Microbial Musings Entry #1 : "Could Methanogens Replace Mitochondria?"

     

TLDR; Here, we'll be looking into whether methanogens could give rise to complex life on other planets. We also look into how this unfamiliar form of life may develop, leading to some interesting results. 

     Recently, I was browsing through the official speculative evolution discord server and came across an interesting question. In it, Silly_Milly asks whether or not methanogensis (the coupling of hydrogen / acetate / methyl oxidation with the reduction of CO2) could provide enough energy to support "eukaryote like complexity". In other words, would methanogenesis allow microbes to achieve larger genome sizes? 

     However, in order to answer their question, we first have to ask ourselves why eukaryotes are able to support large genome sizes in the first place. As many of you might know, the answer is mitochondria. 

     Roughly 2.1 billion years ago, the common ancestor of mitochondria had forged an mutualistic arrangement with an archaeal host. This provided them with shelter from the elements and from competition. 

     Since they no longer had to invest energy towards supporting an active, free-living lifestyle, mitochondria have undergone a dramatic reduction in genome size and have greatly decreased their rate of ATP consumption. However, their overall rate of ATP production had remained the same, providing them with far more energy then they knew what to do with. 

     Instead of stockpiling this excess ATP for themselves, populations of mitochondria work together, exporting it and donating it to their hosts. This increase in stored energy would have allowed early eukaryotes to develop more costly adaptations that would serve to increase the reproductive fitness of both the host and the endosymbionts. In addition, mitochondrial populations can be scaled up in order to keep up with the energetic demands placed upon them by their host, enabling eukaryotes to support genomes of progressively greater size and relative complexity. 

     So to simplify, the reason eukaryotes are able to harbor large genomes has more to do with how mitochondria allow them to efficiently scale up energy production, rather than something that is unique to aerobic respiration.

     Therefore, if we were to imagine a hypothetical, eukaryote-like cell with methanogens in place of our oxygen reducing / lactic acid fermenting mitochondria, they would still be able to function in a similar manner to their real-life counterparts. However, since methanogenesis produces ATP yields that are far lower than that aerobic respiration (0.5-2 moles of ATP per mole of substrate Vs. the 30-32 moles of ATP generated from the aerobic consumption of one mole of pyruvate), a greater number of methanogens would be required to produce the same amount of ATP. As a result, "methano-eukaryotes" would have to obtain far more resources and chemical energy from their environment than true-eukaryotes would in order to achieve similar energy budgets. 

     With that said, plenty of eukaryotic cells on the modern day Earth support populations of mitochondria numbering in the thousands, so its well within the realm of possibility that our methano-eukaryote could harbor large populations of endosymbionts as well. However, it's also important to note that the caloric and nutritive demands mitochondria place upon their hosts had once played an important role in stalling their evolutionary development of eukaryotes throughout much of the Proterozoic, back when essential biogenic elements and oxygen were more difficult to come by. Because of this, methano-eukaryotes on similarly nutrient-starved exoplanets would have an even greater challenge diversifying and developing costly adaptations.

     Additionally, the presence of oxygenic photosynthesis on alien planets will largely restrict methanogens to anoxic sediments and other environments that greatly limit the availability of oxygen, such as geothermal springs. However, in a recent study published in 2011, researchers found that methanogens in the McMurdo Dry River Valley can survive in oxygenated soils by upregulating the detoxification of oxygen and ROS (reactive oxygen species). This uses up a significant portion of their meager energy budget, but seems to enable them to slowly metabolize, grow, and reproduce within aerobic environments. 

*NOTE : Due to our hypothetical microbe's ability to scale up respiration, they would have more than enough energy to invest in upregulating these processes. Because of this, they might still be able to support relatively fast rates of cell division under oxygenated conditions. Additionally, there's also the chance that the host might start out as a facultative aerobe, much like how mitochondria did. This would allow them to potentially shield their endosymbionts from oxygen, either through the consumption of oxygen during respiration or the use of their own detoxification pathways.  

     Another problem we have to address involves the substrates required for methanogenesis. In aerobic environments, hydrogen gas is in limited supply and is often restricted to the presence of trace gases. While organisms use radiolytic hydrogen in the atmosphere for growth, the energy this provides is incredibly meager and only serves to supplement the cell's ATP requirements. As a result, I wouldn't expect a eukaryote-analogue to thrive primarily off of hydrogen in an aerobic habitat. Instead, acetate and methylated compounds might serve as better donors, since they can be easily sourced from detritus.

     Alternatively, the host cell could have originally started out with the ability to produce its own acetate from more abundant carbon sources in the environment, thereby providing their endosymbionts with a readily available source of fuel. In one scenario, the host might be capable of acetic fermentation. During which, sugars are broken down into pyruvate which is later decarboxylated and converted into acetyl CoA. Afterwards, the acetyl CoA can be used to produce Acetyl phosphate which is later used to phosphorylate an ADP molecule, thereby producing ATP and acetate. 

     This process is incredibly ancient and may go as far back as LUCA, so it's likely to develop readily throughout the universe. Additionally, acetic acid bacteria are incredibly successful and already form a ton of close associations with methanogens, so there is precedent for an endosymbiotic merger developing between the two.

