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I was kind of always against an opinion that bacteria are not worth being checked. Yeah, they require big distances for variety, but quite a lot of them are very well visible even from hundreds of meters in a ship hovering the planet. Yes, they're cheap, but it's still 5m including discovery bonus and if you fly those 1000 (?) m between the colonies in your ship, they're rly fast to scan as they seem to meet relatively often (in the plains at least). Not always though. Sometimes it's dark and sometimes bacteria color does not differ them much from the ground. I've checked a couple of brown dwarfs systems recently and was unlucky enough to stack all the bonuses i can imagine: dark icy bodies (+ice itself is dark color) with bacteria colors nearly matching ground colors. One is pictured above and is quite invisible from any reasonable disctance.
Obviously looking from your ship cabin is useless in such cases. What helped a little is howering at slow speed (like 50 m/s) at an altitude of 20-30 m and trying to spot life with external camera. It worked if it's not too dark. If too dark (small star + far planet) what also worked sometimes is to find a real noon spot on the ground, on icy bodies that place will sometimes have some kind of glow, which i usually don't like much as you can see stuff worse due to it - but it does help in the real darkness. I still scanned all of the little beasts, even if it did ended in a couple of times with just mad jumping and sending scan pulses around just in case there's a bacteria nearby. But maybe sometimes some stuff can indeed be skipped. Was nearly as fun as requesting those carrier jumps on a Sat evening (about 45 mins now), but still, i'm heading for the brighter places.
On a note, testing DBS as a carrier based explorer (scout?), and it's a success! Taking off from a planet to land in another area is fast, jump is still 25 ly, i even kept docking computer (2t fuel tank won't change much) and i'm not sure if i want to remove SRV hangar. Tested auto landing on a planet, nah, it's way too slow. You either hover the surface at low altitude, either fly like an helicopter (e. g. in the mountains), up and down at variable speeds, sometimes hitting the ground a bit (got a little above 100 MJ shields - they near 50% after a couple of hits), and you don't land, you just throw the thing at the ground hoping no big stones are below and if they are, you fly 20 m and throw again. Also speedy = you can fly fast enough even with deployed landing gear saving those seconds deployment takes.