#lokiarchaeota

[lokiinmediasideblog]

I find it hilarious when something is named after Loki it's usually because "there was a lot of confusion surrounding it."

^^ A previously discovered dinosaur also named after Loki

Lokiarchaeota:

Loki's Castle Hydrothermal vents:

[fishyfishyfishtimes]

Sirpaverse overview

I want to talk more about the world Ahti II inhabits, but to do that it needs a brief introduction! This is that introduction. I don’t really have a name for the world, so I’m going to be calling it Sirpaverse; that's the name I refer to it with my friends, who are funnily enough most familiar with Sirpa rather than Ahti II.

The Context

I have pretty out-there dreams. If you've kept up with every post that starts with "I had a dream-" then you'll be familiar with that fact already! I often explore and see strange animals, places and people, occasionally with names, even. I like to remember my nightly adventures, so I tend to write and draw the things I’ve seen. Eventually, since I'd gathered quite a roster, I made a big lineup of characters from my dreams in 2021, and liked them so much that I decided to compile them and a bunch of things I’d seen in dreams into one world. That's Sirpaverse! Worldbuilding is a fun exercise for me so this is mostly just for fun :)

The very basis of the world is based on Karl Popper’s theory of three worlds and Plato’s theory of forms, I’ll go through them briefly. Popper’s three worlds indeed consists of three worlds of being in our one universe: World 1, the objective reality and physical world, World 2, the subjective perception of the world done by conscious living beings, both conscious and subconscious processes involved, and World 3, concepts, theories, stories and creations formed by humans. A stone and gravity are of World 1, love and dreams are of World 2, and Donald Duck and the theory of evolution (note: the theory itself) are of World 3.

Plato’s theory of forms meanwhile ponders that there exists these basal ideas or forms that are more real than our subjective perception of the world — they are the essence of everything we see, for example an apple can be red, green, small, shiny, half-eaten, or rotten, but we still recognize it as an apple. The idea of apple!

The World

The world is made up of three realms: the physical world, the idea world and the spirit world. The worlds are technically separate but occupy the same universe and influence each other greatly. The spirit world overlaps with both the physical and the idea world, which has given rise to sentient life in both. 

The Physical World

The physical world is… our universe. You already know all about that. There’s the Earth and it’s a pretty nice place to live, with such reoccurring guys as Enchytraeidae worms, bristlemouths, beetles, common yeast, parasitoid wasps, Lokiarchaeota-archaea, basidiomycetes, beetles, lanternfish, giant tube worms, tiny tube worms, tubeless worms, cyanobacteria, beetles, and also humans! Everything is made up of atoms, they are tangible, real, concrete.

Along with the physical building blocks, every single object and being also has nonphysical idea/concepts hanging on (just like Plato said!). The concepts are less like actual building blocks — no one actually put the ideas together deliberately — they’re more like unspoken instructions, a consequence of the object existing! Living beings meanwhile have ideas/concepts in their DNA which influence how we look in tandem with our physical DNA. I’ll get back to that later. When us sentient animals die, our soul separates from our physical body and it’s left hanging out in the world. 

The Idea World

The idea world is a realm where the basal ideas of everything exist. Everything there is a shifting, infinite, intangible soup of those basal concepts from the physical world! It’s a world where the idea people reside. The idea people are as varied as there are things in the world, they have a “core self”, which takes the form of eye(s), and to build upon that they pull concepts into their own selves. They can look very abstract or very normal (what is normal to them is somewhat different to what we find ordinary: this just means they look like a thing that we know) depending on their tastes, and oftentimes an idea person looks a bit different to every observer because of their lack of a physical form. They also have supernatural powers innate to their being, which they find as easy to use as blinking (each one has two!).

The idea people are not bound by bodily needs like hunger or tiredness or thirst, although they can have social needs — idea people are sophont creatures that more or less match the intelligence and awareness of a human of the same age… of course, the idea people do not die naturally and can live forever if they want to, and so their intelligence grows with age until they become very difficult to understand by human standards. Idea people tend to get bored of existing after a few hundred thousand years at which point they can decide to die and “recycle” their bodies. Whether the soul of the idea person immediately moves into an afterlife or the same soul remains but forgets all their past memories, the idea people don’t really know. All they know is that in the exact same spot, a “baby” with one additional eye appears, and that baby will grow up to have their own unique personality. Occasionally one-eyed baby idea people will also spontaneously appear, but again, ehh… the idea people don’t actually know why or how that happens. They think it might have something to do with things happening in a different inaccessible world. 

The Spirit World and Related Beliefs

Spirit world is the final world! And uh… sadly nothing is known about it. Supposedly souls go there when they pass on, but no soul that has gone there has ever returned. As a result there are lots of different beliefs about what happens to a soul when they pass on, religions often seek to answer this very question! There’s several, I haven’t come up with all of them yet, but two major ones are Muffyism and the Children of Sun and Moon.