(Above) Here's a quick doodle depicting an endosymbiotic relationship between a facultative aerobe / acetate fermenter and an acetolactic methanogen. The end result of this partnership is 2 net ATP from glycolysis (the conversion of sugars to pyruvate), 1 ATP from the breakdown of acetyl phosphate, and an additional 2 ATP for every mol of acetate used up in methanogenesis. 

     In short, a methanogen could serve as the basis of energy production for a eukaryote-like organism, but its evolutionary avenues would be somewhat impeded upon by nutritive requirements, substrate availability, and low energy conversion efficiency during respiration. However, a relationship between an acetate fermenter and a methanogen could resolve the problem of acquiring substrates.

Sidenote : In researching this topic, I realized that hydrogenosomes (highly-derived mitochondria that allow eukaryotes to survive in anaerobic habitats) produce similar amounts of ATP to methanogens; averaging at around 1 mol of ATP per every mol of substrate. As a result, these organisms might provide us with a window into how methano-eukaryotes might develop. However, its important to keep in mind that these organisms are restricted primarily to anoxic sediments, which would greatly curb their evolutionary avenues (animal and plant analogues aren't likely to develop under meters of marine sediment or within the guts of termites). 

(Above) A random assortment of anaerobic protists 

that are reliant upon hydrogenosomes for ATP.

DISCLAIMER : feel free to use this idea in your own work, but be sure to provide credit. Additionally, I should note that this might make its way into a future project of mine as well. 

Citations :

  

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7289024/#:~:text=Depending%20on%20the%20substrates%2C%20methanogens,such%20that%20the%20overall%20Gibbs'

 

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0020453

https://www.sciencedirect.com/topics/medicine-and-dentistry/hydrogenosome#:~:text=1%20ATP%20is%20generated%20per,Succ.%2C%20succinate%3B%20Succ.

A video of some anaerobic ciliates collected from the digestive tracts of termites : https://www.youtube.com/watch?v=dLAdNOQCiik

Microcosmos Updates Entry #3 : Microbial Partnerships in Depositional Habitats

     TLDR; While taking some time to flesh out the interactions between microbes in depositional environments further inland, I've developed some interesting ecological interactions. These might end up being applicable to both lake bed environments rich in organics, as well as the marine habitats I had discussed in the previous entry.

Now that I've finished fleshing out the broader ecological interactions in marine depositional habitats, I've had a moment to think. What sorts of behavioral and structural adaptations would these organisms have? Would they be distinct from microbes on Earth inhabiting similar environments, or would they experience extreme convergent evolution? 

     In order to answer this question, it's important to note that prokaryotes face severe energetic constraints due to their inability to effectively scale up respiration. Since there is an upper limit to how much energy these organisms could obtain, there are only so many structural modifications that they can invest in before maxing out their energetic carrying capacity.  

     This limited evolutionary flexibility often results in prokaryotes developing the same morphotypes over and over again, selecting for those that fall within their budget and provide clear ecological benefits (bacilli, cocci, spirilla, vibrio, etc.) Because of this, it's likely that our prokaryote analogues will be "pigeon-holed" into developing the same basic cell shapes when faced with similar environmental pressures. However, this isn't to say that there isn't room for contingency. 

     From time and time, we find cases in which structures and behaviors have arisen within a single prokaryotic lineage, only to have never reemerged again (and with no discernable reason). A good example of this are cannulae; hollow, proteinaceous appendages found in the genus Pyrodictium. These structures are incredibly durable, flexible, and heat-resistant. 

     Additionally, they permanently connect cells to their progeny, providing a network through which chemical signals and public goods could be exchanged, all without giving unrelated populations a competitive edge (This remains a speculative behavior for now, but there is a precedent for this idea, considering that cannulae are anchored directly to the periplasmic space.)

     Given the role cannulae play in fortifying biofilms and (might) have in shuttling nutrients, it would seem that many organisms would benefit from developing structures with similar properties. However, as of the time this has been posted, no such instance of convergent evolution has ever been observed. 

     The same also goes for hami; tiny, grappling-hook like appendages that are commonly found amongst some groups of archaea. Despite being incredibly useful in allowing biofilms to resist strong currents, they have never been recapitulated in bacteria (At least, as far as we're aware of.)

(Left) In this electron micrograph, cannulae (yellow) can be seen emerging from the periplasm (purple) of the hyperthermophilic archaeon Pyrodictium. (Right) Some images of hami taken with the aid of electron cryotomography.

     As a result, we can infer that our alien microbes will exhibit many of the same cell morphologies and physiological adaptations as their terrestrial counterparts, but will also have unique structural and behavioral traits scattered throughout. With that said, I've been working on developing a few adaptations that would explore this theme of limited contingency. 

     However, before we jump in, I should offer a bit of a disclaimer. Trying to predict new behaviors and morphological adaptations for fictional microbes is a deceptively challenging process. Due to the strong pressures placed upon prokaryotes to make use of untapped resources and ecological associations within biofilms, there is a pretty high likely hood that whatever you come up already exists. It's also important to note that the absence of evidence is not the same proof of absence. In other words, just because you don't observe something you predicted, that doesn't mean it's not there.

     The techniques used to study "microbial dark matter" and to model microbial ecology in the laboratory are still in their infancy. As a result, we're constantly learning new things all the time, even about organisms in well-studied environments.   

