Kurzgesagt – In a Nutshell
Kurzgesagt – In a Nutshell
Embedded Files
Sources – Deep Biosphere
Sources – Deep Biosphere
We thank our experts for their feedback:
Steven D’Hondt
Professor of Oceanography, University of Rhode Island (USA)
Karen G. Lloyd
Professor of Earth Science, University of Southern California (USA)
We found a new planet, home to octillions of the most extreme beings living in the most absurd and deadly hellscape.
We refer mainly to two habitats, the deep oceanic subsurface (500m - 5,000m deep) and the deep continental subsurface (8m - 5,000m deep). That means, 4 x 1029 + 3 x 1029 bacteria and archaea may live in these habitats (= 700 octillion).
Keep in mind that the numbers can have a very wide range. There are different approaches to this question. In the source we mention below, you will find further sources for estimating these figures.
#Flemming, H.C. & Wuertz, S. (2019): Bacteria and archaea on Earth and their abundance in biofilms. Nature Reviews Microbiology, Vol. 17
We have to simplify a lot in this script. The structure of the earth is very different, e.g. there are different rocks or different interaction processes (such as groundwater) with the world on the surface. The following picture gives a rough overview of various environmental conditions and exchange processes. In addition, many living creatures have hardly been researched and accordingly many processes, e.g. how they can feed and survive, are still very vague.
#Onstott, T. C. (2017): Deep Life: The Hunt for the Hidden Biology of Earth, Mars, and Beyond. Princeton University Press
https://books.google.de/books/about/Deep_Life.html?id=F2KYDwAAQBAJ&redir_esc=y
Its volume is at least twice as large as all the Earth’s oceans, home to more microbes than on the rest of the entire planet combined.
As with the number of bacteria themselves, we have referred here to two main habitats: “Continental subsurface” and “Marine Crust”.
#Magnabosco, C. et al. (2019): 17 - Biogeography, Ecology, and Evolution of Deep Life. Deep Carbon. Past to Present
As we have described above, 7 x 1029 bacteria and archaea live in these two habitats. It is estimated that 1.2 x 1030 live on the entire earth. That means that 60% live in only these two habitats. If other habitats such as oceanic sediments were included, the number would increase even further.
#Flemming, H.C. & Wuertz, S. (2019): Bacteria and archaea on Earth and their abundance in biofilms. Nature Reviews Microbiology, Vol. 17
Their total biomass is 20 times greater than all humans, livestock, and animal wildlife.
Animals (including humans, of course) account for only around 0.4% (or 2 billion tons = 2 Gt) of the Earth's total biomass in carbon (546 billion tons). The following chart is based on a source below.
All Archaea and bacteria make up 77 Gt in total. If we assume (as explained above), that around 60% of these live in the two habitats deep oceanic subsurface and deep continental subsurface, this means that 46.2 Gt of the carbon is stored by archaea and bacteria. That is around 23 times more than all animals (2 Gt).
#OWID (2019): Humans make up just 0.01% of Earth's life — what's the rest?
#Bar-On, Y.M. et al. (2018): The biomass distribution on Earth, PNAS Vol. 115 (25)
Plants exploit this paradise and produce more than 30 times the biomass of all of Earth’s animals each year, in a constant cycle of growth and decay.
The total biomass of animals is around 2 Gt. Plants produce around 65.8 Gt of biomass annually, i.e. around 30 times more.
#Bar-On, Y.M. et al. (2018): The biomass distribution on Earth, PNAS Vol. 115 (25)
#Richardson, K. et al. (2023): Earth beyond six of nine planetary boundaries. Sciences Advances, Vol. 9 (37)
https://www.science.org/doi/10.1126/sciadv.adh2458
Quote: “By 2020, potential natural NPP would have risen to 71.4 Gt of C year−1 because of carbon fertilization, a disequilibrium response of terrestrial plant physiology to anthropogenically increasing CO2 concentration in the atmosphere, whereas actual NPP was 65.8 Gt of C year−1 due to the NPP-reducing effects of global land-use (see the Supplementary Materials).”
Only a tiny fraction of the biomass is buried deeper in the ground, supplying juicy resources for almost half a billion years.
Here we refer to the first land plants that appeared almost 500 million years ago. Then, as now, they are part of a carbon cycle that covers virtually the entire planet. This biomass can reach deeper layers through tectonic processes as well as groundwater.
#Galvez, M. E. & Pubellier, M. (2019): 10 - How Do Subduction Zones Regulate the Carbon Cycle?Deep Carbon. Past to Present
Quote: “The core, mantle, and crust contain more than 99% of Earth’s carbon stocks.1 The remaining 1% is in the fluid Earth, split between the biosphere, atmosphere, and oceans. But this distribution must be considered as a snapshot in time, not a fixed property of the Earth system. Continuous exchange of carbon between fluid (ocean, atmosphere, and biosphere) and solid Earth (mainly mantle and crust) has modified the size of the fluid and solid carbon reservoirs2 over geological time, regulating atmospheric composition and climate.3,4 The subduction zone, where converging tectonic plates sink below one another or collide, is the main pathway for this exchange.”
