Mysql connector allows to specify many properties in the jdbc URL for different purposes. Some features are only available this way. However when a query is performed through Spring jdbcTemplate, the properties set in the URL have no effect.
For example, using "jdbc:mysql://localhost:3306/mydb?includeThreadNamesAsStatementComment=true" with 5.1.15 connector can show the Java thread name in the "show processlist" output, a great feature for debugging. If jdbc API is used directly the thread name shows up as expected, but not so if the query is made through jdbc template.