     Okay, with that out of the way, let's explore some speculative adaptations and ecological associations. In keeping with the theme of marine depositional environments, I'll be focusing on anoxic sediments in waters that lack euxinia. 

     As covered in the previous post, many of the microbes in these habitats have to navigate the difficult task of pairing the oxidation of sulfide to the reduction of nitrate. This means scaling several millimeters or centimeters of sediment in order to acquire both. 

     The most common way in which this is preformed on Earth and Leeuwenhoek is through physically migrating from one end of the redox gradient to the other. In doing so, cells collect a bit of sulfide and then oxidize it for energy upon reaching a source of nitrate. In many ways, this isn't too dissimilar from how whales will hunt for krill in deeper waters, before occasionally resurfacing to respire. However, much like whales filling up their lungs with air, many filamentous microorganisms are able to take a "gulp" of nitrate and store it within vacuoles for later use. This enables them to continue carrying out respiration in sulfidic sediments and to stockpile nitrate in the event the competition renders it difficult to come by. 

     As a result, organisms like Thioploca and Beggiatoa essentially operate as "little nitrate shuttles", gathering nitrate from the surface and bringing it down with them into sediments where electron acceptors are difficult to find. This offers smaller prokaryotes that are incapable of stockpiling nitrate the incentive to steal it through endobiosis (the act of living within another organism). 

     By boring into the host and adhering to the surface of the gas vacuole, the endobionts would be able to gain access to this highly sought after electron acceptor. Additionally, endobionts might start off as parasitic and later develop mutualistic endosymbiosis with their hosts. By supplying some sort of public good (such as the synthesis of amino acids), they could increase their hosts chances of survival and thereby increase their own reproductive fitness.

*NOTE : Of all of the speculative adaptations / associations listed here, this is admittedly the most unlikely to develop. However, non-motile sulfur oxidizers belonging to the genus Thiomargarita have been found to contain endobionts and it has been suggested that they might be there to harvest nitrate. However, little has been determined about the precise nature of this relationship, so it's still unclear as to whether or not they are after electron acceptors. 

     Alternatively, giant sulfide oxidizers could also serve as modes of transport for epibionts (organisms attached to the surface of a larger host, known as a "basibiont"), much like a whale transporting marine lice and barnacles. In so doing, they could carry them back and fourth, from the bottom of the redox gradient to the top. This in turn would supply them with the high energy sulfide and nitrate required to speed up their metabolism. In exchange, the epibionts (much like the endobionts mentioned earlier) may offer their host some sort of public good in order to increase their combined reproductive fitness. 

*NOTE : Some gliding filamentous prokaryotes seem to support populations of epibionts. With that said, there is at least some precedent for gliding sulfide oxidizers partnering up with smaller organisms and offering them transportation. 

     Lastly, filamentous sulfide oxidizers may produce chemical signals that attract diverse, free-swimming microbes which supply them with waste electrons. In so doing, the swarming cells can reap the beneficial effects of nitrate reduction without having to spend energy on traveling long distances. Meanwhile, the host gets to supplement its diet with electrons obtained from a wide variety of substrates. 

*NOTE : As mentioned in the previous entry, this process is widely observed occurring between cable bacteria and a host of free-swimming prokaryotes. Additionally, interspecies electron transfer is ubiquitous across both prokaryotic domains and has evolved several times, providing further support for this idea. 

A.) A pair of filamentous sulfide-oxidizers that have been colonized by a population of endobionts (The pink blob represents a nitrate vacuole and the smaller objects attached to it are the endobionts.) B.) A collection of sulfide oxidizers, sporting a number of epibionts. C.) An "electrotrophic" sulfide oxidizer surrounded by a diverse assortment of free-swimming organisms. 

*NOTE : This sketch won't make its way into the book. The quality of the artwork will be far better in the finished version.  

Citations :

https://schaechter.asmblog.org/schaechter/2008/02/archaeal-macaro.html

https://schaechter.asmblog.org/schaechter/2015/09/pictures-considered-29-archaeal-ninjas.html

https://experts.umn.edu/en/datasets/giant-sulfur-bacteria-host-intracellular-endobionts

Video of a filamentous bacterium with epibionts : https://www.youtube.com/watch?v=pBZk7Fgx-aw&list=PLGbE8ME5yo4AKJDlQwGOOBxQpWrTJSWd2&index=28

Microcosmos Updates Entry #2 : Deep Sea Depositional Environments

     TLDR; In the previous entry, we introduced some of the ecosystems present on Leeuwenhoek and added a few more to our list. These new ecosystems would begin as depositional environments. In which, organic matter from more productive habitats would accumulate in waters with minimal access to sunlight, giving rise to vast communities of decomposers and chemoautotrophs (those that use chemical energy to fix inorganic carbon and construct biomolecules). Here, we'll be examining how these ecosystems might function, starting with marine depositional environments : 

     Along coastlines, organics generated within photosynthetic mats would be carried upwards into the water column by passing tides. Once shuttled into deeper waters, much of this organic matter would begin to drift downward, sedimenting on the ocean floor. 

     Since Leeuwenhoek is a "microbial planet", these environments would lack bioturbation (sediment-mixing) from burrowing animals, allowing organics to pile up into massive debris fields. In some cases, this layer of detritus could grow to be several meters thick, providing a vast habitat from microorganisms. 

