Plant diseases are not very common in planted aquariums, however, Java fern can be infected by a fungus; Synchytrium cfr. stachydis. The fungus grows inside of the plant tissue and causes gall lesions to form on the surfaces of the leaves and rhizomes. This interferes with the growth of the plant and eventually leads to most surfaces being covered and death of the plant. The galls appear as green protrusions that causes twisting of the leaf surface. It can appear as more sparse dots before forming denser clusters over time. This causes deformation of younger leaves and twisted growth. In the long run, the fungus is a slow but sure death sentence for the plant. There is no confirmed known cure, which furthers the severity of the disease.
An except from Tri-Ology Vol 58 Number 2 (2019) published by the Florida Department of Agriculture and Consumer Services details the Synchytrium fungus below:
Identifying the disease
Galls start as rather innocuous small galls. When they are sparsely distributed, some folks mistake them for Java fern spore capsules (pictured below).
The dots in the picture above are not fungus galls, but the usual sporophytes found on the bottom side of Java fern leaves. Sporophytes are usually brown or black, circular, and are evenly distributed across the bottom side of leaves. This is different from the fungus galls which can form on either the top or bottom surface of the leaf and rhizome and are green in color. The galls also causes twisting and deformation of the leaf surface which natural Java fern sporophytes do not.
As the gall density increases, the java fern plant gets increasingly deformed. The galls feel crunchy to the touch.
Fungus galls smoother this entire young leaf.
Galls causes dents and deformation of the leaf surface.
How it spreads
This disease is spread by contact and spores contained within the gall structure. It spreads to adjacent Java fern by contact. It will spread to different sub-species of Java fern. The spread happens slowly, so it can take quite a while for adjacent plants to be infected. It does not spread to other plant species.
The fungus spores are very resilient, so even after every bit of infected Java fern plants are removed from a tank, the tank can still have spores that can infect newly introduced plants. It may take many weeks before new galls appear, so the confirmation whether a tank is already 'clean' or not can take a long time. The fungus Synchytrium's land cousins are known to have spores that last many years. This has been especially damaging to aquatic plant farms. Dealers ignorant of this issue may continue to sell infected plants and the condition can be hard to spot by new aquarists.
In one case, a commercial grower removed all affected leaves from the infected Java fern and grew the plant emersed, and the new leaves came out clean. However, upon submerging the plants in water, the fungus galls resurfaced after a few months. This is an indication that when a plant is infected, the fungus can lay dormant in the rhizome for a long time, and resurface when the opportunity arises.
There is no known cure for this fungus at this point. For the land species of this fungus that affects potato plants, there is no approved chemical treatment. The main method of dealing with this fungus disease is exclusion - i.e. not having any infected plants to start with.
For a tank that already contains Java fern plants with the disease, a complete tear down and restart with new materials is the only sure solution. Synchytrium fungus spores last for years in dormancy. Newly infected plants also take months to show more obvious symptoms, so it brings tremendous difficulty in testing whether a tank is truly free from the disease or not. Bleaching previously used equipment does seem to work, but organic materials such as aquasoil should not be reused.
Hobbyists are advised to inspect all purchased Java fern closely to avoid infecting their tanks in the first place. Tissue culture sources will be one way to side-step this issue, but tissue culture Java fern is not commonly commercially sold.