Are you trying to isolate bacterial strains that produce antibiotics? You take culture supernatant from each isolate and add it to a culture of the target bacteria (You are more likely to get positive results with a Gram positive test species than a Gram negative one). You can do the test in a 96-well plate format in liquid culture, or add a drop of culture medium to a lawn of bacteria on an agar plate, or soak a filter disc in the culture medium and place it on a lawn of bacteria. In the liquid culture format, you look for inhibition of growth based on turbidity of the medium after a day, either by eye or with an A600 measurement. With agar plates, you look for clearing of the culture around the spot where the culture medium or filter disk was placed.

For enzymes produced by bacteria, you need to set up an assay for the enzyme activity, preferably something easy to read out, like a color change. Again, this can be done in liquid or solid culture, either with the bacterial isolates present or with just culture supernatant.

The highest throughput methodology that can be set up easily without a lot of fancy automation uses 96-well assay plates to grow the isolates in liquid culture and 96-well plate-based assays for the active substance. Hand-held multichannel pipettors can be used for the liquid transfer between plates if automated systems are not available. Whether this is practical depends on what you mean by high-throughput. It's OK for hundreds to thousands of tests, but gets pretty tedious for tens of thousands or more. 

The answer depends on you actual task. Do you want to screen large number of isolates from certain environment  for potential antibiotics/enzymes of wide range of activity, or you need to find antibiotic compound against certain type of bacteria?

Thanks Adam for your precious time and suggestion.

Hi Alex,

Yeah..i want to screen large number of isolates and my intention is to develop bacterial antagonists against fungal pathogens(ex:fusairum ) which   cause decease to crops (ex:chickpea). so i am thinking of screen large number of isolates by high throughput method..so would you suggest me in detail

Dear Naresh,

If you are interested in isolating large number of CFU against Fusarium sp., its bettee you go for Kirby Bauer's modified method as described in Microbiological methods by Cappuchino & Sherman. Use 18' inch petri plate, add either of Glucose yeast extract agar (Peptone-5g, Yeast extract-5g, Agar-20g, Distilled water-1litre, pH-5.0) or readymade potato dextrose media (HiMedia Mumbai) to plate hermatically. Spread plate the dilution of Fusarium on surface of solidified agar surface. Using a metallic cavity borer (10mm diameter), cut out agar plugs. Now to the well formed you can add your extract. After 48-72hours you can check inhibition of growth around the  antibiotic containing well. You can compare no of extract's activity on one plate also.

For enzyme activity assay you can choose specific substrate degradation by enzyme extracts at the absorption maxima of the probable extract formed. e.g. Lignin peroxidase activity can be measured by action of this enzyme on veratryl alcohol to form veratryldehyde, while measuring the veratryldehyde formed at 310nm spectrophotometrically. Its basic you can find in Practical Microbiology by Maheshwari and Dubey title of S.chand publishers.