#Osterholz, H. et al. (2022): Terrigenous dissolved organic matter persists in the energy-limited deep groundwaters of the Fennoscandian Shield. Nature Communications, Vol. 13 (4837)
https://www.nature.com/articles/s41467-022-32457-z#Sec6
Quote: “Groundwater is the earth’s largest active source of freshwater1 containing a vast store of poorly characterized dissolved organic matter (DOM)2, an actively cycled key component in the global carbon cycle. As the water moves into deeper layers, nutrients and available organic carbon are removed, severely limiting the energy supply to the deep biosphere life estimated to contain 2–6 × 1029 cells3 that is approximately one quarter of the global microbial biomass.4
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Despite a considerable terrestrial fingerprint31, the Baltic Sea DOM carries freshly produced matter comprising e.g., proteins, amino acids, and carbohydrates44. These compounds are preferentially respired in the subsurface water column and may adsorb to sediment grains leading to the strongly terrigenous DOM signature entering the deep fractures.”
Above us pressing solid rock weighting tens of thousands of tons of solid rock, with pressures as intense as at the bottom of the Mariana Trench.
The hydrostatic pressure (blue line), i.e. in simplified terms, the pressure of the water column above you, is around 10 MPa per kilometer. This makes around 110 MPa for the Mariana Trench (around 11km deep).
Similarly, there is a lithostatic pressure for rocks in the crust (brown line). This is around 25 MPa. That is around 100 MPa at 4km.
#Cas, R. & Simmons, J. (2018): Why Deep-Water Eruptions Are So Different From Subaerial Eruptions. Frontiers in Earth Science, Vol. 6 (198)
Down here the temperature is on average 120 degrees, even hotter if a magma plume is nearby.
The extent to which the temperature rises can vary greatly. For the purposes of simplicity, we have taken the upper end of the range here (30°C/km).
#Hoinkes, G. et al. (2005): METAMORPHIC ROCKS | Classification, Nomenclature and Formation
https://www.sciencedirect.com/science/article/abs/pii/B0123693969004780
Quote: ”Geothermal gradients describe the temperature increase with depth (Figure 2). Typical geothermal gradients are in the range of 15–30°C km."
To make things worse some rocks are mixed extreme amounts of salt. Hell.
There are rock formations that were created by the evaporation of seawater and thus partly produced crystalline salt or contain brines.
#Stan-Lotter, H. et al. (2011): Deep Biosphere of Salt Deposits. Encyclopedia of Geobiology. https://link.springer.com/referenceworkentry/10.1007/978-1-4020-9212-1_67
Quote: “A total of about 1.3 million cubic kilometers of salt were estimated to have been deposited during the late Permian and early Triassic period alone (250–192 million years ago; Zharkov, 1981); newer research has discovered additional vast salt deposits, which were previously unknown – especially deposits below the Gulf of Mexico, and extensive Miocene salt (about 20 million years old) underlying the Mediterranean Sea, the Red Sea, and the Persian Gulf (Hay et al., 2006). The thickness of the ancient salt sediments can reach 1,000–2,000 m. When Pangaea broke up, land masses were drifting in latitudinal and northern direction. Mountain ranges such as the Alps, the Carpathians, and the Himalayas were pushed up by the forces of plate tectonics. In the Alpine basin and in the region of the Zechstein Sea, which covered northern Europe, no more salt sedimentation took place after the Triassic period.”
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Although the microbial content of ancient rock salt is low – estimates range from 1 to 2 cells/kg of salt from a British mine (Norton et al., 1993) to 1.3 105 colony forming units (CFUs) per kg of Alpine rock salt (StanLotter et al., 2000), and up to 104 CFUs per g of Permian salt of the Salado formation (Vreeland et al., 1998), equivalent to a range of 1 pg to 10 µg of biomass per kg of salt - the reports showed that viable haloarchaeal isolates were obtained reproducibly by several groups around the world. The data support the hypothesis that the halophilic isolates from subterranean salt deposits could be the remnants of populations which inhabited once ancient hypersaline seas; in addition, they provide strong evidence against the notion that the recovered strains could be the result of laboratory contamination, since the isolates were obtained independently from different locations.
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While there is no direct proof that haloarchaea or other microorganisms have been entrapped in rock salt since its sedimentation, it would also be difficult to prove the opposite, namely that masses of diverse microorganisms entered the evaporites in recent times (see also McGenity et al., 2000, for further discussion).
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Grant et al. (1998) discussed several possibilities, such as the formation of resting stages other than spores – since archaea are not known to form spores – or the maintenance of cellular functions with traces of carbon and energy sources within the salt sediments, which would imply an almost infinitely slow metabolism. At this time, there are no methods available to prove directly a great microbial age, whether it be a bacterium or a haloarchaeon.”
#Payler, S. J. et al. (2019): An Ionic Limit to Life in the Deep Subsurface. Frontiers in Microbiology, Vol. 10(426)
https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.00426/full
Quote: “The ionic composition of deep subsurface waters is particularly important in evaporite deposits where the dissolution of salt minerals can lead to fluids becoming highly concentrated in ions. Evaporites are ubiquitous in the deep subsurface, underlying 35–40% of the US with some sequences being hundreds of meters thick (Davies and LeGrand, 1972). This makes them a significant potential habitat in the terrestrial subsurface. Furthermore, evaporite deposits are widely exploited as a mineral resource, hence a better understanding of geochemical and biological processes occurring within them will carry important economic implications. Little is known about the variability in brine composition in evaporite deposits and their impact on deep subsurface microbiology. Work carried out on the microbial communities in evaporite sequences has generally focused on halite-rich environments. In these environments both halophilic archaea and bacteria have been identified, with the order Halobacteriales being a prominent feature (e.g., Denner et al., 1994; Vreeland et al., 2000; Radax et al., 2001; Fish et al., 2002; Stan-Lotter et al., 2002; Mormile et al., 2003; Gruber et al., 2004). Gypsum horizons found 200 m below the Dead Sea were also found to contain Halobacteriales (Thomas et al., 2014). Whilst the literature on deep subsurface halite-rich environments is limited, it is worth noting that evaporite sequences consist of many soluble salt minerals assemblages that include no or little halite. Therefore, waters through the entire evaporite sequence will be more chemically diverse than those typically encountered in the halite dominated sections.