Muffyism teaches that a godly semiaquatic bird, Muffy, dove into the endless dark primordial sea for a beakful of mud, with which she shaped the earth under our feet. Muffy laid down on the barren land to lay her eggs, and from these eggs hatched the stars, the sun, the moon, the moss, the trees, the fish, the animals on land, and finally, birds. Muffyists believe that once you die, your soul returns to her nest under the care of her wings — after all, we are all her children.

The Children of Sun and Moon/Moon and Sun worship the very celestial bodies, or gods that control them, depending on the creed. Sun and Moon are closer than lovers, closer than any living being could be, and in their shared joy they created the Earth (and the rest of the planets) and every living being on Earth as their children, friends, witnesses of their eternal shared existence, a bit of all of the above. When you die and pass on, your soul leaves into space, and becomes a star. As a star you can influence the world still, like grant wishes to your offspring!

Belief in reincarnation is also very popular in the Sirpaverse, but I don’t have any specific religion whose main belief is that — yet. In older times, worship of magically powerful people who were described more as gods than human in myths was pretty big also! King Ahti the First is one of such figures: the Sea God of Fish and Seals, who fell into the waters from the rainclouds to unite the Osmerian Kingdom so many centuries ago. The rule of Ahti the Second’s family relied on this divine right principle for the longest time! After all, these people are obviously demigods, they deserve to rule. Now, uhhhh…… it’s certainly much less popular. Historians agree that Ahti the First did exist, but his godly powers have come into some question! The Osmerian monarchy stays pretty quiet about that whole deal...

Ghosts

 The interesting part about living in Sirpaverse is that people know for certain that they will become ghosts when they die! Unfortunately it’s not all too interesting. Death is a very big change and to cling to any semblance of normalcy the mind comes up with self-imposed rules, such as “gravity is a force that impacts you” and “you can’t see ultraviolet”. These take a while to unlearn. Ghosts are often impacted by the world around them even when they can’t interact with the world themselves, which can lead to lots of stumbling and hitting your head on objects and people swaying their arms around. Fortunately ghosts have one power, they are able to possess objects and living things and use them as vessels! It does still take practice and skill, taking control of something physical can be tricky indeed… but they can do it, and are even somewhat able to get briefly close to a feeling of normalcy via having A Body of any kind. Ghosts often describe that their senses shift with each object, some amplifying or even adding new senses or dampening others.

Ghosts, ownership and the law is pretty complicated. In times of old people would usually pass on from this world immediately, often due to beliefs that the longer you stay the harder it is to leave, and so there was no confusion about wether or not stuff should be handed to relatives or if the ghost can still keep them, etc.. I haven't really ironed the whole ghost thing yet fully, but I think ghosts are considered a non-person in the eyes of the law and have been for a long time (the decision of what to do with a dead person's possessions is up to the closest relatives or previous agreements made while alive), which there is and has been pushback against. After all, why should a person immediately leave, when their life might've been cut short of all the potential joys!?? Can't they hang onto their possessions for just a bit longer????

Magic

Is it really a fantasy world with merfolk and crazy weird animals if there’s no magic? 

Magic or applied physics as it is known formally, is, at its core, altering the physical world by changing the basal ideas behind everything. Or, that’s how it actually works! People in-universe don’t actually know that, so shhhh... all doing magic seems to require is a soul, so all kinds of sentient animals enjoy the added benefits of magic, including people. It’s an extremely handy way of doing work, making items, altering the self, anything really, the issue is that it’s also very hard! To perform magic, one needs to focus on the thing they want to change or make, and fully concentrate on it, feel it in their soul —  doing simple tricks is easier, but the more complicated you want something the trickier it becomes. It’s one thing to turn a brown toad blue (change the “brown” into “blue”) but it’s a whole other thing to change a brown toad into a blue, long-legged and bird-winged toad creature! The usual learning curve that people expect with other skills is much shallower and really kicks in much later with learning magic, so if you want to learn to be good at it, it pretty much ends up being your trade and life’s mission. Most people only know one or two “mandatory” spells and leave it at that. 

Fortunately it’s not all horribly inaccessible or an impossible skill to acquire. Magic is easier if you use phrases, items, symbols or do poses that help you return to the correct mindset and feeling — beginners are often taught “magic words” for this reason. Magic spells (long strings of magic that each does a specific thing, think code) can also be put into physical vessels and activated using much less demanding spells — sometimes no magic at all! Ironically the invention of electronic machines brought magic closer to the average person’s everyday life than ever before, even if people know less magic on average than centuries ago. 

