The most obvious symbolism, and one that runs throughout the play is the use of the soil or earth as a metaphor for the actual kingdom of England itself. This isn't an original image, since one of the common understandings of the role of a monarch is that he IS his people, he IS the land -- hence the use of the royal "We" instead of "I," used by Richard II very frequently in this play. He considers himself, as King, to be the land.
So, in this scene the Queen sits in the garden with her waiting women, sad and without occupation. The gardeners enter, and as the Queen listens to their conversation, it becomes clear that the Gardener is likening an unweeded garden to the state of affairs in England. The Gardener suggests that the King should have behaved more like a dedicated gardener and make sure to pull the "weeds" and kill the "caterpillars" (those subjects who are causing mischief in the "garden") so that the "fairest flowers," "wholesome herbs" and "fruit trees" might flourish.
It is significant that the Gardner, quite a low man on the totem pole in the kingdom, has common sense advice, through the extended gardening metaphor that he employs, for the King. He sees that King Richard has been the author of his own demise:
He that hath suffer'd this disorder'd spring
Hath now himself met with the fall of leaf.
The weeds which his broad-spreading leaves did shelter,
That seem'd in eating him to hold him up,
Are pluck'd up root and all by Bolingbroke.
The Gardener extends his use of metaphors here to include a timely symbol of the King's reign. The King oversaw a very "disorder'd spring," so that he must reap the consequences at the present, during the "fall of the leaf." In this way, Shakespeare implies that it is the natural order of things, just as one season follows another, for a King who has misused his power such as Richard to be swept away and replaced. This is the way of Nature in the garden, and the way of the world at large.