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The culturing experiments demonstrate that the ability of the brines to support microbial growth varies. Organisms grew successfully in 44XC, Billingham and 215 when amended with carbon sources, showing these brines were habitable.”
Sandstone, limestone or basalt are so porous that up to 40 percent of their volume is actually empty space.
University of Wisconsin–Madison (retrieved 2024): Understanding Porosity and Density
Quote: “Porosity is the percentage of void space in a rock. It is defined as the ratio of the volume of the voids or pore space divided by the total volume. It is written as either a decimal fraction between 0 and 1 or as a percentage. For most rocks, porosity varies from less than 1% to 40%.
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The porosity of a rock depends on many factors, including the rock type and how the grains of a rock are arranged. For example, crystalline rock such as granite has a very low porosity (<1%) since the only pore spaces are the tiny, long, thin cracks between the individual mineral grains. Sandstones, typically, have much higher porosities (10–35%) because the individual sand or mineral grains don’t fit together closely, allowing larger pore spaces.”
But even much denser rocks like granite, can be split open by cracks and fractures.
Even if the graphic shows basalt instead of granite, you get an overview of the different habitats of organisms.
#Flemming, H.C. & Wuertz, S. (2019): Bacteria and archaea on Earth and their abundance in biofilms. Nature Reviews Microbiology, Vol. 17
In this hot, moving pressure cooker minerals are forged and baked, and organic molecules are created and destroyed. An insane menu for anyone brave enough to try to survive down here.
How organic molecules could arise from inorganic things such as minerals is often discussed in theories on the origin of life. Questions of the origin of life and the deep biosphere are therefore very closely linked.
For some theories of the origin of life, the process of serpentinization is a central component. Put simply, a chemical transformation of the rock takes place under the influence of water and certain temperatures, as is known from hydrothermal vents (black smokers or white smokers), for example. These processes could enable the formation of inorganic to organic molecules and thus make life possible.
However, there are also indications that similar processes can also take place in the continental crust.
#Schwander, L. et al. (2023): Serpentinization as the source of energy, electrons, organics, catalysts, nutrients and pH gradients for the origin of LUCA and life. Frontiers in Microbiology, Vol. 14
Quote: “Serpentinization in hydrothermal vents is central to some autotrophic theories for the origin of life because it generates compartments, reductants, catalysts and gradients. During the process of serpentinization, water circulates through hydrothermal systems in the crust where it oxidizes Fe (II) in ultramafic minerals to generate Fe (III) minerals and H2. Molecular hydrogen can, in turn, serve as a freely diffusible source of electrons for the reduction of CO2 to organic compounds, provided that suitable catalysts are present. Using catalysts that are naturally synthesized in hydrothermal vents during serpentinization H2 reduces CO2 to formate, acetate, pyruvate, and methane. These compounds represent the backbone of microbial carbon and energy metabolism in acetogens and methanogens, strictly anaerobic chemolithoautotrophs that use the acetyl-CoA pathway of CO2 fixation and that inhabit serpentinizing environments today. Serpentinization generates reduced carbon, nitrogen and — as newer findings suggest — reduced phosphorous compounds that were likely conducive to the origins process. In addition, it gives rise to inorganic microcompartments and proton gradients of the right polarity and of sufficient magnitude to support chemiosmotic ATP synthesis by the rotor-stator ATP synthase. This would help to explain why the principle of chemiosmotic energy harnessing is more conserved (older) than the machinery to generate ion gradients via pumping coupled to exergonic chemical reactions, which in the case of acetogens and methanogens involve H2-dependent CO2 reduction. Serpentinizing systems exist in terrestrial and deep ocean environments. On the early Earth they were probably more abundant than today. There is evidence that serpentinization once occurred on Mars and is likely still occurring on Saturn’s icy moon Enceladus, providing a perspective on serpentinization as a source of reductants, catalysts and chemical disequilibrium for life on other worlds.
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Serpentinization releases energy, generates reductants, and provides small organic compounds that directly interface with microbial metabolism. It occurs both in terrestrial systems (continental, on land) and in submarine systems on the sea floor, usually close to the borders of tectonic plates (Schrenk et al., 2013; Wang et al., 2014; Preiner et al., 2018). Continental serpentinizing systems, for example those hosted by ophiolites, are a valuable source of information about the process, as deep-sea hydrothermal vents are much harder to access and few Lost City type systems have been discovered so far (Lecoeuvre et al., 2021).”
#Nisson, D. M. et al. (2023): Radiolytically reworked Archean organic matter in a habitable deep ancient high-temperature brine. Nature Communications, Vol. 14 (6163)
https://www.nature.com/articles/s41467-023-41900-8#Sec6
Quote: “Depending on the geologic history of the system, hydrocarbons in these groundwaters can be biotic in origin, from in-situ microbial production or the products of thermal degradation24,25,26 and/or abiotically contributed from a variety of water-rock reactions related to radiolysis, serpentinization and Fischer-Tropsch type synthesis reactions3,20,27. Deep fracture fluids with low water/rock ratios and Ma-Ga residence times can generate and accumulate hydrogen, abiogenic methane and C2+ hydrocarbons produced from these water-rock reactions, which can serve as precursors in the production pathways for various other abiotic and biogeochemical processes1,2,3,5,20,28,29,30.”