And there you have it! Hopefully this serves more as an explanation for how certain things are rather than as further confusion (after all, I just revealed that there are powerful nonphysical beings in another realm), I will build upon this information more, you'll see! :D

[prebioticsoupconnesseuir]

Eukaryogenesis

Presently, it is understood that there are three domains of life. There is the eukarya, which is the domain consisting of the highest degree of complexity per cell and constitutes organisms such as plants, animals, and fungi. The other two are sub-branches of the prokarya, wherein the individual cells are less complex than the eukarya, and these are the bacteria and the archaea. Archaea, specifically, are a relatively new discovery (in terms of the scientific timescale) as their existence was first reported by Dr. Carl Woese in 1977.

Over time, the tree of life has undergone many changes, but the current most popular form is the below image, which was published in Nature Microbiology in 2016 and is based on 16S rRNA sequences (these ribosomal RNAs are ubiquitous in all life, and thus are a solid candidate for tracking evolutionary lineages)

There are two interesting features of this tree. The first is the upper right branch, which consists entirely of candidatus bacterial species. Candidatus indicates the the organism has been identified, but it has not been isolated and grown in a homoculture. Some species may never escape this category as it stands as some are obligate syntrophs, meaning that they cannot be grown without a co-culture that provides necessary nutrients. The second feature is the bottom right corner, in which the archaea and eukarya are located on the same arm, with the eukaryotes branching off just after the Asgard archaea.

An interesting feature of archaeal species is that they are a sort-of middle ground between the bacteria and the eukarya. What I mean by this is that, despite being prokaryotes like bacteria, they contain proteins that are more eukaryote-like. Additionally, the rRNA of some Asgard archaea actually contains elongation segments, something previously considered a trait exclusive to eukaryotes.

With these cursory points in mind, a current hypothesis for an aspect of eukaryogenesis (the origin of eukarya), specifically the aquisition of the mitochondria and/or the chloroplast, is that an archaeal species and a bacterial species were closely symbiotic to the point that the archaea engulfed the bacteria and fully incorporated it into its metabolism and replication cycle. This hypothesis is called "endosymbiosis."

Evidence for the mitochondria and chloroplast having their origins as bacterial species is the presence of a double membrane (one would have been the bacteria's, and one would have been the proto-eukaryote's), their own distinct ribosomes, and their own DNA.

How exactly this occurred is hotly debated, but two methods of engulfment include standard phagocytosis, and the other involves filaments of cytoplasm-containing membrane called "blebs" that could slowly build up around the symbiote. An example of the latter has been observed in the species Candidatus Prometheoarchaeum syntrophicum, strain MK-D1, which is an example of Lokiarchaeota (a subsection of the Asgard archaeota). In the paper "Isolation of an archaeon at the prokaryote-eukaryote interface" by Itachi et al. (2020), it was observed to grow blebs around its syntrophs, namely Halodesulfovibrio bacteria and Methanagenium archeaon.

As might be gathered by its classification as Candidatus, it was incapable of growth without its syntrophs due to an "incomplete" metabolism where the syntrophs covered the crucial gaps.

Based on their results, they proposed their own model for Endosymbiotic Eukaryogenesis, which they dubbed "Entangle, Engulf, Endogenize."

However, it is important to note that these cells were grown in optimized growth conditions. Originally, these cells came from a deep-sea sediment core, meaning that they are more accustomed to minimal nutrient conditions. As such, the optimized growth conditions may have resulted in the formation of these blebs as the cells struggled to self-regulate under overly nutrient-rich conditions. So, as always, more research would need to be done on these cells to make sure the bleb formation was not simply a side-product of lab growth conditions. Furthermore, this only accounts for one aspect of eukaryogenesis and does not account for the formation of the nucleus.

[stellernorth]

desert of maine, pituffik space base, mystery airship, eduardo saverin, ball screws, subculture, gävle goat, catherine princess of wales, rule against perpetuities, italian wolf, psycho (1960), tater tots, lokiarchaeota, chinese water torture, quebec city, list of mythological places, john darnielle, caving, tool use by non-humans, wojtek (bear), island of newfoundland, burial, Eurasian Steppe

[godsofhumanity]

I don't know if it's that interesting but I just found out there are bacteria (archaea) named after some nordic deities like Lokiarchaeota, Thorarchaeota, Baldrarchaeota and so on. And the whole group is called Asgard super group.

dude that's so cool!!!

[currentsinbiology]

The life of archaea

In 2015, researchers published the metagenome of a member of the Asgard group of archaea called Lokiarchaeota (A. Spang et al. Nature 521, 173–179; 2015). These are descended from an ancient lineage of archaea, simple cells lacking a nucleus and distinct from bacteria. This discovery was exciting because the genes were found to have similarities with those of eukaryotes — the group of organisms whose cells have nuclei and other structures, and which include plants, fungi, humans and other animals. That suggested a stronger connection between archaea and eukaryotes than had previously been thought.