*Note : Interestingly, as more organic material is deposited, increased pressures and temperatures deep within the debris field will eventually yield the production of petroleum and coal.

     During early colonization, the organic matter would attract aerobic scavengers, which would end up depleting the available oxygen in the sediment, preventing communities of microorganisms further down from acquiring it. This may also use up the available oxygen in the overlying water as well, leading to widespread anoxia. However, due to tides, storms, and winds at the surface churning the water and providing aeration, this condition will likely be restricted to the lowermost depths and is unlikely to penetrate into the photic zone above.

     In this dark, nutrient-rich habitat, organisms would have to get clever, utilizing other electron acceptors in place of oxygen. These could include nitrate, nitrite, elemental sulfur, sulfate, iron, manganese, carbon dioxide, and a host of trace metals (vanadium, molybdenum, cobalt, chromium, palladium, uranium, arsenic, mercury, etc.). 

     Most of these electron acceptors would be sparse and difficult to come by. As a result, organisms would be forced to fiercely compete for them or to rely more heavily upon less efficient forms of energy production, such as various modes of fermentation. 

     However, in competing for resources, microbes would naturally begin to outcompete those with less energetic systems of slower respiration, forcing them to flee into environments deeper within the sediment. Over time, the addition of progressively more efficient forms of respiration creates a stratified ecosystem in which layers nearest to the surface participate in more efficient forms of energy production and support faster rates of division relative to those at the bottom (This form of ecological stratification is commonly observed on Earth and will likely arise elsewhere as a natural consequence of thermodynamics.) 

*Note : Once stratification occurs, organisms will often form beneficial relationships in which resources and ecological services are exchanged by members of neighboring layers. For instance, methanotrophs (methane-consuming archaea) living alongside methanogens will often use nanowires to exchange electrons with sulfate reducers in order to acquire greater energy yields.

(Above) an image of a "redox ladder" that would be expected to emerge within Leeuwenhoek's marine depositional environments. This is an oversimplified version that leaves out some of the trace metals I mentioned prior. However, this serves more so as a general outline of which groups of microbes are the most dominant within each layer.  

     Returning back to the seabed, the sulfide produced within the sulfidic layer would also cause the debris fields to turn putrid, releasing an odor similar to rotten eggs which would bubble up to the surface. Meanwhile, the hydrogen sulfide would readily react with ferric iron in the sediment to generate pyrite, mackinawite, and other iron-sulfur minerals, causing the substrate to turn pitch black in color. 

(Above) Here we have an image showing the bottom of the black sea. Within this depositional environment, algae residing within oxygenated waters die during the winter and rain down into the anoxic zone, leaving behind glass shells. Collectively referred to as "Siliceous Ooze", this material forms a fine, cream-color crust the overlies the black sediment beneath. In contrast, life on Leeuwenhoek has never evolved the capacity to use silica in this way. As a result, the global ocean contains concentrations of dissolved silica that are orders of magnitude greater than what we observe within Earth's oceans. During winter, this silicic acid experiences decreased solubility and precipitates onto the seafloor, adhering to clay particles and organics. As a result, our depositional habitats on Leeuwenhoek would have a similar coating of minerals. Additionally, if you were to take a cross section of the sediment beneath, you would see many thin, alternating bands of white silica and black, organic rich sediment. These mark the passage of time in yearly intervals, much like the rings of a tree. 

     During the late stages of colonization, sulfide would begin to accumulate in the overlying water column, turning the water euxinic. This would begin to attract sulfide-oxidizing microorganisms which would settle along the surface of the sediment in order to capitalize on the energetically favorable blend of nitrate and sulfide. 

     Since sulfide is the most energetically favorable electron donor in this ecosystem and nitrate is the most viable acceptor, this form of respiration would provide them with unrivaled growth rates and allow them to monopolize more space and resources than there contemporaries. Eventually, they would go on to take over much of the sediment-water interface, creating dense microbial mats (of which, some may resemble the "Thiodendron" consortium in Entry #1).

     Alternatively, within less productive environments (such as those that exist further away from continental margins where most deposition occurs), euxinia would be less widespread. Within these habitats, nitrate would remain constrained to the sediment-water interface and sulfide would only be found deep within the substrate. 

     In order to bridge this gap and attain the highest potential energy yields, many organisms will end up making the trek vertically through the sediment, either through swimming or gliding. Over time, these "nomads" would grow to dominate over the sedentary sulfide oxidizers deeper in the sediment and the nitrate reducers at the surface. In addition, roving herds of filamentous organisms could end up forming large, conspicuous mats along the seabed (much like those of Thioploca and Beggiatoa mentioned in Entry #2). 

      However, stochastic processes (such as viral infections and storms) could threaten to disturb these mats, providing an opportunity for new communities with unique compositions to replace previously established ones. This would cause the microbial mats to bear a "patchy" appearance, with different regions supporting different primary producers, each capable of sulfide oxidation and nitrate reduction. 

