I suspect that you're looking for Tamora Pierce's Street Magic, the second book of the The Circle Opens series, which followed her Circle of Magic series.
Four young misfits from four different social classes are brought together at the Winding Circle Temple in Emelan. They find themselves housed together as they did not "fit in" when they slept in the dormitories with everyone. They are sent to Discipline Cottage to learn and use their new-found magical abilities. All four have ambient magic, as opposed to academic magic, and the power they use comes from ordinary things all around them. Sandry has magic with threads, Tris with weather, Daja with smithing, and Briar with plants.
....
Roach (later named Briar Moss) is a "street rat" in Hajra, Sotat. His mother died when he was four; he was then taken in by the Thief Lord, the leader of the gang Lightning. Each time Roach is caught committing a crime, an "X" is tattooed onto the web of skin between his thumb and forefinger. After his third capture, Roach is sentenced to the docks but is saved by Niko, who stopped the judge and convinced her to allow him to take Roach to Winding Circle. Roach also has the opportunity to choose a new name for himself; he chooses Briar Moss because of his curiosity and experience with plants.
....
While Briar and his teacher Rosethorn are helping the locals in Chammur, Briar realizes that all is not as it should be in Chammur's streets. As a former 'street rat' himself, he tends to have an interest in the affairs of local gangs. He discovers a gang known as the Vipers roaming through territory not their own. After further investigation, Briar discovers that the Vipers are the pet gang of a local Noblewoman.
While Briar investigates the Vipers, he discovers Evvy, a local girl with stone magic. At first, she runs away from him, but she gradually learns to trust him. When Evvy singularly refuses to study with local stone mage Jebilu Stoneslicer, Briar takes her training in hand himself. The Vipers attempt to kidnap her many times, so Lady Zenadia doa Atteneh can use Evvy's powers as a stone mage to further increase her riches. When they finally kidnap her, Briar comes to her rescue.
I don't have a quote onhand, but Lady Zenadia indeed buries the bodies of people who have failed her in her garden, which seems to result in the plants growing even stronger.
Not matching is that Briar's origin as a street rat and realizing the possibilities of his power is in the first book, with Street Magic being released five books and four years later.
