I am looking for certain tests to identify or tests for the presence of secondary metabolites of Marine Bacillus species. Can I use HPLC? what kind? or if not any tests?
Sure, you can use HPLC to detect, as long as it is known what you wanted to analyze. If it is known, you need to prepare the standard solution of that secondary metabolite and identify the retention time. Then you can use the liquid bacterial culture and prepare an HPLC sample. On the basis of HPLC results, you can quantify the amount of your desired chemical.
As Abhijeet said, to use HPLC, you need to target what you want to analyze and prepare standards. The protocols to extract compounds are different and you need to know what you need to analyze and find the extraction method for that particular compound.
But if you want to have a metabolomic profile you need to use GC-MS, LC-MS or NMR.