[netmassimo]

An article published in the journal "Nature" reports a study on an archaeon called Candidatus Prometheoarchaeum syntrophicum, part of the proposed phylum Lokiarchaeota. A team of researchers took samples from the bottom of the Pacific Ocean near the Japanese coasts, managing to cultivate these Archaea contained in a special laboratory environment specifically created. Years of studies made it possible to separate various strains and to discover that some have long and branched protrusions, a feature that led the researchers to suggest that in the past a bacterium became entangled in similar protrusions becoming an organelle of what became over time a eukaryotic cell.

[mylokabrennauniverse]

"More reasons why I love Biology"

Today while I was studying for one of my final exams of my professorate I found it among my notes:

Lokiarchaeota or "Loki" is a proposed  phylum of the Archaea. Superphylum: Asgard or Asgardarchaeota is a proposed superphylum consisting of a group of uncultivated archaea that includes Lokiarchaeota, Thorarchaeota, Odinarchaeota, Heimdallarchaeota.

The Asgard superphylum represents the closest prokaryotic relatives of eukaryotes

The phylum includes all members of the group previously named Deep Sea Archaeal Group (DSAG), also known as Marine Benthic Group B (MBG-B). A phylogenetic analysis disclosed a monophyletic grouping of the Lokiarchaeota with the eukaryotes.

The analysis revealed several genes with cell membrane -related functions.

The presence of such genes support the hypothesis of an archaeal host for the emergence of the eukaryotes; the eocyte-like scenarios.

Lokiarchaeota was introduced in 2015 after the identification of a candidate genome in a metagenomic analysis of a mid-oceanic sediment sample. This analysis suggests the existence of a genus of unicellular life dubbed Lokiarchaeum.

The sample was taken near a hydrothermal vent at a vent field known as Loki's Castle located at the bend between Mohns/ Knipovitch ridge in the Arctic Ocean.

Translated: Lokiarchaeota, represents a missing link in the evolution of complex life. A transition from simple to complex cells

I love Biology!

[maureenlycaon]

There are clades of one-celled organisms named after Norse deities. Seriously. From the first sentence of this Wikipedia entry:

“Asgard or Asgardarchaeota[1] is a proposed superphylum consisting of a group of uncultivated archaea that includes Lokiarchaeota, Thorarchaeota, Odinarchaeota, Heimdallarchaeota.[2] The Asgard superphylum represents the closest prokaryotic relatives of eukaryotes.[3]“

[onesimovillalobos]

