Gathering Bonus?

[Brightamethyst]

[+1 Yield Node Bonus] : 3900 Gathering

What does that mean? For example, if I am farming Annite or Raw Star Quartz what difference does it make if I upgrade from current 3715 to 3900?

You only get the bonus if you meed the stated conditions. If you have at least 3900 gathering you get +1 yield for that node. If you don't meet the requirements (as in this example where 3715, is less that 3900) you don't lose anything, you just don't get the bonus.