We think that octillions of microbes live down here, and naturally they are pretty hardcore. The doomsday preppers of the underworld.
Some have big, bulky genomes, living entirely on their own, basically forming their own ecosystem.
#ScientificAmerican (2023): Subterranean ‘Microbial Dark Matter’ Reveals a Strange Dichotomy
Quote: “In new research published in the journal Environmental Microbiology, a genetic analysis of the mine’s microbes from as deep as 1.5 kilometers beneath the surface reveals a schism in survival strategies. Some microbes have big, bulky genomes that prep them to digest any nutrient that might come their way. Others are so genetically streamlined that they can’t even make some of life’s fundamental building blocks and instead rely on scavenging them or living symbiotically with other species.
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This overpreparation is surprising because there is an energy cost to maintaining so many genes for so many metabolic abilities, Osburn says. But the “prepper” nature of these microbes may be an advantage in the subsurface. “Fractures open; fractures close; things mineralize,” she says. “Many of these organisms are just prepared for whatever energy source comes along.”
#Momper, L. et al. (2023): A metagenomic view of novel microbial and metabolic diversity found within the deep terrestrial biosphere at DeMMO: A microbial observatory in South Dakota, USA. Environmental Microbiology, Vol. 25 (12)
https://enviromicro-journals.onlinelibrary.wiley.com/doi/full/10.1111/1462-2920.16543
Quote: “Similarly, the deep subsurface isolate Desulforudis audaxviator contains the is found globally and maintains genomic potential for an astonishing array of catabolic and anabolic metabolisms including sulfate reduction, carbon and nitrogen fixation, heterotrophy, and others (Becraft et al., 2021; Chivian et al., 2008). Our findings support the growing body of evidence that in many subsurface biomes there is a dichotomy of small, ultra-streamlined genomes adapted to low energy environments and syntrophic relationships, and larger, bulky genomes with diverse metabolic capabilities, poised to take advantage of an injection of higher energy electron acceptors (Anantharaman et al., 2016; Jungbluth et al., 2013, 2017; Lau et al., 2014; Mehrshad et al., 2021).
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Indeed, MAG and metabolic reconstruction of the DeMMO microbiome shows similarities to other studied subsurface sites in that we see an abundance of CPR with small, ultra-streamlined genomes and larger, bulky genomes with versatile metabolic capabilities, potentially leading an episodic lifestyle, poised to scavenge various nutrients, when available (Anantharaman et al., 2016; Jungbluth et al., 2013, 2017; Lau et al., 2014). Metabolically these groups have the potential for widespread carbon utilization and fixation, sulfur, and metal-based metabolisms, and potential roles in rapid drawdown of injected TEAs such as nitrate and oxygen.”
Like the bacterium Desulforudis audaxviator. It synthesises its own food by nibbling carbon or sulfur from the rock and turning it into organic substances.
As the picture shows, the metabolism is very complex. We simplify a lot here, but it is important to note that Desulforudis audaxviator takes many of its nutrients from the rock, such as the mineral smectite (a clay mineral), pyrite (an iron sulfide mineral better known as “fool's gold”) or calcite ("limestone").
#Chivian, D. et al. (2008): Environmental Genomics Reveals a Single-Species Ecosystem Deep Within Earth. Science, Vol. 322
Quote: “This bacterium was shown in a previous geochemical and 16S rRNA gene study (11) to dominate the indigenous microorganisms found in a fracture zone at 2.8 km below land surface at level 104 of the Mponeng mine (MP104).
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This gene complement was consistent with the previous geochemical and thermodynamic analyses at the ambient ~60°C temperature and pH of 9.3, which indicated radiolytically generated chemical species as providing the energy and nutrients to the system (11), with formate and H2 as possessing the greatest potential among candidate electron donors, and sulfate (SO4 2– ) reduction as the dominant electron-accepting process (11).
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“Its genome indicates a motile, sporulating, sulfate-reducing, chemoautotrophic thermophile that can fix its own nitrogen and carbon by using machinery shared with archaea. Candidatus Desulforudis audaxviator is capable of an independent life-style well suited to long-term isolation from the photosphere deep within Earth’s crust and offers an example of a natural ecosystem that appears to have its biological component entirely encoded within a single genome.
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Other factors that may confer fitness in this environment are the ability to form endospores (table S16) and the potential for it to grow in deeper, hotter conditions (table S9) than provided by MP104.”
#Jungbluth, S.P. et al. (2017): Genomic comparisons of a bacterial lineage that inhabits both marine and terrestrial deep subsurface systems. PeerJ, Vol. 5
https://pubmed.ncbi.nlm.nih.gov/28396823/
Quote: “Chivian and colleagues (2008) reconstructed the first complete genome from a terrestrial member of this firmicutes lineage, provisionally named “Candidatus Desulforudis audaxviator” MP104C, via metagenome sequencing of a very low diversity sample from a deep gold mine in South Africa. The “Ca. D. audaxviator” genome revealed a motile, sporulating, thermophilic chemolithoautroptroph genetically capable of dissimilatory sulfate reduction, hydrogenotrophy, nitrogen fixation, and carbon fixation via the reductive acetyl-coenzyme A (Wood-Ljungdahl) pathway (Chivian et al., 2008). Thus, “Ca. D. audaxviator” appears well suited for an independent lifestyle within the deep continental subsurface environment.”