     Because of this, we might also see a wide diversity of lineages, each with their own unique strategies for linking the two processes together. As opposed to migrating, some organisms for instance may use insulated, electrically-conductive wires to transport electrons from sulfide to nitrate, much like the muticellular cable bacteria found in terrestrial oceans. Others, similar to Lysinibacillus varians GY32 (shown below), may form giant, hyper-polyploid cells (those containing many genomes) that span the redox gradient. Alternately, smaller organisms may swarm around these biological wires in order to use them for vertical electron transport, much like free-swimming prokaryotes associated with cable bacteria do today.

      

(Upper Left) Here's an image of Electrothrix, a well studied cable bacterium. Note the unusual raised edges along its surface. These contain proteinaceous filaments which act as insulating wires. (Upper Right) This is an image of L. varians GY32. Unlike the cable bacteria which are multicellular, the filaments of this organism are comprised of a single, gigantic cell which stretches from the sediment-water interface to the sulfidic sediments below. In doing so, soluble electron acceptors diffuse along its membrane and slowly carry waste electrons into oxidized sediments where they can be released through the use of nanowires. These appear as "little hairs" lining the outside of the cell. Additionally, a thick cell wall serves to insulate the cell and prevent electron loss as they are transferred from sulfide to nitrate. (Bottom) This is a selection of free-swimming prokaryotes commonly associated with cable bacteria. In forming these relationships, the swarming microorganisms are able to avoid competing for electron acceptors with their sedentary counterparts by "feeding" their waste electrons to the cable bacterium. Meanwhile, the host is able to benefit through the exchange of free energy in the form of waste electrons.  

     Lastly, some microbes may use a radically different approach. As a opposed to traveling up and down through the sediment, developing systems of relaying electricity, or relying upon other organisms to transport electrons for them, some colonies of microorganisms might develop structures referred to as "veils" that transport resources through "bioconvection". 

     By generating currents through the rotary action of their flagella, cells within the veil could create currents that mixing the water. This in turn would provide them with a continuous source of sulfide and nitrate. In addition, some organisms might take advantage of this ecological service, attaching to the veils so that they could benefit from the transport of resources.   

(Top) A closeup of a veil constructed by the giant sulfide-oxidizing bacterium Thiovolum majus. The cells are linked by stalks made up of interwoven polysaccharides. (Bottom) An image of a T. majus veil from further away. These large, translucent structures grow along the sediment-water interface, capturing oxygen from the water column above and sulfide from the sediment below. 

Now that we've covered marine depositional ecology, let's leave behind the seafloor behind and check out what's going on the water column.

     Within deep waters, slowly-sinking detrital snow and dissolved organic matter could serve as the basis for planktonic communities. Unlike planktonic microbes in aerated, coastal waters, those within the anoxic portions of the water column would make use of nitrate as their preferred acceptor. 

     However, nitrate reducers might not be the only organisms in the water column. Although nitrate is a thermodynamically superior electron acceptor to sulfate, sulfate-reducers can still persist within the interiors of detrital snow particles where nitrate has been depleted. This would afford them some protection from their nitrate reducing neighbors, allowing them to coexist. Additionally, if sulfide is present (either in the environment or within particles colonized by sulfate reducers), planktonic communities would readily use it due to its status as a high-energy electron donor.  

NOTE : This is a commonly described phenomenon within anoxic environments on Earth, but this begs an interesting question as to why these microenvironments are dominated by sulfate reducers and not those that use iron or manganese. Perhaps the reason lies in the abundance of sulfate in the water column (relative to iron and manganese) or perhaps these metal reducers just haven't been observed yet within detrital particles. For now, I'm inclined to agree with the latter and will probably include them on Leeuwenhoek when doing some of my illustrations for the book.

     Lastly, in sulfide-rich, hypoxic (low-oxygen) environments, we may find microaerophiles that supplement their diets with hydrogen sulfide. This would provide them with an energetic boost, thereby offering them a bit of a competitive edge over their less metabolically-versatile neighbors.

     Anyways, this is where we'll end for now. Tune in next time for a deep-dive into how depositional environments in enclosed bodies of water differ from those in the ocean.  

Citations :

https://sci-hub.st/10.1017/s0025315400044945

https://www.nature.com/articles/s41467-023-37272-8

https://www.researchgate.net/publication/350127413_Long-distance_electron_transfer_in_a_filamentous_Gram-positive_bacterium 

https://www.researchgate.net/publication/283730886_Biophysical_basis_for_convergent_evolution_of_two_veil-forming_microbes

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8359478/

Microcosmos Updates Entry #1 : "Visualizing Habitats on Microbial Planets"

     

TLDR ; All throughout the universe, many worlds are likely to take on evolutionary routes different from our own, remaining permanently microbial. However, while there is good evidence to imagine this will be the case, it's much harder to imagine what life on these worlds would be like. However, by studying the ecosystems that once flourished in Earth's distant past and those that exist in the modern day, we might find our answer.  

     In my book Microcosmos, I plan to discuss how life will develop elsewhere in the universe. However, as opposed focusing on planets similar to our own, the worlds I describe have gone down a different evolutionary path. Instead, their biospheres have never achieved primary endosymbiosis (or at the very least, a form of endosymbiosis in which the endosymbiont gives up ATP or some other cofactor, as mitochondria do with their eukaryotic hosts). As a result, the organisms on these planets had never developed the necessary adaptations that would aid them in scaling up their energy production and supporting larger genomes. 