Uno de los pasos más importantes en esa escalera que es la historia de la evolución biológica tuvo lugar hace aproximadamente 2.000 millones de años, con la aparición de los primeros seres eucariotas: organismos unicelulares que contienen un núcleo diferenciado. De este primer linaje eucariota surgirían posteriormente todos los organismos superiores que conocemos en la actualidad, incluidos los hongos, las plantas y los animales. Sin embargo los orígenes y mecanismos que dieron lugar a la vida compleja tal y como la conocemos hoy en día, siguen velados por datos aún desconocidos para los científicos.No obstante, hace algunos años, los microbiólogos analizaron las secuencias de ADN de unos sedimentos marinos que arrojaron nueva luz sobre la incógnita. Dichos sedimentos fueron recuperados de un respiradero hidrotermal conocido como el Castillo de Loki -bautizado así por el dios nórdico del fuego- en el Océano Ártico. La secuenciación de las moléculas de ADN allí halladas revelaron que estas derivaban de un grupo de microorganismos previamente desconocido. Y aunque las células de las que se originó el ADN no pudieron aislarse y caracterizarse directamente, los datos mostraron que estaban estrechamente relacionadas con las arqueas, por lo tanto, los investigadores nombraron al nuevo grupo Lokiarchaeota.Las arqueas, junto a las bacterias, son los linajes más antiguos conocidos de organismos unicelulares. Sorprendentemente, los genomas de la Lokiarchaeota indicaron que podrían exhibir características estructurales y bioquímicas específicas de los organismos eucariotas. Esto sugirió que Lokiarchaeota podría estar relacionado con el último ancestro común de los eucariotas. De hecho, lo que el análisis filogenómico del ADN de Lokiarchaeota del Castillo de Loki sugería era una fuerte evidencia de que este nuevo grupo podía estar emparentado con uno de los descendientes de los últimos antepasados ​​comunes de los organismos eucariotas a de las arqueas a su vez.El profesor William Orsi, del Departamento de Ciencias de la Tierra y del Medio Ambiente de la universidad Ludwin-Maximilian de Munich, en cooperación con científicos de la Universidad de Oldenburg y el Instituto Max Planck de Microbiología Marina, han podido examinar directamente la actividad y el metabolismo de la Lokiarchaeota. Y los resultados de sus experimentos, los cuales se recogen en el artículo titulado Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments publicado recientemente en la revista Nature Microbiology, apoyan la relación sugerida entre Lokiarchaeota y eucariotas, y proporcionan pistas sobre la naturaleza del entorno en el que evolucionaron los primeros eucariotas.La hipótesis del hidrógenoEl escenario más probable para el surgimiento de eucariotas es que aparecieron resultado de una simbiosis en la que el huésped era una arquea y el simbionte era una bacteria. Según esta teoría, el simbionte bacteriano dio lugar posteriormente a las mitocondrias: los orgánulos intracelulares que son responsables de la producción de energía en las células eucariotas. Esto significa que los antepasados ​​de los eucariotas surgieron, de facto, directamente de las arqueas y no formaron un dominio separado en el árbol de la vida. De hecho Christa Schleper, profesora de la universidad de Viena y una de las autoras de los primeros estudios realizados sobre Lokiarchaeota, declaraba en el momento de su hallazgo que: "es como si acabáramos de descubrir los primates, es decir, los parientes más próximos vivos de los seres humanos, que también nos dan ideas interesantes sobre la naturaleza del último antepasado común. Sin embargo, el antepasado común de Lokiarchaeota y Eucariotas data de mucho más atrás, aproximadamente 2.000 millones de años".El escenario más probable para el surgimiento de eucariotas es una simbiosis en la que el huésped es una arquea y el simbionte una bacteriaUna hipótesis para explicar este paso evolutivo propone que el huésped arquea dependía del hidrógeno para su metabolismo, que el precursor -bacteriano- de la mitocondria metabolizaba. Esta "hipótesis del hidrógeno" plantea que las dos células asociadas presumiblemente vivían en un ambiente anóxico que era rico en hidrógeno, y si se hubieran separado de la fuente de hidrógeno se habrían vuelto más dependientes entre sí para sobrevivir, lo que podría conducir a un evento endosimbiótico. "Si los Lokiarchaeota, como descendientes de este supuesto arqueón o célula primordial, también dependen del hidrógeno, esto respaldaría la hipótesis del hidrógeno", explica Orsi. "Sin embargo, hasta ahora, la ecología de estas arqueas en su hábitat natural era una cuestión especulativa".Orsi y su equipo, ahora por primera vez, caracterizaron el metabolismo celular de Lokiarchaeota basándose en la información que se desprende de los núcleos de sedimentos obtenidos del fondo marino de una extensa región anóxica -sin oxígeno- en la costa de Namibia. Lo hicieron analizando el ARN presente en estas muestras. Las moléculas de ARN se copian del ADN genómico y sirven como planos para la síntesis de proteínas. Por lo tanto, sus secuencias reflejan patrones y niveles de actividad genética. Los análisis de las secuencia revelaron que Lokiarchaeota en estas muestras superaba a las bacterias entre 100 y 1000 veces. "Eso indica fuertemente que estos sedimentos son un hábitat favorable para ellos, promoviendo su actividad", comenta Orsi.De este modo el investigador y sus colegas pudieron establecer cultivos de enriquecimiento de Lokiarchaeota de las muestras de sedimentos en el laboratorio. Esto les permitió estudiar el metabolismo de estas células utilizando isótopos de carbono estables como marcadores. Los resultados demostraron que los microorganismos hacen uso de una red compleja de vías metabólicas basadas en el hidrógeno.Además, los datos confirmaron que Lokiarchaea, de hecho, usa hidrógeno para la fijación de dióxido de carbono. Este proceso mejora la eficiencia del metabolismo y permite que estas especies mantengan altos niveles de actividad bioquímica, a pesar de las condiciones de energía limitada de su hábitat natural anóxico. "Nuestra evidencia experimental es la hipótesis del hidrógeno para la primera célula eucariota", añade Orsi. "En consecuencia, los primeros eucariotas podrían haberse originado en sedimentos marinos ricos en hidrógeno y agotados en oxígeno, como aquellos en los que Lokiarchaeota moderna es particularmente activa hoy en día" concluye.

https://www.nationalgeographic.com.es/ciencia/lokiarchaeota-hipotesis-hidrogeno-y-surgimiento-celula-eucariota_15082

[sciencespies]

Evolution: A revelatory relationship

https://sciencespies.com/biology/evolution-a-revelatory-relationship/

Evolution: A revelatory relationship

A crane is used to deploy the rig used to recover sediment cores from the seabottom. Source: W. Orsi

A new study of the ecology of an enigmatic group of novel unicellular organisms by scientists from Ludwig-Maximilians-Universitaet (LMU) in Munich supports the idea hydrogen played an important role in the evolution of Eukaryota, the first nucleated cells.

