What happens to Bacteria at a low pH?
pH affects the structure of all macromolecules that compose bacteria, and indeed all cells.

Here's a shortlist of examples:

Lipids

Lipids are hydrolyzed by extreme pH levels. They undergo chemical reactions and fall apart into constituent molecules, which may be toxic. The membrane is made of lipids; if it is disrupted, the cell ceases to exist.

Nucleic acids

At low pH, RNA and DNA hydrolyze - bonds are broken between individual bases (phosphodiester bonds) and nitrogen bases break off from the (deoxy)ribose groups. Structures and hydrogen bonding (necessary for DNA replication or transcription of genes) are impaired.

In alkaline conditions, DNA typically denatures but remains intact. Structures and hybrogen bonding are still strongly impaired though.

Protein

Low or high pH environments affect ionization of amino-acid functional group ionization. This affects hydrogen bonding in such a way as to denature the molecule, because it adopts very different conformations. This of course renders the protein or enzyme non-functional, and may cause it to aggregate or become cytotoxic. If any one of the hundreds of essential enzymes fails to function correctly, a bacterium will die.

Potentials across membranes

Changes in pH have drastic effects on proton concentrations both in and outside the bacterium. Respiration depends on a concentration gradient of protons. Low or high pH will make it difficult for cells to establish a potential (different in concentration across a membrane). This gradient must be upkept for a bacterium like E.coli to generate energy, and it's difficult if protons are being neutralized or are in sheer excess!

Any one of these is enough to have a bactericidal or bacteriostatic effect! This is also why cells that do live in slightly alkaline or acidic environments have to specialize, and they have narrow windows of pH that they can survive under, because they have to compensate so much to counteract the protonation or lack-thereof in their environments.