Patches that could be added to cell stage

[50gens]

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.^[1]

1. Underground microorganisms (also called deep biosphere(1), dark biosphere(2)^[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

(4)Through her studies on the fluid found between the cracks in the crust, she says that in some areas the fluid contains about the same number of microbes as standard deep-sea water collected at ocean depths of 4,000 meters (2.5 miles): around 10,000 microbial cells per milliliter. In other regions, such as at the Juan de Fuca Ridge in the Pacific Ocean where Lever found his microbes, there are fewer cells, around 8,000 microbes per milliliter. And in other regions, such as in non-oxygenated fluid deep in hydrothermal vents, there can be around 10 times more.

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)

The empty spaces these microbes live in are called cracks(4)(1.6.1.3)(8) or fractures (6) for rocks and pore networks (7.1) for sediments. These gaps are filled with water (4)(8)(1.6.1.3) or air(6)

(7.1)the availability of void space often constrains microbial activity as cells require pore networks with spaces large enough to pass through

(8)As seawater entrains deep in the crust, it travels through cracks in the rock, some microfine and others as large as, or even larger, than spaghetti noodles.

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(1.6.1.3)

(1.6.1.1)At first the sediment has 50 to 60 percent porosity; as it is compressed, fluids are expelled to form cold seeps or gas hydrates

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.

(1.4.3)An increased pressure compresses lipids, making membranes less fluid. In most chemical reactions, the products occupy more volume than the reactants, so the reactions are inhibited by pressure.

(1.4.4)High temperatures stress organisms, increasing the rates of processes that damage important molecules such as DNA and amino acids. It also increases the energy requirements for repairing these molecules. However, cells can respond by changing the structure of these molecules to stabilize them.

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)

(5)(…)he believed that during the process of forming coal, the bacteria had dried up and entered suspended animation. “…The microorganisms found in coal are actually survivors, imprisoned in the coal at the time it was formed, from material which originally was probably very rich in microorganisms since it was peat-like in nature,” he wrote in the Journal of Bacteriology. (…) This dessicated condition we now call anhydrobiosis, and it is in such a state that organisms like water bears can withstand the vacuum of space and bombardment with radiation. Lipman’s coal (…) is at least 300 million years old.

But not all cells are in hibernation, the fact that they have active protein and DNA repair mechanisms indicate that they are living(3)

(1.6.1.1)In the top few meters, metabolic rates decline by 2 to 3 orders of magnitude, and throughout the sediment column cell numbers decline with depth

(5)The biomass turnover rates – the time in which it takes to replace the molecules in a cell – were measured on the order of hundreds to thousands of years. “We do not know whether the microbes of these subsurface environments reproduce at these slow rates of biomass turnover,” wrote Frederick Colwell and Steven D’Hondt in a review called Nature and Extent of the Deep Biosphere in 2013, “or live without dividing for millions to tens of millions of years.” (…) They were still actively, if extremely slowly, living. Their generation times ranged from months to over 100 years. But this estimate was likely low, the authors conceded. The generation time of E. coli in the lab: 15 to 20 minutes. (…) The amount of carbon they consume for maintenance and repair each year is just 2% of the cell’s own carbon content.

(1.4.5)In the subsurface, cells catabolize (break down molecules for energy or building materials) 10,000 to one million times slower than at the surface.(…) It was thought, at first, that most underground cells are dormant. However, some extra energy is required to come out of dormancy. This is not a good strategy in an environment where the energy sources are stable over millions of years but decreasing slowly. The available evidence suggests that most cells in the subsurface are active and viable. A low energy environment favors cells with minimal self-regulation, because there are no changes in the environment that they need to respond to. There could be low-energy specialists. However, there is unlikely to be strong evolutionary pressure for such organisms to evolve because of the low turnover and because the environment is a dead end.

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.

(7.4)Many of the organisms used in fermentative technology are common in subsurface environments, e.g., Bacillus, Clostridium, and Desulfovibrio species.

(11)As luck would have it, the team had found something more interesting than they ever hoped: cyanobacteria (sometimes called blue-green algae), which are found almost everywhere on Earth with at least a small amount of sunlight. But there was no sunlight.