One of the most consequential developments in the history of biological evolution occurred approximately 2 billion years ago with the appearance of the first eukaryotes—unicellular organisms that contain a distinct nucleus. This first eukaryotic lineage would subsequently give rise to all higher organisms including plants and animals, but its origins remain obscure. Some years ago, microbiologists analyzed DNA sequences from marine sediments, which shed new light on the problem. These sediments were recovered from a hydrothermal vent at a site known as Loki’s Castle (named for the Norse god of fire) on the Mid-Atlantic Ridge in the Arctic Ocean. Sequencing of the DNA molecules they contained revealed that they were derived from a previously unknown group of microorganisms.

Although the cells from which the DNA originated could not be isolated and characterized directly, the sequence data showed them to be closely related to the Archaea. The researchers therefore named the new group Lokiarchaeota.

Archaea, together with the phylum Bacteria, are the oldest known lineages of single-celled organisms. Strikingly, the genomes of the Lokiarchaeota indicated that they might exhibit structural and biochemical features that are otherwise specific to eukaryotes. This suggests that the Lokiarchaeota might be related to the last common ancestor of eukaryotes. Indeed, phylogenomic analysis of the Lokiarchaeota DNA from Loki’s Castle strongly suggested that they were derived from descendants of one of the last common ancestors of Eukaryota and Archaea.

Professor William Orsi of the Department of Earth and Environmental Sciences at LMU, in cooperation with scientists at Oldenburg University and the Max Planck Institute for Marine Microbiology, has now been able to examine the activity and metabolism of the Lokiarchaeota directly. The results support the suggested relationship between Lokiarchaeota and eukaryotes, and provide hints as to the nature of the environment in which the first eukaryotes evolved. The new findings appear in the journal Nature Microbiology.

The most likely scenario for the emergence of eukaryotes is that they arose from a symbiosis in which the host was an archaeal cell and the symbiont was a bacterium. According to this theory, the bacterial symbiont subsequently gave rise to the mitochondria—the intracellular organelles that are responsible for energy production in eukaryotic cells. One hypothesis proposes that the archaeal host was dependent on hydrogen for its metabolism, and that the precursor of the mitochondria produced it.

This “hydrogen hypothesis” posits that the two partner cells presumably lived in an anoxic environment that was rich in hydrogen, and if they were separated from the hydrogen source they would have become more dependent on one another for survival potentially leading to an endosymbiotic event. “If the Lokiarchaeota, as the descendants of this putative ur-archaeon, are also dependent on hydrogen, this would support the hydrogen hypothesis,” says Orsi. “However, up to now, the ecology of these Archaea in their natural habitat was a matter of speculation.”

Orsi and his team have now, for the first time, characterized the cellular metabolism of Lokiarchaeota recovered from sediment cores obtained from the seabottom in an extensive oxygen-depleted region off the coast of Namibia. They did so by analyzing the RNA present in these samples. RNA molecules are copied from the genomic DNA, and serve as blueprints for the synthesis of proteins. Their sequences therefore reflect patterns and levels of gene activity. The sequence analyses revealed that Lokiarchaeota in these samples outnumbered bacteria by 100- to 1000-fold.

“That strongly indicates that these sediments are a favorable habitat for them, promoting their activity,” says Orsi. He and his colleagues were able to establish enrichment cultures from the Lokiarchaeota in the sediment samples in the laboratory. This enabled them to study the metabolism of these cells using stable carbon isotopes as markers.

The results demonstrated that the microorganisms make use of a complex network of metabolic pathways. Moreover, the data confirmed that Lokiarchaea indeed use hydrogen for the fixation of carbon dioxide. This process enhances the efficiency of metabolism, and allows these species to maintain high levels of biochemical activity, in spite of the energy limited conditions of their anoxic natural habitat. “Our experimental evidence the hydrogen hypothesis for the first eukaryotic cell,” says Orsi. “Consequently, the earliest eukaryotes could have originated in oxygen-depleted and hydrogen-rich marine sediments, such as those in which modern Lokiarchaeota are particularly active today.”

Explore further

Biology of our ancient ancestor takes shape

More information: William D. Orsi et al, Metabolic activity analyses demonstrate that Lokiarchaeon exhibits homoacetogenesis in sulfidic marine sediments, Nature Microbiology (2019). DOI: 10.1038/s41564-019-0630-3

Provided by Ludwig Maximilian University of Munich

Citation: Evolution: A revelatory relationship (2019, December 27) retrieved 28 December 2019 from https://phys.org/news/2019-12-evolution-revelatory-relationship.html

This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no part may be reproduced without the written permission. The content is provided for information purposes only.

