Dr. Shirayama is an expert of marine biology. His main target organisms are meiobenthos, which is microscopic multicellular animals. He has studied ecology of deep-sea meiobenthos and taxonomy of meiofaunal taxa, such as nematodes, kinorhynchs and loriciferans. He has been also trying to apply the meiobenthos as an indicator of environmental condition. Recently he expanded his field to global environmental issues especially ocean acidification. He also played a leading role in an international research project aiming to compare the coastal biodiversity in the global scale in a comprehensive international marine biodiversity research project, Census of Marine Life.