(6)At first he thought it a mistake. He recalls fretting: “My Ph.D. is going nowhere; my adviser is going to kill me.” (…) Metagenomic analysis suggests that they are descendants of rock-dwelling lineages who make their living in tough environments, such as in the desert or within shadowy caves.

(11)“How can they survive?” The answer, it turns out, relates to hydrogen. (…) “This proposed mechanism relies on traits that are conserved across cyanobacterial lineages, and might thus reflect the lifestyle of the non-photosynthetic ancestor of cyanobacteria.”

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.

(10)Analysing enzyme activities, lipid biomarkers and gene expressions allowed the researchers to determine that some of the microbes rely on breaking down organic matter for sustenance. They’re likely feeding on scraps of organic molecules, such as fragments of amino acids and traces of fats, seeping in with water via cracks in the oceanic crust.

(1.6.1)In rock, chemicals are mainly carried through an aquifer system that cycles all of the ocean’s water every 200,000 years. In sediments below the top few centimeters, chemicals mainly spread by the much slower process of diffusion

(3)the organic carbon available to them represents about 1% of the carbon that is fixed by photosynthesizing organisms on the surface

This is more prominent in shallow waters

(1.6.1.1)Passive margins (continental shelves and slopes) are under relatively shallow water. Upwelling brings nutrient-rich water to the surface, stimulating abundant growth of phytoplankton, which then settles to the bottom (a phenomenon known as the biological pump).[68] Thus, there is a lot of organic material in the sediments. The population of microbes is orders of magnitude greater than in the abyssal plains

In some regions, oxygenated water reaches down to the cracks(4) if it wasn’t used up in the layers above (1.6.1.1), but most of the times there is no oxygen.

(1.4.1)The electron acceptor with the highest redox potential is oxygen. Produced by photosynthesis, it is transported to the ocean floor. There, it is quickly taken up if there is a lot of organic material, and may only be present in the top few centimeters. In organic-poor sediments it can be found at greater depths, even to the oceanic crust.

There are two alternatives when there isn’t oxygen. The first is anaerobic respiration.

(12.1) Once all of the oxygen is consumed, organisms begin using substrates like nitrate, manganese oxides, and iron oxides as the electron acceptor in anaerobic respiration. However, these substrates tend to be low in concentrations throughout sediments. Sulfate, on the other hand, is relatively high in abundance in comparison, so sulfate reduction is the main form of respiration after oxygen is consumed. Methanogenesis is the next form of metabolism after sulfate reduction. (…) sulfate reduction and methanogenesis could occur simultaneously in marine sediment

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.

(1.4.1)Some organisms break down organic compounds using fermentation and hydrolysis, making it possible for others to convert it back to carbon dioxide

(7.4)End-product inhibition of fermentation necessitates that the hydrogen production must be balanced by hydrogen removal. Therefore, hydrogen, as a product of fermentation, is normally a transient substance, being rapidly utilized as an electron donor.

Hydrogen seems to be important to subterranean microbes. It is both used and generated. Hydrogenase reaction is reversible (7.6)

(7.6)Hydrogenase gene abundances in subsurface environments, per megabase, are nearly an order of magnitude higher than for surface environments [57], highlighting the importance of hydrogen cycling in many subsurface microbial communities.

(7.6) Hydrogen-based metabolisms are thought to have been critical to life on early Earth; however, with the advent of oxygenic photosynthesis, hydrogen-based life became confined to specialized niches [26]. Hydrogen appears to be the main source of energy for autotrophs in many subsurface environments, especially those that have no, or a limited supply of carbon from photosynthesis

There are 5 ways of breaking up marine snow which generate hydrogen. ^[3]

And there are 9 ways of using that 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.

(1.4.1)Multiple species can combine fermentation with methanogenesis and iron oxidation with hydrogen consumption

There are also a few ways non biological ways hydrogen is absorbed/consumed by the environment^[4]. In Thrive, the biomass that can be supported under the ground can be calculated during planet generation.

