The current game includes all the layers of oceans, also beaches and glaciers. But three more can be added, which are underground, the atmosphere, and a place above the atmosphere.
Underground microorganisms (also called deep biosphere(1), dark biosphere(2) or intraterrestrials(1.1)
The biomass under the ground is 15% of total biomass of Earth(1.5). The percentage of microscopic life that resides here is even higher, but sources conflict on this matter, it is 70%(2)(3), 90%(1.5) or 95% divided between marine subsurface(%55) and terrestrial subsurface(39%)(1.2). One source says the microbes here contain between 15 and 23 billion tons of carbon, or 245 to 385 times the carbon mass of humans(2). The main takeaway is that it is a lot and not negligible.
The number of microbes per volume is comparable to the oceans
The genetic diversity is the same as the surface, but it decreases with depth (1.5). Life from all three of the domains (Archaea, Bacteria, and Eukarya) (1.5) and maybe viruses(1.4.5) exist here.
The deep biosphere starts a few meters below the seafloor, where the soils are not bioturbed by sea creatures. (1.1) The zone starts at a deeper altitude in land. Life was found as deep as of 5 km’s in continents and 10.5 km’s below the ocean surface(1.6)
A typical clay for example, has a porosity more than 50%(9.2), meaning it is more than 50% air (or water if it is wet). The sediments under the oceans are also like that, but as the depth increases, the sediment gets more compact and the space between mineral grains becomes less(220.127.116.11)
cold seep: a water at 60 °C/140°F denser than the water surrounding it, containing a lot of salt, hydrogen sulfide or hydrocarbons
gas hydrate: a solid formed by water and other molecules
The volume of the deep biosphere is double the volume of all the oceans combined.(1.6)(2). A single aquifer can contain up to 4% the water in the oceans.(4)
At the bottom of the oceans (3800m), the pressure reaches 38 megapascals, where the water boils at 400°C(1.4.3). The cells can survive pressures 26 times that(1.4.3), but the highest temperature a cell was recorded surviving was 122°C(1.4.4) and the theoretical limit is 150°C (1.4.4)
Those pressures and temperatures affect the cells in some ways.
The cells can be found here in two conditions, hibernation and extreme slow metabolism. If the cells simply ended up there and decided to hibernate until the conditions got better, the conditions will probably never get better (but seeing some cells extinct on the surface returning to surface in the game may be interesting)
But not all cells are in hibernation, the fact that they have active protein and DNA repair mechanisms indicate that they are living(3)
The cells that live in the subsurface are related to the ones that live in the surface. Life may have appeared deep down, and migrated upwards.
There are two types of ways microorganisms in deep biosphere make energy. The first is decomposing marine snow, same stuff that happens in the oceans but at a slower rate.
This is more prominent in shallow waters
In some regions, oxygenated water reaches down to the cracks(4) if it wasn’t used up in the layers above (18.104.22.168), but most of the times there is no oxygen.
There are two alternatives when there isn’t oxygen. The first is anaerobic respiration.
80% of methane is generated by methanogenesis(1.4.1) and 90% of the methane is oxidised by microbes (when it diffuses to a place that has enough oxygen) before it reaches the surface(1.4.1). The second alternative to oxygen is fermentation.
Hydrogen seems to be important to subterranean microbes. It is both used and generated. Hydrogenase reaction is reversible (7.6)
There are 5 ways of breaking up marine snow which generate hydrogen. 
The same species that creates the hydrogen can use it, or one species can use the hydrogen another species produces, which is called a syntrophic relationship (7.6). In case of acetate production, a species creates acetate and hydrogen which requires energy, and another species takes the hydrogen, and gives back some of the energy it generates from that hydrogen.(7.6)
The second type of energy generation is chemosynthesis. The environments that don’t depend on photosynthesis for the source of carbon or hydrogen are called subsurface lithoautotrophic microbial ecosystems (SLiMEs)(7.6). The species Candidatus Desulforudis audaxviator (has no connections to the surface)(1.7) uses the sulfate as an energy source and that sulfate is formed due to radiation(13.2). There are 5 non biological ways hydrogen is generated.
One study says that the hydrogen generated by radioactive materials in the crust breaking the water into hydrogen and oxygen is enough to sustain 10% of the currently observed subsurface microbe population.(7.7) Microbes can use the hydrogen generated bioticaly and abioticaly at the same time. Cells can do more than one type of chemosynthesis.
There are also a few ways non biological ways hydrogen is absorbed/consumed by the environment. In Thrive, the biomass that can be supported under the ground can be calculated during planet generation.
Life on Earth may have started under the ground.
The other rocky bodies in our solar system that may have or had life are Mars (its crust had the same amount of hydrogen as Earth during the heavy bombardment period, and it had suitable temperatures for life), Titan and Enceladus (they have hydrogen)(7.8)
It may seem like the subterranean life merely feeds from the surface, or does its own thing, but it can also influence the surface.
How may a subsurface patch be added to Thrive? There can be a porous rock texture, the movement of cells being restricted like in Pacman.
Fermentation and anaerobic respiration can be added, making less ATP than normal respiration. There is already chemosynthesis and rusticyanin. Methane and hydrogen can be added as compounds. An organelle version of hydrogenase can be created with endosymbiosis between two syntrophic species.
