Collecting flora and fauna isn't important to finishing the game, but it's an activity that'll keep you busy for a while.

The Atlas Discoveries section of your Collections database will tell you what you've already discovered. It doesn't tell you what you haven't discovered, though, because you haven't yet discovered it!

Fauna

Each planet has 3 large land fauna species you can scan. At most difficulty levels you'll need to scan 3 individuals of each species, but at the Easy level you can usually get by with scanning just one of each species.

A couple of planets also have a subsurface fauna species in addition to the standard 3 species. When one of these spawns you'll see a lightning bolt, and when you're close to one you'll see a yellow paw print on your minimap, You can't scan these critters, but you'll get credit for them if you get close enough.

The fauna are unusual in that when you lose sight of them, they tend to disappear. They're not a permanent part of the environment like most things are.

Usually the biggest problem is finding the critters. You'll find some while doing your other activities, so that's helpful. Otherwise, you need to check out various ecosystems to try to find them. Some fauna prefer rivers, some prefer forests, etc.

Something that can help is to pick up an analyzer at an observatory (you don't need to be on a scanning mission from the observatory to use it). Not all observatories will have an analyzer, in part because not all observatories are reasonably close to where the fauna hang out. The analyzer is too heavy to fly with, so you'll want to stay reasonably close to the observatory.

When you've got an analyzer in tow, your minimap will show fairly distant fauna as shimmering white squares in the outer ring. As you get closer, the square turns into a white dot. When you're really close, you'll see a white pawprint in the inner ring. Note that the analyzer will indicate all kinds of fauna, not just the kind the analyzer is built for. If you do locate one of the analyzer's preferred species, "collecting data" with the analyzer also performs the usual scan into the Equinox DNA database, so you don't need to do that separately.

Some of the critters may take considerable exception to your trying to scan them. In my experience, the easiest way to deal with those species is to scan them immediately after plucking Legion infection off of them. Apparently the animal is still recovering and not inclined to make a fuss. Because of this, I'll often do my fauna scanning before clearing the extractors and their clouds (especially where I know the fauna can be hostile).

That brings up another way to locate fauna. Occasionally an observatory will ask you to remove Legion infection from a land animal. In that case, they'll tell you what kind of animal and exactly where to find it. You can go there, pluck the infection, and scan the animal. Once in a while, there also will be other critters nearby.

Biological samples

Most planets have 5 different biological samples to locate, but Haven and Sonatus only have 4. Each planet has two rare sample types.

Common samples will appear in clusters within their ecological niche. Sometimes you'll find 3 together, sometimes as many as 20. Chances are good that you'll come across all of them in your normal travels on the planet, so just keep an eye out and snag one sample of each new type you find. Common samples are stored in your hold, in the "organics" category. I try not to completely fill the organics section of my hold if I haven't collected all of the common sample types on the current planet -- it'd be disappointing if I found a new type but couldn't grab a sample because my hold was full.

On the planets with subsurface fauna, one of the sample types will be a sample from that fauna. If you can stay close enough to one of those animals for long enough, you can grab a small piece of it. Good luck holding onto your souvenir, but fortunately you don't need to hold onto it to get credit for the discovery. The sample will be held by your tractor beam, not collected in your hold, and is too heavy to fly with.

Rare samples are carried by your tractor beam, not in the hold, and are too heavy to fly with. One rare type is occasionally requested by observatories, and the other rare type is occasionally requested by workshops.

The rare samples requested by observatories are very delicate. I know you hear a lot of "be careful with [whatever]" from the outposts, but in the case of the rare samples requested by observatories, they mean it. Tug a little too hard when dislodging it, or get into combat while carrying it, or whatever, and the sample will perish before you can deliver it. Fortunately, you don't need to actually deliver the sample to get it credited as being discovered.

Because of the delicacy of those sample types, only observatories located fairly near a suitable ecosystem will offer the mission to retrieve that sample type. You may need to try a number of observatories, and go through many mission requests at each one, before you get the mission you need. When you do get the mission, you'll be shown exactly what you're looking for and where to find it. It's possible you'll stumble across one on your own, but many of those rare species tend to be located in places you're not likely to have visited.

The rare samples requested by workshops are very hardy. There's no need to be careful with those. Here too, you'll be told what you need and where to find it, plus you'll be told how to get it. You might flinch at the instructions for obtaining the sample, but there's no alternative. The chances of stumbling across one of those samples is extremely low, so be sure to ask the workshops for missions. Occasionally a workshop might not have such a mission; I suspect that occurs when there are multiple workshops on a planet and another workshop is closer to the appropriate ecological niche.

Finally, I'll note that some of the planets have a vexing plant species in addition to the standard ones. These will be added to the Atlas Discoveries in your Collections database as you encounter them.