If the conditions get too extreme or if there is no food around, it kills itself to survive, by forming an endospore. It divides into a big and a small part, and swallows the small part again, forming a cell, within a cell. The outer cell then sheds its water and kills itself, leaving the spore to float around, maybe for thousands of years until it finds a good place to spring to life again.
#Basta, M. & Annamaraju, P. (2023): Bacterial Spores. StatPearls
https://www.ncbi.nlm.nih.gov/books/NBK556071/
Quote: “Endospores can resist inactivation from ethanol treatment.[3] They also can survive high temperatures for up to 150°C, making specific Gram-positive species heat resistant. Further, bacterial spores can show typical viability signs at temperatures near the absolute zero. Endospores are resistant to the chemical agents, e.g., triphenylmethane dyes, and can even protect the bacterial cells against ultraviolet radiation, extreme pH gradients, drought, and nutrition depletion.”
#Romero-Rodríguez, A. et al. (2023): Targeting the Impossible: A Review of New Strategies against Endospores. Antibiotics, Vol. 12(2)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9951900/
Quote: “Endosporulation (indistinctly used as endosporulation or sporulation) is a complex process of morphological differentiation that culminates in the output of a dormant cell type that is exceptionally resistant to severe environmental conditions, surviving for prolonged periods without water or nutrients [2,3]. This process is highly ancient, perhaps arising near the phylogenetic root of bacteria [4,5].”
#Al-Hinai, M. & Jones, S. (2015): The Clostridium Sporulation Programs: Diversity and Preservation of Endospore Differentiation. Microbiology and molecular biology reviews: MMBR, Vol. 79 (1)
Other microbes down here prefer a bit of company, like the archaea with the clunky name Candidatus Altiarchaeum hamiconexum, that have a unique double membrane covered in weird materials that protect them against the extremes.
They shoot out nano-sized grappling hooks to stick to the surfaces. They seem to live in cracks and fissures filled with deep water, completely devoid of oxygen, harvest carbon dioxide to create biomass and may sort of breathe hydrogen.
Although this organism was discovered at shallow depths around 40m, it is possible that it originates from deeper depths due to the water in which it lives.
Probst, A. J. & and Moissl-Eichinger, C. (2015): “Altiarchaeales”: Uncultivated Archaea from the Subsurface. Life, Vol. 5 (2)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500143/
Quote: “Fairly soon after this discovery, another biotope of Ca. A. hamiconexum and of the string-of-pearls communities was found. In contrast to the first biotope, this cold, sulfidic groundwater emanated from a 36.5-m deep, drilled hole (Mühlbacher Schwefelquelle; [3,4]). This aquifer delivers ~5400 L of sulfidic freshwater per hour and transports thereby subsurface microbes from the deep to the surface, thus allowing indirect access to the subsurface.”
The exact function of the hooks is not entirely clear, they could serve as a connection between conspecifics or other surfaces, or even as a form of communication.
Probst, A. J. et al. (2014): Biology of a widespread uncultivated archaeon that
contributes to carbon fixation in the subsurface. Nature Communications, Vol. (5) 5497
https://www.nature.com/articles/ncomms6497
Quote: “However, both genomes from the German site (SM1-MSI) and from the US site (SM1-CG) harbor genes for hamus (plural hami) subunits. Hami are specialized cell surface appendages with barbwire like filamentous structures and nano-grappling hooks at their distal end (diameter approx. 60 nm; Fig. 3a).”
Probst, A. J. & and Moissl-Eichinger, C. (2015): “Altiarchaeales”: Uncultivated Archaea from the Subsurface. Life, Vol. 5 (2)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500143/
Quote: “Although the hami are probably the best-characterized cell surface appendages of an uncultivated organism, many questions remain unanswered, particularly those that necessitate cultivation and establishment of a genetic system of the organism. First of all, it is unclear, if and what other types of proteins are involved in the hami-anchorage and formation and how hami formation is regulated within the cell. In addition, any components of the outer membrane remain unknown, which holds true for most of the other, rare, double-membraned Archaea, such as Methanomassiliicoccus luminyensis [14].
To date, also a possible function of the hami besides attachment remains elusive. Most microbes have developed pili or flagella to strongly attach to different surfaces [15], and such structures seem to provide enough adhesion power due to van-der-Waals forces prevailing at such small dimensions. The hami, however, are highly structured and bear a grappling hook at the end, whose specific function is unknown so far. The structural analyses of the protein have indicated the possible capability towards conformational change [12], but it remains to be analyzed whether the hami are involved in signal transduction or may even mediate electron transfer, as discussed recently [7].
Since biofilm formation usually requires some communication between cells (quorum sensing) [16] and the porous biofilm of Ca. A. hamiconexum thriving in groundwater with high flow rates may not allow communication via small molecules between cells, we hypothesize that the hami could fulfill such a communication role, i.e., via tractive forces. The hooks may ensure anchorage to another cell or another (a)biotic surface. We speculate that traction applied to the hooks by cells in an environment with high pressure and flow rate could initiate an intra-cellular signal cascade. Such a signal cascade could enable cells to form biofilms via cell division and initiate other factors, like production of extracellular polymeric substances (EPS).”
