For the megaAVR microcontrollers, the pull-ups are enabled by default at power-up. The software can enable or disable all ports simultaneously using the Pull-Up Disable (PUD) bit in the Special Function I/O (SFIOR) register.
Unlike megaAVR microcontrollers, the AVR Dx families provide a pull-up option for each pin individually. The pull-up is disabled at Reset and can be enabled by software using the Pull-Up Enable bit in the PORTx.PINnCTRL register.