You definitely need a chat with Jonathan, and the best time is after you have some recent examples of his behavior and the impact on the team that was felt. You should discuss how he is losing influence by always being the naysayer and that you always have more influence when you are a problem solver versus problem explainer. When people always talk negative, others stop listening. Have a discussion as to what would be the opposite behaviors and ones that would position him for even greater influence in the future.