Isolation and identification of soil species - (Jun/19/2014 )
Can anyone offer any advice or suggestions for isolating and identifying microorganisms from soil?
So far I was thinking of stirring the soil in a solution like 1X PBS and then streaking onto a variety of plates such as PEA, DES ,McConkey and TSA.
Then isolating and sub culturing and eventually identifying.
The identification part, I am not sure if I should try biochemical tests or 16S sequencing??
Our lab was traditionally chemistry synthesis but now we are becoming interdisciplinary with microbiology so we don't have PCR/sequencing capabilities as yet or biochemical identification assays, so cost would be a factor as these things need to be purchased or outsourced.
Any suggestions of advice would be great.
If you just want to find out the diversity, currently people are doing next generation sequencing style approaches in attempts to catalogue the stuff that is there.
If you want something cultured, then you will need to have a range of conditions, temperatures, humidity, light exposure, carbon sources, nitrogen sources, phosphates...etc for both agars and broths. I would go with 16s sequencing, it is relatively cheap (max $20/isolate, but depending on where you are, probably a lot cheaper than that)
Note that so far less than 10% of the diversity is capable of being cultured
I will look into sequencing options.