     This also means that they wouldn't have had the chance to develop analogues of animals and plants, let alone protists. Instead, what we're left with are essentially "worlds of bacteria". In which, organisms continue to rapidly diversify, but are held back by the same evolutionary pressures that have limited the development of bacteria and archaea here on Earth. 

     In order to explore the potential for evolution on these planets, I've made a theoretical model, dubbed "Leeuwenhoek" (named after the French microbiologist Antonie Van Leeuwenhoek). This current model has a mass slightly greater than that of Earth, a vast global ocean, and a moon that is smaller and orbits a bit further out than our own, resulting in weaker tides. 

     I addition to simulating how a planet would develop if complex life had never evolved, I also wanted to use this opportunity to see what might happen if the minerology of the planet were altered as well. For this reason, I decided to make Leeuwenhoek a "low-metallicity planet". 

     For in-universe context, Leeuwenhoek orbits Tau Ceti, a real star in the constellation Cetus. However, Tau Ceti has a relatively low metallicity percentage, at around 25-31% that of our sun. From this, we can extrapolate that Leeuwenhoek and other hypothetical planets orbiting Tau Ceti would start out with similar elemental abundances. 

     Following there formation, these planets would have also undergone differentiation, with denser materials sinking deeper into the mantle and lighter elements drifting upwards towards the surface. Since Leeuwenhoek is a bit larger than our planet, at around 1.7 Earth masses, this effect would be more significant. As a result, an even greater fraction of the iron and other heavy elements would have become incorporated into the core and mantle. This would have left the crust starved of many of the ingredients required for life (Leeuwenhoek has a global productivity rate ~15% that of modern levels observed on Earth). 

*Note : Productivity is the rate at which carbon is removed from the atmosphere by living organisms and turned into biomass. This is done by plants, algae, cyanobacteria, and other primary producers.

     Despite this, microorganisms would still flourish and go on to carve out a number of unique ecosystems in and along the planet's surface. These include coastal microbial mats dominated by photosynthesizers akin to cyanobacteria, terrestrial microbial mats that form vast plains along the margins of continents, as well as a number of more exotic cases, such as those inhabiting desert varnish and snow mounts.

For context, here's a complete list of the kinds of microbial ecosystems one might find on Leeuwenhoek:

*Note that while many of these ecosystems have proxies on Earth, they may not behave the same or have the same biogeographical distributions as their terrestrial counterparts. This can be due to a number of different reasons, ranging from minimal interactions with protists and fungi to differences in global nutrient cycling (all of which will be described in the book).

1. - mesophilic (temperate) and psychrophilic (cold) "matland" (A term used to describe microbial mats on land. It can also come in a variety of different morphotypes based on regional variations in rainfall and temperature. These include rugose, pinnacled, and uniform surface textures.)
2. - Matland fueled by geothermally-enriched groundwater
3. - "dark matland" (An assemblage of slow growing microcolonies and isolated cells on or within the sediment. These communities are especially prevalent within the ultraoligotrophic soils of continental interiors.)
4. - endoliths (communities inside of rocks)
5. - hypoliths (communities underneath rocks)
6. - desert varnish (A community of microbes that creates a complex sheet of organics and metal oxides on mineral surfaces.)
7. - grit crust (A kind of matland that stabilizes loose pebbles to form a ground covering similar in appearance to asphalt. They also play an important role in weathering minerals to form new soils, much like other matland communities.)
8. - phototrophic mats along coastlines, tidal flats, and shallow seas
9. - planktonic communities in shallow seas and along coasts (As organic matter is produced within microbial mats along the sediment, passing waves carry it upwards into the water column, providing pelagic communities with energy and nutrients. Since most of this material is concentrated along continental shelves and becomes more diffuse further away from the coast due to sedimentation or consumption by microbes, communities in the open ocean are typically extremely sparse or non-existent.)
10. - oligotrophic seafloor habitats with sparse assemblages of slow-growing cells and microcolonies
11. - springs and calderas
12. - cryoconite holes (water-filled pockets that form within ice sheets, containing microbes, detritus, and sometimes volcanic ash)
13. - snow mounts containing slush and brine
14. - extinct and active hydrothermal vent systems of varying geochemistry
15. - freshwater ponds and lakes
16. - streams and rivers
17. - Communities with the deep subsurface (highly variable / based on regional minerology, temperature, etc.)
18. - etc.

     In order to create this list, I pulled inspiration from ecosystems that persist on Earth today that have little interaction with plants and animals. I also took a number of my ideas from various paleontological sites that were preserved prior to the Avalon explosion (the initial diversification of animal life that took place during the late Neoproterozoic). 

     It's also important to note that throughout much of the Archean and Proterozoic eons, the crust was thinner and less malleable, leading to less subduction and uplifting. As a result, large mountain ranges wouldn't have formed and less erosion would have taken place, greatly reducing the rate at which essential nutrients would have been cycled. In addition, low oxygen levels would have led to reduced oxidative weathering along the surfaces of continents. This in turn would have prevented "redox sensitive metals" (such as nickel, vanadium, molybdenum, etc.) from becoming freely accessible for organisms to use. 

     Both of these factors are now thought to have made the early Earth a low-productivity world, with some estimates suggesting productivity levels as low as 1-10% that of modern levels. As a result, the early Earth served as a good stand in for Leeuwenhoek, given that both planets would have imposed similar pressures.  

