Food poisoned water being cleaned by either pump or pipe

That's actually a somewhat low amount of food poisoning. Did some rough math, you're only going to have about 1300 germs in each 5kg unit coming out from the sieve. And food poisoning starts dying off at 40C. The germs may just be "dying off", due to low population, while in transit to your clean water storage.

Not sure what you are trying to point out in the screenshot, if you are talking about "zero surface germs" on the "status" page, that's normal when you are on the pipe overlay. Maybe a bug, but the germs are there and the germs tab is for the pipe, not the contents. Neither will show germs, but they are there.

The pipe/germ overlay is weird. You can't see germs directly on the pipe overlay because it only sees the pipe, and it just shows the mass of it's contents and what type.

You can't see the x-ray vision or germs (no highlights) in the germs overlay (besides entry points of pipes are highlighted on the exterior). You have to open the germ overlay and trace the pipe blindly using the tooltip. It's highly annoying, especially if you have air in the pipes or pipes that cross a lot.

Clean water kills germs, especially at that temp. It doesn't spread much either, in my experience. It kinda just stays where it enters (a really deep well would effectively be clean even with germs at the top). Still, better to do it proper for the long term, or just feed it to your pincha peppernut surrounded in clorine.

As I recall, pipes have never displayed the germ count, which could be considered a bug. Because of that the screenshots tells very little.

The water sieve uses an ElementConverter, which indeed transfers germs, or at least has code mentioning the transfer of germs (didn't explicitly test this right now).

The dripping clean water doesn't actually hit the surface of the water. It hits the bottom. Since you add so little germs each second and it's killed in water, it might have all died by the time it reach the surface. If you check the cell at the bottom under the water intake I suspect it's not completely germ free.

9 hours ago, Nightinggale said:

The dripping clean water doesn't actually hit the surface of the water. It hits the bottom. Since you add so little germs each second and it's killed in water, it might have all died by the time it reach the surface. If you check the cell at the bottom under the water intake I suspect it's not completely germ free.

Maybe I am remembering it wrong, or they have changed it, but I remember my accidental germ contamination on my first game being isolated to the top of the tank. Top or bottom, I guess it doesn't matter. Just have your pump on the opposite side and it's probably fine for a while.

I suspect the same. Take a look at the germs overlay. Probably a speck or two of germs.

31 minutes ago, tommytom2k2 said:

Maybe I am remembering it wrong, or they have changed it, but I remember my accidental germ contamination on my first game being isolated to the top of the tank.

"Normal" liquids like toilet accidents will hit the surface. The problem with such liquids is that they take up the cells meaning they push gases away. The pipe output will not form cells of liquids, but rather drops. They will not push gases away. Instead they fall until they hit the floor. This means they can fall through water and hit the bottom.

This inconsistency is actually rather important because some advanced setups like oil boilers depend on this working the way it works. Also it's a good thing the drops doesn't push gases away because that would quickly cause havoc, not to mention being exploitable for overpowered gas pumps.