No large creatures can evolve later in life, but this place has implications for the beginning of life. The players may start in the underground patch if “subsurface abiogenesis” is chosen as the origin of life.
Microbes in the air (bioaerosols)
The microbes live inside water droplets suspended in air.
There aren’t a lot of cells in the air
So how may this be added to Thrive?
It is above the other patches. If the microscopic creature of the player adapts to surviving in high altitudes it can move between the patches in the surface. If the oceans boil (like in Venus), the atmosphere becomes the only playable patch remaining. After that point, it becomes the sky whales discussion
Hey developers, what do you think about this achievement?
Microbes in space (panspermia)
A meteor can hit a planet, ejecting its rocks into space, and rocks from a planet can hit another planet, like in the case of Allan Hills 84001,which was a Martian meteorite that hit Earth, but it didn’t have Martian microbes on it. But if Mars was habitable, could a rock from Earth (which we know has microbes) hit Mars, and seed it with life?
jerk: change of acceleration
How may space environments be added to cell stage? Since cells always hibernate(17), there is no point to playing on an asteroid. But there may be pop up that says “A rock from this planet hit another, which was carrying your species. Do you want to switch to playing there?” And clicking yes would move the player to a surface patch of a different planet in the same solar system.
If the player plays in a moon like Enceladus, the cells can move to the other moons of the same gas giant as they are ejected with the plumes.
There is also radiopanspermia(cells in atmosphere going to space), but without the protection of a layer of rock or the magnetic field of a gas giant, radiation becomes an issue(18)
If the cracks are like two 2d planes parallel to each other, the cells situated between them could be shown having the same 2d freedom of movement as it exists in the game right now. The background would have the same color as the rock that is just behind. But showing the cracks from that angle has problems with indicating the places where it isn’t wide enough for the cell to move, or where three junctions meet.
Or there can be a sideways view.
This can show both the cracks and the pores in the sedimentary rock. It can work in different scales, as the crack size increases the cell finds itself in a place similar to the oceans, as the gaps become smaller, the cell can try to fit there, more fluid membranes able to fit smaller gaps. But this has one disadvantage. If the cell moves through a small crack in a cristaline rock, the game would show it moving in a 1 dimensional route(if a predatory cell is ahead, your only option is going back), when in reality, it is 2d.
Perhaps a combination of these could be used for crystaline rocks. If the distance becomes too small, or 3 junctions meet, you switch to sideways view. If another cell is on the path you want to take, you switch to front view.
The metabolisms are slower, maybe the time between the evolving sessions can be increased or the dna points may be decreased
Two new substances can be added, gas hydrates are just aestethic. Cold seeps can have high salt(not in the game yet) or hydrogen sulfide content.
The cell membrane is made less fluid by default.
There is iron, glucose and hydrogen sulfide. Oxygen usually doesn’t exist, is oxygen in the game?
Two new compounds may be added, hydrogen and methane. They can be digested with hydrogenase and methanase.
After you consume glucose, you may generate hydrogen or methane. Things to discuss if chosing how you break down glucose(fermentation, methanogenesis) is added to the game.
Glucose becomes less as you get down the surface, but hydrogen has a constant source (radiolysis). Chemosynthesis is the same.
A cell generating hydrogen can be followed by a cell consuming hydrogen, but syntrophy is trickier. It would require sharing compounds with another cell, and chosing to break down glucose into acetite. Syntrophy can maybe result in endosymbiosis and an organelle for hydrogenase, endosymbiosis not in the game yet.
If the enviroment removes hydrogen, then the number of cells that consume hydrogen in a given patch becomes less, this would be calculated by the game.
The starting location may be in subsurface
Size is a constraint, multicellular life can’t advance.
There are two ways of adding it.
The cells in the air aren’t simulated. But if you are in the surface, you can go to other patches not directly adjacent to your patch by flying.
The cells are simulated, and there is an air patch. The cells live inside water droplets suspended in air. The map the player plays in may be quite small. Conversation starter:
After meteor impacts, a pop up apears asking if the player wants to move to another planet.
It has more marine snow than other areas, but more pressure and less oxygen, making basic cell processes less effective and bio-luminescence extra effective. It spawns diagonally down from the standard Sea Floor patch. It has a 10% chance to spawn below another Gaping Trench patch. If there is not a Gaping Trench patch below it, there will always be a Deep Sea Floor or a Deep Sea Hydrothermal Vents patch below it. Gaping Trench patches also have a 1% chance of spawning under or next to a Cave Patch or Deep Sea Cave Patch.
Deep Sea Floor and Deep Sea Floor With Hydrothermal Vents
Has even more marine snow and pressure and even less oxygen than the Gaping Trench, but also more Ammonia, Phosphate, and Hydrogen Sulfide. Nothing can spawn directly below it, or next to it. It can only spawn directly below Gaping Trench patches. Bio-luminescence is even more effective. The Hydrothermal Vents variant is warmer and has more resources.
Like Hydrothermal Vents, but near the surface, with 50% light. Every 100 Million years, it has a 10% chance to erupt, increasing all resources, along with the temperature and hostility.
Volcanic Shoreline/Volcanic Island
If an Underwater Volcano patch erupts next to certain patches, they become Volcanic Shorelines, Volcanic Islands, and Volcanic Estuarys.