     At first, I assumed that both planets would have had relatively nutrient-poor surfaces, with areas of slightly higher productivity scattered throughout (these include environments with active erosion, such as coastlines, rivers, streams, hydrothermal vents, springs, and calderas.) However, in doing some research, I came to realize that some other environments on the early Earth may have been especially good at concentrating organic carbon and stimulating microbial ecosystems.  

     For example, Roper Seaway in Northern Australia dates back to 1.38 billion years ago and represents a deep-water marine habitat in which carbon from the photosynthetic mat-dominated coastlines was later deposited. Within this environment, organic carbon would be degraded by a host of microorganisms, causing the water to become temporarily euxinic (rich in hydrogen sulfide). 

     Meanwhile, Borden Basin of Northern Canada dates back to 1.2 billion years ago and seems to bear similarly high depositional rates. However, unlike the Roper Seaway, Borden Basin was once a massive inland lake that was totally cut off from the ocean. Instead, this body of water was connected to a braided delta. 

     As within all flowing rivers, the continuous movement of water erodes source rock and liberates key nutrients, allowing for significant amounts of productivity. This in turn would have generated large amounts of organic matter which would have flowed into Borden Basin where it would undergo deposition and serve as food for microorganisms. Over time, this community of microbes became so robust that they were able to change the water chemistry, causing intermittent periods of euxinia in the lower-water column (much like what was observed in Roper Seaway). 

A 200-meter-tall rock face near Borden Basin, containing high concentrations of organic 

carbon (Those dots to the left of the rock formation are people!) The alkalinity of the Borden Basin had also played a role in favoring interactions between organic carbon and sulfide, creating bonds which would have made much of this organic detritus difficult for microbes to break down (Hence why so much of it survived to the present and underwent fossilization.)  

     In both cases, productive environments were able to generate high levels of organic material which then fed into massive depositional environments, creating novel microbial habitats. As a result, it would only be reasonable to assume that environments on nutrient-starved, microbially-dominated worlds would likely have similar features, paving the way for all sorts of interesting microbial adaptations. 

     For instance, stratified lakes on Leeuwenhoek with permanently anoxic bottom layers (similar to Lake Cadagno in Sweden) could contain euxinic zones that reach high enough into the water column to come into contact with sunlight. Within this unique habitat, anoxygenic photosynthesizers would form massive swarms, turning the water layer they inhabit a deep shade of emerald green or purple. In some cases, photosynthetic microorganisms might actively swim in order to maintain their ideal depth in the water column. In other cases, they could control their buoyancy with the aid of gas vacuoles, hovering in the water like trillions of hot air balloons. Additionally, some may even form intricate partnerships with their motile neighbors, exchanging nutrients for transportation. In doing so, these small phototrophs might develop sophisticated modes of chemical communication, "puppeteering" their hosts and encouraging to chase after the ideal levels of sunlight (as observed in green sulfur consortia). 

   (Top) A diver emerging from a meromictic lake with a collection tube containing purple sulfur bacteria. (Bottom) A green sulfur consortium (Check out the video about them that I linked below in the citations if your interested!)

* Note : Meromictic lakes receive water from precipitation as well as ground water. Since this groundwater is more saline due to interacting with minerals in the subsurface (such as dolomite), it is far more dense that the water in the uppermost portion of the lake. This prevents the two layers from mixing. As a result, if the bottom layer is rich in organics and all of the oxygen within it gets depleted by scavenging microbes, it can become permanently euxinic / anoxic due to a lack of aeration. This creates a stable environment for anoxygenic phytoplankton (Environments with similar conditions include Lake Cadagno as well as The Black Sea.) 

     Meanwhile, along the bottoms of Leeuwenhoek's euxinic lakebeds and depositional coastal habitats, we might also find massive microbial mats, similar to those mentioned in Entry #2. In some cases, these mats might even span hundreds of miles along the seabed, harboring a host of strange and unique symbiotic relationships and microorganisms.

     This is where we'll leave off for now, but be sure to look out for more posts on Leeuwenhoek's ecology moving forward. 

Citations : 

https://www.sciencedirect.com/science/article/abs/pii/S0012821X20303289

https://www.sciencedirect.com/science/article/pii/S0009254116303254

https://www.sciencedirect.com/science/article/abs/pii/S0301926812000812

https://www.youtube.com/watch?v=KF6rClLH4n4&t=88s

https://www.youtube.com/watch?v=GvQrH8qas0Q&t=9s

Microbe Spotlight #3 : "The Magic Sphere"

TLDR; A strange consortium begins its life by becoming an aquarium for a swimming community of microbes, transitioning into a living greenhouse, and ends its life cycle by turning into stone. 

     While scrolling around online in search of some new blogs and science news outlets to follow, I came across a strange defunct site from the early 2000's. The website was titled "Microbiological-Garden.net" and was a non-commercial project made by the University of Oldenburg in Germany. Within it were a series of slide-shows, each telling stories about strange microbes and the research techniques used by those who study them.

(Above) Screenshot from www.microbiological-garden.net

     As I continued exploring the website, I came across a few obscure topics that I'm hoping to discuss in future posts, but the one that fascinated me the most was the story titled "magic microbial spheres". Wondering what on Earth that could be, I opened it up and I certainly wasn't disappointed. 