#Biology

[lokiinmediasideblog]

Tournament of Lokis: Round 1

May the Lokiest Loki win!

Propaganda:

Lokiceratops:

Lokiarachaeota:

[garudabluffs]

Even the human genome has been laterally invaded. Its sequencing has revealed the boggling reality that 8 percent of our human genome consists of viral DNA inserted sideways into our lineage by retroviruses. Some of those viral genes, as illuminated by a French scientist named Thierry Heidmann and his colleagues, have even been co-opted to function in human physiology, such as creating an essential layer between the placenta and the fetus during pregnancy. Ford Doolittle’s reticulated tree.

The Scientist Who Scrambled Darwin’s Tree of Life

How the microbiologist Carl Woese fundamentally changed the way we think about evolution and the origins of life.

(But) he is the most important biologist of the 20th century that you’ve never heard of.

“What made Woese the foremost challenger and modifier of Darwinian orthodoxy — as Einstein was to Newtonian orthodoxy — is that his work led to recognition that the tree’s cardinal premise is wrong. Branches do sometimes fuse. Limbs do sometimes converge. The scientific term for this phenomenon is horizontal gene transfer (H.G.T.). DNA itself can indeed move sideways, between limbs, across barriers, from one kind of creature into another.”

“The cells that compose our human bodies are now known to resemble, in telling ways, the cells of one group of archaea known as the Lokiarcheota, recently discovered in marine ooze, almost 11,000-feet deep between Norway and Greenland near an ocean-bottom hydrothermal vent. It’s a little like learning, with a jolt, that your great-great-great-grandfather came not from Lithuania but from Mars.”

“...The ribosome is a 3-D printer.” [ READER COMMENT “ The "tape reader" that Brenner was referring to was not an audio tape or videotape, but the punched paper tape that was used to communicate with the early computers. The programs and data were input on punched paper tape, and the output was punched by the computer.” I do agree that today the 3-D printer is the analogy that communicates. David Quammen used the analogy that was familiar in his growing-up years. }

“ Even the human genome has been laterally invaded. Its sequencing has revealed the boggling reality that 8 percent of our human genome consists of viral DNA inserted sideways into our lineage by retroviruses. Some of those viral genes, as illuminated by a French scientist named Thierry Heidmann and his colleagues, have even been co-opted to function in human physiology, such as creating an essential layer between the placenta and the fetus during pregnancy.”

Comments 266

“I'm afraid that the ribosome is actually more like a tape reader than a 3D printer. The "folding instructions" for a protein are essentially inherent in its linear sequence, and it folds spontaneously as it spools out of the ribosome. Finally, Woese fought the idea that eukaryotes were directly derived from Archaea, and would have hated the Lokiarchaeota concept, which I believe is correct and is one of the most exciting area of science today. No doubt I'll have further quibbles as I read the book, but from the reviews I've read it sounds like it gets things right.”

+ “The 1960 'insight' from Brenner and Crick is incremental, rather than revolutionary. In 1957, Crick gave a talk in which he postulated a continuous RNA template with instructions specifying the sequence of amino acids in a protein: "...the template would consist of perhaps a single chain of RNA."  (Crick, FHC. 1958. Symp Soc Exp Biol. 12: 138-163; quote from p. 156.). What was new in 1960 was that this was not part of the structure of the 'microsomal particle' (not yet given the name 'ribosome') and so the tape and the tape reader  (or the program and the computer...) were distinct.”

++ Ana Luisa Belgium Aug. 16  “For all those out there who like me felt disappointed when reading here that Woese had discovered something fundamental and then failed to see what more precisely because of the many anecdotes and lack of definitions in this article: fortunately Wikipedia writers have more pedagogical/vulgarizing talent than the author of this piece, so after having read their article about Archaea, here's an attempt to try to summarize Woese's discovery: - 4 billion years ago, for the first time there was water on planet earth - hundreds of billions of years later, the first living organisms were "born". They had only one single cell, so are called "unicellular organism". As they're very small, they're also called "microbes". - before Woese, those microbes were called bacteria (viruses don't have a cell structure, so aren't independent life forms) or prokaryotes, the predecessors of eukaryotes, unicellular organisms that have a nucleus, contrary to bacteria - eukaryotes then got together, forming multicellular organisms such as plants and later on mammals - Woese discovered that some bacteria actually had much more in common with eukaryotes than others, especially genetically, and put them in a new category, called "Archaea" - eukaryotes and archaea have a common ancestor X, and X and bacteria have a common ancestor Y

-contrary to what Darwin thought, the genome of microbes doesn't evolve in a linear way, as different "species" existing simultaneously intermingle. Is that it ... ?”