"Carbon fixation" is the process in which the inorganic carbon dioxide is converted into organic building blocks.
Probst, A. J. & and Moissl-Eichinger, C. (2015): “Altiarchaeales”: Uncultivated Archaea from the Subsurface. Life, Vol. 5 (2)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4500143/
Quote: “Based on lipid measurements that showed a very low delta 13C value, it was concluded that Ca. A. hamiconexum is an autotrophic organism that uses a modified reductive acetyl-CoA pathway to turn carbon dioxide into organic compounds [7]. The so-generated acetyl-CoA is ultimately available for gluconeogenesis and production of various sugars and serves as the precursor for lipid biosynthesis [7]. The Wood-Ljungdhal pathway is also present in the genome of Ca. A. hamiconexum recovered from Crystal Geyser in the USA [7]. Moreover, this pathway is also found in the IM-C4 Altiarchaeales genome, which indicates that it may be a general feature of this clade and confirms the importance of this group regarding autotrophic carbon cycling in the subsurface.”
The conditions in the deep biosphere are so harsh that other microbes share the hard work by forming consortia. They knit themselves together in a biofilm – a very thin, sticky net that shields them against the extremes.
These microbes are miniature cells, often small genome, but each good at one thing.
One type of microbe eats methane and excretes its electrons. A second type eats these electrons and converts sulphate into sulfite that is then eaten by a third microbe and so on. Some eat iron, others use electrons to turn nitrogen or carbon dioxide into biomass.
We simplify a lot here, but biofilms are not a simple cluster of certain organisms, there are complex relationships within biofilms as well as division of labor. Much is still unclear, but there are probably exchange processes in which the microbes "help each other out" with different metabolic outputs. What exactly this relationship looks like is still the subject of research.
In the context of microbial metabolism, "breathing" or "eating" are said to be electron-accepting or electron-donating processes. So when a microbe "eats" methane, we mean that methane donates it an electron. When a microbe "breathes", it gives an electron to a specific substance.
#Parrilli, E. et al. (2022): Biofilm as an adaptation strategy to extreme conditions
Rendiconti Lincei. Scienze Fisiche e Naturali, Vol. 33
https://link.springer.com/article/10.1007/s12210-022-01083-8
Quote: “Biofilm is the oldest most successful and widely distributed form of life on earth (Westall et al. 2001), in fact, current estimates suggest that up to 80% of bacterial and archaeal cells reside in biofilms (Flemming and Wuertz 2019).
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It is likely that biofilms provided homeostasis in the face of the unstable and harsh conditions of the primitive earth (pH and exposure to ultraviolet (UV) light, extreme temperatures) helping the development of complex interactions between individual cells.
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By generating a matrix, bacteria in biofilms create a physically distinct habitat that provides protection and produces nutrients and gases gradients (Flemming et al. 2016). These gradients create microenvironments with specific physical and chemical properties allowing the presence of microorganisms with very different physiological requirements (Flemming and Wingender 2010; Hung et al. 2013). In biofilms present in shallow aquatic environments, for example, microorganisms are distributed according to their metabolic properties.
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Physiological heterogeneity in biofilms allows the three-dimensional organization of mixed-species biofilms. In many cases, the presence of one group of organisms determines the ability of the other group to survive in the biofilm For example, phototrophic microorganisms generate and release organic substrates, and neighboring species use these substrates for their metabolic activity (Ward et al. 2008). In a mixed-species biofilm, a division of labor, based on their functional ability, between species belonging to a different taxonomic group is frequently reported (van Gestel et al. 2015; Joshi et al. 2021).
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A further advantage of biofilm as a collective organization is the improved ability to acquire nutrients from the environment. It is achieved through resource capture and retention of cellular products and debris that can be used as a reservoir. This advantage is related to the matrix’s ability to promote the accumulation of nutrients (Flemming and Wingender 2010) and to create an extracellular digestion system made by different hydrolytic enzymes. Indeed, the hydrolytic enzymes present in the biofilm are not only a supply for the microorganisms that produce them but also become a resource for all members of the biofilm community (Worm et al. 2000; Nicolaisen et al. 2012), this phenomenon has been called the 'social function of extracellular hydrolysis' (Flemming et al. 2016).
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It is widely accepted that biofilm formation offers protection of cells from hostile environmental conditions such as ultraviolet radiation, extreme pH, high salinity, extreme temperature, high pressure (Yin et al. 2019), and tolerance to desiccation (Flemming and Wingender 2010).”
#Flemming, H.C. & Wuertz, S. (2019): Bacteria and archaea on Earth and their abundance in biofilms. Nature Reviews Microbiology, Vol. 17
https://www.nature.com/articles/s41579-019-0158-9
Quote: “It was the pioneering work of Marshall194, Fletcher195, Characklis196 and Costerton197 that led to the biofilm concept, which describes bacterial attachment and its consequences as a specific form of microbial life. Microorganisms, including archaea, although only recently acknowledged17–19, can also attach to interfaces, grow and eventually aggregate in layers, termed biofilms. Such aggregates of cells can develop at any interface, even one formed by the cells themselves. From an evolutionary point of view, it is interesting that the biofilm mode of life enables self-organization of its members and the development of emergent properties — that is, properties that are not predictable from the study of free-living bacterial cells — that involve novel and coherent structures, patterns and properties, as observed in other collective, complex systems10,198. this is analogous to the difference between individual trees and a forest but fundamentally different in the sense that, for many microorganisms, residing in a biofilm may be only one of several phases in their life cycle. Biofilms form structures with multicellular aspects and division of labour, enabling both synergistic and antagonistic interactions. Certainly, biofilms represent a higher level of organization among microorganisms than is possible for single, suspended cells10.