     Out of all of the microbial consortia I've read about thus far, this might take the cake as being one of the most unusual. To begin, let's start by discussing how these "magic spheres" form and go through their life cycle. 

     In the beginning, a number of different heterotrophic bacteria aggregate and self-assemble into a hollow sphere which is supported with the aid of extracellular matrix. Once formed, the cells forming the sphere fill the space inside with hundreds of their flagellated progeny, which swarm within it like shoals of fish swimming within an aquarium.

     While this behavior is incredibly bizarre, another microbe (Vibrio splendidus 12B01) has also been shown to form a similar structure. In both cases, the movement of these bacteria appears to mix the contents of the water inside so that nutrients permeating the sphere are evenly dispersed throughout. In contrast, a colony of bacteria that is comprised of a solid mass of sedentary cells would gradually become so large that nutrients couldn't diffuse far enough to reach the interior, causing those within the deepest parts of the colony to starve and suffocate. So, by mixing the water in this manner, these magic spheres are able to push past that upper size limit and get significantly larger than normally-structured communities of bacteria. 

(Top) An image depicting the flow of nutrients within the spheres of Vibrio splendidus 12B01.

(Bottom) Alternatively, some prokaryotes (such as the Pseudomonas Aeruginosa colony shown here) create biofilms with intricate channels that allow water to flow throughout the interior and supply the cells with oxygen and other essential metabolites. 

     However, unlike the spheres of Vibrio splendidus 12B01, the mixed-species spheres appear to attract filamentous cyanobacteria and the diamond-shaped diatom Navicula which are able to sense it over large distances (presumably through sensing some sort of pheromone the spheres release). Once in contact, the diatoms and cyanobacteria pierce the membrane and enter the sphere, joining the community of swimming bacteria inside. Much like the tiny swarming heterotrophs, the photosynthesizers also continuously move within the sphere, perhaps to aid in circulating nutrients. 

                      (Above) The growth of cyanobacteria within the magic spheres over time.

 (Above) Navicula sp.

     While the benefits of this relationship are difficult to determine, it's possible that living within the sphere could offer protection against phagocytotic predators and antimicrobials emitted by other competitors. Secondly, microbial photosynthesizers and heterotrophic bacteria have long since been known to engage in syntrophy (exchanging metabolites) with one another. 

     During this process, the photosynthesizers offer the heterotrophs organic byproducts of their light-independent metabolic reactions that would be too energy intensive to recycle back into the Calvin cycle. In exchange for this waste, the heterotrophic bacteria may provide some other metabolite (such as amino acids) in order to promote the health and growth of their partner. Since this behavior is widespread amongst communities containing algae and cyanobacteria, it's reasonable to assume that they same might be occurring within the magic spheres as well. 

     Regardless, as the communities mature, the spheres begin to undergo some extraordinary changes. At first, the cyanobacteria and diatoms make up a relatively small portion of the community, but as they photosynthesize within it, they gradually begin to fill the sphere with their progeny, turning it into a living, microbial greenhouse. Eventually, after a few months have passed, the spheres begin to darken as the cyanobacteria become more densely packed. 

     As this occurs, the growth of the cyanobacteria and diatoms begins to interfere with the circulation of nutrients, causing the symbiosis within the sphere to gradually fall apart. In response to the environmental stress, the free-swimming bacteria and photosynthesizers break free from the sphere in order to migrate to new habitats. During which, the swarming heterotrophic bacteria are able to once again consolidate, giving rise to the next generation of magic spheres. 

     Meanwhile, the punctured remains of the membrane are left abandoned. The polysaccharides that were left behind as the cyanobacteria and diatoms glided across its inner surface gradually drive the formation of calcite crystals which expand to fill the interior. 

     Sometime later, the sphere's membrane begins to break down, peeling back like a mold and revealing the sphere of calcite within, known as an "ooid". In a sense, the magic sphere concludes its lifecycle by turning into stone. A befitting end for such an other-worldly and ethereal structure.

(Above) A diagram depicting the complete life-cycle of the magic spheres.

     Apparently, after doing some further researcher, I found that these magic spheres typically reside within the lamina of microbial mats that grow along tidal flats and salt marshes. Definitely something I'll have to look out for as I collect and film more samples this summer. 

Side Note : Ooids have been found along beaches all over the world and are generally assumed to form as grains of detritus or calcium carbonate are held aloft by the churning of tides and accumulate calcite as they tumble throughout the water column. However, this process may also play an important role in generating ooids. This is especially interesting, given the role ooids play in serving as habitats for "euendolithic" microbes (those that bore into solid rock) and may have had in providing a home for microbes on the early Earth.

(Above) Euendolithic cyanobacteria growing within

ooids (collected in the Bahamas)

Citations :

https://www.researchgate.net/publication/248984979_Biomicrospheres_Generate_Ooids_in_the_Laboratory

https://www.youtube.com/watch?v=krKBQ-j_oeI&t=120s 

https://royalsocietypublishing.org/doi/10.1098/rstb.2019.0077 

https://www.researchgate.net/publication/23792051_Molecular_and_morphological_characterization_of_cyanobacterial_diversity_in_the_stromatolites_of_Highborne_Cay_Bahamas