+++ “ Carl could not have known that co-evolution is a common way in which evolution occurs. Using this approach, the current Tree of Life is now portrayed somewhat differently (See supporting Figure 1 - https://onlinelibrary.wiley.com/doi/pdf/10.1002/bies.201800036). When evolution began in the Pre-cellular period the Euryarchaeta co-evolved with the Bacteria and the Crenarchaeota co-evolved with the Eukarya. This process likely ended when the oldest bacteria (the PVC – Planctomycetes- Verrucomicrobia – Chlamydia group) and the Eukarya developed nuclei which prevented access to the DNA of the Bacteria and the Eukarya. Thus, the archaea never became nucleated.” https://onlinelibrary.wiley.com/doi/abs/10.1002/bies.201800036 http://rsob.royalsocietypublishing.org/content/7/6/170041

This article is adapted from “The Tangled Tree: A Radical New History of Life,” published by Simon & Schuster.

... {we now know that roughly eight percent of the human genome arrived not through traditional inheritance from directly ancestral forms, but sideways by viral infection—a type of HGT.}

[surroundedbyselcouth]

Now THIS is the kind of content I expect to see in my scientific papers:

“Here we describe the ‘Asgard’ superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota” 

A+ microbe naming scheme.

[wildcat2030]

We Might Finally Have Found Where Complex Life Came From

See on Scoop.it - Knowmads, Infocology of the future

It sounds like something out of Norse mythology, but new evidence suggests that all complex life on Earth, including humans, might have evolved from Asgard - a large group of microbes that were once found all over the world. These microbes have been named Loki, Thor, Odin, and Heimdall, after the gods of Norse mythology, and a new study suggests that they could be part of the family tree from which we all evolved. These Asgard microbes might even be our oldest ancestors. The debate over how complex life started on Earth has been raging for centuries. On our planet, there are three kingdoms of life: bacteria, archaea (which includes thermophiles and other extremophiles), and eukaryotes. We belong to that third kingdom, the eukaryotes, along with all other multicellular life, including animals, fungi, and protists. Not only are eukaryotes more complex than the other two kingdoms, we're also a lot newer. While bacteria and archaea both seem to have arisen around 3.7 billion years ago - not too long after the planet was formed - it was roughly another 1.5 billion years or so before eukaryotes appeared, and no one is quite sure where they came from. The leading hypothesis is that, at some point, an archaea host took up a bacterium, and the symbiotic relationship between the two ultimately led to eukaryotes. That bacterium is suspected to belong to a class called alphaproteobacteria, which, over time, ended up becoming mitochondria - the 'powerhouse' of the cell. But, until recently, no one had any idea about the archaea species that swallowed this bacteria. And that's important, because the big, lingering, question is this: was it a primitive archaeon that took on the bacterium, or had the archaeon already become more complex? Was this symbiosis the cause of eukaryotism, or a consequence of it? That's an important question, because the answer will ultimately tell us where we came from. And we might finally be getting closer to figuring it out. The first clue came in 2015, when Thijs Ettema from Uppsala University in Sweden discovered a new type of archaean called Lokiarchaeota - or Loki for short - in sediment at the bottom of the ocean between Greenland and Norway. They didn't actually find any of these microbe cells themselves, but they discovered traces of its DNA at depths of 2,300 metres (7,545 feet), and an analysis of their genome revealed that they were the closest living relatives of all eukaryotes, as Ed Yong reports for The Atlantic. Then, last year, a team from the University of Texas in Austin found traces of DNA from a closely related archaeon, which they called Thorarchaeota (or Thor), in North Carolina. Now, in a paper published this week in Nature, a collaboration between Ettema, the Texan team, and other researchers from around the world, has found the DNA of even more of Loki's relatives in some of the most remote corners of the world, including Yellowstone National Park, deep-sea vents near Japan, and a hot spring in New Zealand.

[netmassimo]

Un articolo pubblicato sulla rivista “Nature” riporta uno studio su un archeo chiamato Candidatus Prometheoarchaeum syntrophicum, parte del phylum proposto Lokiarchaeota. Un team di ricercatori ha prelevato campioni dal fondo dell’Oceano Paficico vicino alle coste giapponesti riuscendo a coltivare questi archei contenuti in uno speciale ambiente di laboratorio creato appositamente. Anni di studi hanno permesso di separare vari ceppi e di scoprire che alcuni hanno sporgenze lunghe e ramificate, una caratteristica che ha portato i ricercatori a suggerire che nel passato un batterio sia rimasto impigliato in sporgenze simili diventando un organello di quella che col tempo è diventata una cellula eucariota.