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Microbial aggregates are extremely diverse, ranging from tiny, patchy microclusters or colonies, monolayers and confluent biofilms of varying thickness to highly heterogeneous structures, such as microbial mats or biofilms in hot springs, marine snow or dense, granular sludge. it remains debatable how many cells are needed to make a biofilm, similar to the question of how many trees it takes to make a forest. However, it is safe to assume that there is a continuum between single sessile cells and the point at which they divide and form small clusters, microcolonies and larger aggregates.
Microbes that use methane as an energy source, for example, are called "methanotrophs". Biomes of such organisms in the deep biosphere marine sediments play an important role in the global methane cycle.
#Ruff, S.E. et al. (2019): In situ development of a methanotrophic microbiome in deep-sea sediments. The ISME Journal, Vol. 13
https://www.nature.com/articles/s41396-018-0263-1#Abs1
Quote: “Emission of the greenhouse gas methane from the seabed is globally controlled by marine aerobic and anaerobic methanotrophs gaining energy via methane oxidation. However, the processes involved in the assembly and dynamics of methanotrophic populations in complex natural microbial communities remain unclear.”
Kietäväinen, R. & Purkamo, L. (2015): The origin, source, and cycling of methane in deep crystalline rock biosphere. Frontiers in Microbiology, Vol. 6
https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2015.00725/full
Quote: “In addition to methane-producing archaea, the deep subsurface environments host microbes utilizing CH4 for their sole source of carbon and energy, called methanotrophic microorganisms (Figure 1). Electron acceptors can vary from oxygen to sulfate, nitrate and nitrite, iron and manganese (Hanson and Hanson, 1996; Orphan et al., 2002; Raghoebarsing et al., 2006; Beal et al., 2009; Knittel and Boetius, 2009; Ettwig et al., 2010; Haroon et al., 2013).”
#Kucera, J. et al. (2020): A Model of Aerobic and Anaerobic Metabolism of Hydrogen in the Extremophile Acidithiobacillus ferrooxidans. Frontiers in Microbiology, Vol. 11
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7735108/
Quote: “However, the importance of H2 as an electron donor for acidophiles in the subsurface and geothermal springs as well as deep-sea hydrothermal vents remains unknown. Also, most of the information that has been published on acidophilic life in the subterranean environments has come from the research of abandoned deep mines and caves (Johnson, 2012). Recently, drill cores taken from the largest known massive sulfide deposit have confirmed the presence of members of hydrogen, methane, iron and sulfur oxidizers, and sulfate-reducers many of which are acidophilic (Puente-Sánchez et al., 2014, 2018).
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Acidophilic bacteria growing aerobically on H2 include obligate autotrophs Acidithiobacillus spp. (iron/sulfur-oxidizing At. ferrooxidans, At. ferridurans, At. ferrianus, and sulfur-oxidizing At. caldus), iron/sulfur-oxidizing facultative autotrophs Sulfobacillus spp. (Sb. acidophilus, Sb. benefaciens, and Sb. thermosulfidooxidans), and iron-oxidizing facultative autotroph Acidimicrobium ferrooxidans (Drobner et al., 1990; Ohmura et al., 2002; Hedrich and Johnson, 2013; Norris et al., 2020).”
Their metabolism is up to a million times slower than microbes at the surface.
#Jørgensen, B.B. (2011): Deep subseafloor microbial cells on physiological standby. Proceedings of the National Academy of Sciences of the United States of America, Vol. 108 (45)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3215010/
Quote: “A typical metabolic rate of microorganisms in ecosystems on the surface of our planet, such as soil, lake water, or seawater, is 0.1 to 10 fmol C⋅cell−1⋅d−1, corresponding to 10−3 to 10−1 g C metabolized per gram cell C per hour (Fig. 1). The mean metabolic rate for deep subsurface bacteria is typically four orders of magnitude lower: 10−5 to 10−3 fmol C⋅cell−1⋅d−1 (6, 7), corresponding to 10−7 to 10−5 g C⋅g−1 cell C⋅h−1.”
With this lifestyle it seems that extreme microbes can live for centuries, maybe even for millions of years!
We have to put the “millions of years” into perspective here. One of our experts explained to us that some of the living beings upset our previous views or theories about “What is life?”. He says that both could be possible, but we don't know yet.
Beyond that, however, there are signs that entire communities or even single endospores could be millions of years old.
#Jørgensen, B.B. (2011): Deep subseafloor microbial cells on physiological standby. Proceedings of the National Academy of Sciences of the United States of America, Vol. 108 (45)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3215010/
Quote: “The answer is that the average cell may divide once in 1,000 y. Such a slow growth means relatively more energy spent on maintenance metabolism, however, so the growth yield is probably lower than for laboratory cultures and the potential generation time therefore as long as several thousand years.”
