If he replied with his first name only I believe that you have grounds for addressing him by his first name. Emails have introduced a great deal of informality into communications. When I email total strangers and sign off with my full name and title they often reply by addressing me by my first name. So, I think your professor would have little ground for pulling you over starting an email with his first name if that is how he signed off.
My bigger concern is that someone at your stage of education cannot work out these things for yourself. If you feel uncomfortable addressing him by his first name then address him formally. He can hardly have grounds to complain over that. If you feel unsure about whether to be formal, as you seem to prefer, or to be informal, as you seem to have been indirectly invited, you could easily start emails to him with bland openings such as "Hi", "Hello", "Good morning", etc. My guess is the way you begin your emails comes very, very low down on his list of concerns.
It also worth pointing out this is a matter of etiquette. It has nothing to do with the science of biology even if the question relates to a biology professor. You would probably have the same issue if it were another professor. Therefore, not only should you have the ability to resolve this problem yourself you should have posted it in the correct forum.