) and filtration method (for water analysis) more accurate, efficient and economical method of microbial bio-burden estimation as per harmonized pharmacopeia.
Because of the difficulty in studying organisms at the genus/species level , the well developed fingerprinting technique that begins with an genetic DNA extraction from soil / water samples by using methods like DGGE, ARISA . The molecular fingerprint analysis can be used to monitor bacterial complexity/diversity, the relative abundance and dynamics of these microscopic communities is at a landscape level in the real world essentially looking at the problem at a much lower resolution.
TGGE would be another one that has some advantages in comparison with DGGE. Alternatively, you would be able to use sequencing up to three variable regions of 16S rRNA by pyrosequencer. Pyrosequencer would give you more data on species in comparison with illumina platform. If you want to analyze more length of 16S rRNA gene, it would be better to use Sanger sequencer. Choosing platforms and DNA sequencing methods would be depends on the dept of analysis, level of identification (genus, species etc), the resolution of results etc you expect for your study.
For me, the most efficient method is RFLP, it is very simple, cheap and fast.
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