Inagaki, F. et al. (2015): Exploring deep microbial life in coal-bearing sediment down to
~2.5 km below the ocean floor.Science Research, Vol. 349 (6246)
https://www.science.org/doi/abs/10.1126/science.aaa6882
Quote: “Microbial life inhabits deeply buried marine sediments, but the extent of this vast
ecosystem remains poorly constrained. Here we provide evidence for the existence of
microbial communities in ~40° to 60°C sediment associated with lignite coal beds at
~1.5 to 2.5 km below the seafloor in the Pacific Ocean off Japan. Microbial methanogenesis
was indicated by the isotopic compositions of methane and carbon dioxide, biomarkers,
cultivation data, and gas compositions. Concentrations of indigenous microbial cells below
1.5 km ranged from <10 to ~104 cells cm−3. Peak concentrations occurred in lignite
layers, where communities differed markedly from shallower subseafloor communities
and instead resembled organotrophic communities in forest soils. This suggests
that terrigenous sediments retain indigenous community members tens of millions
of years after burial in the seabed.”
#Cano, R.J. & Borucki, M. K. (1995): Revival and Identification of Bacterial Spores in
25- to 40-Million-Year-Old Dominican Amber. Science, Vol. 268 (5213)
https://www.science.org/doi/abs/10.1126/science.7538699
Quote: “The results of the morphological, biochemical, enzymatic, and molecular characterization of isolate BCA16 support the hypothesis that a viable B. sphaericus spore
was indeed recovered from the abdominal contents of P. dominicana entombed in 25-to 40-million-year-old amber.”
If they are not hunted to death, of course. Because kilometers deep in limestone habitats, there seem to be spaces big enough for multicellular predators. We found asexual worms, 100 times longer than microbes, hunting and devouring bacteria. It's not clear if they originated down here or if mini earthquakes opened up fractures for water to carry them into the deep.
Detailed information about this critter can be found here:
#Borgonie, G. et al. (2011): Nematoda from the terrestrial deep subsurface of
South Africa. Nature, Vol, 474
https://www.nature.com/articles/nature09974
#Weinstein, D.J. et al. (2019): The genome of a subterrestrial nematode reveals adaptations to heat. Nature Communications , Vol 10 (5268)
https://www.nature.com/articles/s41467-019-13245-8
Quote: “As the founding genome sequence of the Halicephalobus genus, H. mephisto illuminates previously unexplored territory. H. mephisto separated from Caenorhabditis at least 22 million years ago52,64, and likely over 100 million years ago65, though calibrating the nematode molecular clock is difficult because of their poor fossil record64. Our data suggest that nematodes access the deep subsurface from surface waters facilitated by seismic activity66. This transition from surface to deep subsurface would be expected to exert strong selective pressures on their genomes, which in nematodes are particularly evolutionarily dynamic6,7,10–12.”
#Borgonie, G. et al. (2019): New ecosystems in the deep subsurface follow the flow of water driven by geological activity. Nature Scientific Reports, Vol. 9 (3310)
https://www.nature.com/articles/s41598-019-39699-w
Quote: “In situ seismic simulation experiments were carried out and show seismic activity to be a major force increasing the hydraulic conductivity in faults allowing organisms to create ecosystems in the deep subsurface. As seismic activity is a non-selective force we recovered specimen of algae and Insecta that defy any obvious other explanation at a depth of −3.4 km.”
But there are other fierce predators like rotifers or arthropods in the depths, hunting immortal microbes.
#Magnabosco, C. et al. (2019): 17 - Biogeography, Ecology, and Evolution of Deep Life. Deep Carbon. Past to Present
Quote: “Following the discovery of subsurface Nematoda, other multicellular eukaryotes including Platyhelminthes, Rotifers, Annelids, and Arthropoda and unicellular Protozoa and Fungi have been identified at depth in the South African subsurface (Reference Borgonie, Linage-Alvarez, Ojo, Mundle, Freese and Van Rooyen (164). Recent efforts to identify the source and transport of these eukaryotes underground point to freshwater sources and seismic activity (Reference Borgonie, Magnabosco, Garcia-Moyano, Linage-Alvarez, Ojo and Freese (165).
Borgonie, G. et al. (2015): Eukaryotic opportunists dominate the deep-subsurface biosphere in South Africa. Nature Communications, Vol. 6 (8952)
https://www.nature.com/articles/ncomms9952
Quote: “We report on the discovery in deep-subsurface fissure biofilm
of Protozoa, Fungi, Platyhelminthes, Rotifera, Annelida, Arthropoda and additional Nematoda.”
Like “breathing” nitrogen or eating methane.
#Shao, M.-F. et al. (2010): Sulfur-driven autotrophic denitrification: diversity,
biochemistry, and engineering applications. Applied Microbiology and Biotechnology, Vol. 88
https://link.springer.com/article/10.1007/s00253-010-2847-1
Quote: “Sulfur-driven autotrophic denitrification refers to the chemolithotrophic process coupling denitrification with the oxidation of reduced inorganic sulfur compounds. Ever since 1904, when Thiobacillus denitrificans was isolated, autotrophic denitrifiers and their uncultured close relatives have been continuously identified from highly diverse ecosystems including hydrothermal vents, deep sea redox transition zones, sediments, soils, inland soda lakes, etc.
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Denitrification refers to the dissimilatory transformation of nitrate or nitrite to N2 concomitant with energy conservation (Knowles 1982). Denitrification, in combination with nitrogen fixation, nitrification, and ammonification, constitutes the global nitrogen cycle. From a bioenergetic point of view, denitrification allows a microorganism the respiratory type of life in anaerobic conditions (Kluyver and Donker 1926), where the N oxide (nitrate, nitrite, NO, or N2O) instead of O2 serves as terminal acceptor for electron transport phosphorylation.”
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