Polymer hydrogels and methods for selective retrieval of microbial targets from microwells and other cell culture devices. The methods use semi-permeable, photodegradable hydrogel membranes that permit exchange of nutrients and waste products but seals motile bacteria and other microbes within microwells. Light exposure can be used to degrade the hydrogel membrane in a targeted manner and release the microbes from targeted microwells for further study.