Hi,
The decomposition of POM is simulated in AEM3D and consumes oxygen so this is possible as long as you get the algal growth, death and POM decay calibration correct.
One thing that may be useful is to use the undocumented dead_pom flag in your phyto file.
If you set this to true an additional POM group is created for the dead cells. This allow you to specify different decay and settling rates from the standard POM group.
Chris