For measuring certain metabolites you can also try with freeze-drying. But if you want to monitorize enzyme activities lyophyllization is not a good option.
in the case of organic extract can use rotary evaporator as agood option in the case of aquatic extract , reduce the volium by use water path and then use the freeze drier
if your scope is to analyze the composition of the extract you could choose between freeze-dry procedure if your extract is aqueous and under nitrogen gas in an ice bath if your extract is organic or organic/aqueous (for example in the case of polyphenolic extract)
First of all you have to evaluate what type of compunds you want to extract and thus their stability to oxigen, temperature, light, and so on...
After you could use freeze-drier apparatus for small, but also big, volume of aqueous extracts, or nitrigen gas is small volume paying attention, if the case, to light and temperature
In a less endowed laboratories simple distillation can be used. This reduces the extract volume to a small volume that can be evaporated on water bath or left in desiccator. The disadvantage is that some of the components are likely to be decomposed.