(7.5)Abiotic hydrogen consumption typically occurs at high temperatures (well above those where microbial processes can operate), during magma cooling and in hydrothermal systems through the reduction of carbon dioxide to form methane and other hydrocarbons [44]. However, there are processes that can naturally occur within microbial temperature ranges, such as low-temperature methanation through the Sabatier reaction, or Fisher–Tropsch-type synthesis, e.g., in the Chimaera seep in Turkey [45], where the reactions occur at temperatures below 50 °C. In the presence of chromium mineral catalysts, this could convert significant amounts of hydrogen to methane over geological time scales [46]. Although not technically consumption of hydrogen, a recent study found that sorption of hydrogen to clay can be a significant hydrogen sink [47].

Life on Earth may have started under the ground.

(7.8)It has been suggested that submarine hydrothermal vents above serpentinites on early Earth provided suitable hydrogen gradients, as well as geochemical, temperature, and pH conditions, to be a candidate location for the origin of life on Earth [141]. In addition to hydrogen, this process will supply electron donors such as methane, formate, acetate, and ammonia, and essential elements such as transition metals and transition-metal sulfides [123]. Along with phosphate (dissolved in seawater), this process could supply all the elements essential for life

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.

(4)“The crust plays a significant role in influencing the chemical composition of the ocean and the atmosphere, ultimately influencing cycles on earth,” says Lever. Some of the compounds created by oceanic crust microbes from rock are water soluble, and will eventually enter the ocean. Sulfur, for example, is present in magma—but after the microbes use it for energy, it’s converted to sulfate. Then it dissolves and becomes an important nutrient in the ocean food chain.

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.

2. Microbes in the air (bioaerosols)

The microbes live inside water droplets suspended in air.

(14.2.2)Unlike other bioaerosols, bacteria are able to complete full reproductive cycles within the days or weeks that they survive in the atmosphere, making them a major component of the air biota ecosystem. These reproductive cycles support a currently unproven theory that bacteria bioaerosols form communities in an atmospheric ecosystem.[2] The survival of bacteria depends on water droplets from fog and clouds that provide bacteria with nutrients and protection from UV light

There aren’t a lot of cells in the air

(15.4) a global scale meta-analysis of bacterial abundance across biomes indicated ∼5 × 10^19 cells may occur globally in the atmospheric boundary layer, compared with ∼1.2 × 10^29 in oceans and 2.6 × 10^29 in soils globally

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?

@50gens

Adventurous dust - Have a raindrop or a snowflake form around you in cell or multicellular stage

3. 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?

(16.2)Recent experiments have found organisms that can survive both the acceleration and jerk involved in reaching escape velocity. (…)While very small, these non-zero results show that some lifeforms could survive the impact from a major impact event.

jerk: change of acceleration

(16.1)While concerns over the heat of ejected rocks and the possible sterilizing effects it would have on the microbial life attached, it has been theorized that for rocks even less than 2 kilograms such as ALH84001, internal parts may never reach temperatures greater than 40 °C.

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)

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1. also dry land, but I didn’t researched that ↩︎

2. not to be confused with shadow biosphere ↩︎

3. I didn’t understand why was nitrogen fixation was given under “hydrogen generating” reactions, it takes 8 hydrogen ions and results in a single hydrogen molecule ↩︎

4. no table was given for this ↩︎

[Topcode]

Wow, that’s a lot of cool stuff. But I feel like this could use some more detail on implementation.

[Evolfire (Gustovata)]

I like the idea of more patches

[50gens]

Here are suggestions on how they may be added.

subsurface

@50gens

cracks in the rock, some microfine and others as large as, or even larger, than spaghetti noodles

• The texture needs to be different.

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.

Air
There are two ways of adding it.

1. 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.
2. 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:

@50gens

what do you think about this achievement?

@50gens

Adventurous dust - Have a raindrop or a snowflake form around you in cell or multicellular stage

Space

• After meteor impacts, a pop up apears asking if the player wants to move to another planet.

[TristanMisja (DoubleU)]

That was a really well written post.

[CatSquared]

Here’s a few other ideas:

Gaping Trench

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.

Underwater Volcano

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.