In short, "upstream" capabilities are tapping the backbone itself, via the willing assistance of the telcos (who still have remained mostly silent on all of this) as opposed to "downstream" collection, which requires going to the internet companies directly. The internet companies have been much more resistant to government attempts to get access to their accounts. And thus, it's a big question as to what exactly the NSA can collect via its taps on the internet backbone, and the NSA and its defenders have tried to remain silent on this point, as you can see from the redactions above.
However, as Kevin Bankston notes, during Thursday's Senate Intelligence Committee hearing, Dianne Feinstein more or less admitted that they get emails via "upstream" collection methods. As you can see in the following clip, Feinstein interrupts a discussion to read a prepared "rebuttal" to a point being made, and in doing so clearly says that the NSA can get emails via upstream collections:
Dianne Feinstein Accidentally Confirms That NSA Tapped The Internet Backbone
from the but-of-course dept