The article says that tree roots released massive nutrients into the oceans during the period of decay causing algae bloom depleting the Oxygen and triggering the extinction. Why just the roots and not the entire trees? Wouldn't the entire tree be decayed and end up in the ocean?
There was no soil yet at this time. Plants rooted directly into rock, turning the surface into gravel/sediment, weathering and runoff carried minerals and carbon away into the water. The landscape's stability depends on the roots, and so during mass extinction events, minerals and carbon get dumped en masse from the continents into the sea, and atmospheric CO2 levels drop because of weathering.
That part is relatively well established. This paper looks at the transport of phosphorus in particular, from terrestrial rock into marine ecosystems.
Plants can't take up phosphorus in its mineral bound form. Modern trees have micro-organisms living on their roots that release P (and N etc) from the soil. In certain periods of the Devonian era, P would have been primarily liberated from the rock by acids let off by the plant roots as they decayed.
