While standing on a well lit cobble space outside at night, I noticed that the server was spiking badly on CPU (~130% with one player only vs ~ 60%-70% normally with multiple players). The effect stopped during the day, so I assumed it was a lighting issue.

After trying a few things like extinguishing fires and checking other areas that were well lit and full of entities and finding no problems, I realised that the problem area had a couple of saplings waiting to grow. When I accelerated that with bone meal, the second both of them were oak trees the CPU usage dropped sharply back to 50%