Another example of the parasitic Candidatus Nanohaloarchaeum antarcticus attached to its host, Halorubrum lacusprofundi.
Image Credit: Joshua N Hamm
The Bible is silent on the subject of microorganisms because they were unknown to the Bronze Age authors. But now we know better than them, we can see other ways in which they refute several basic creationist dogmas.
Firstly, there is the problem that creationists always struggle with when they don't avoid it altogether - that of parasites and how they fit into a world 'designed' by an omnibenevolent god who wishes to minimise the about of suffering in the world. More on this later…
Then the fact that archaea and bacteria could be different forms of life which arose independently showing that abiogenesis is not only possible but may have happened twice on Earth. And as they both have the same genetic 'code' this suggests that the 'code' was inevitable, not some special creation requiring a magician to produce it.
But that's a minority view; the consensus being that they have a common ancestor from which they diverged about 3.5 billion years ago.
Archaea are a fascinating group of single-celled microorganisms that constitute one of the three domains of life, alongside bacteria and eukaryotes. They were initially thought to be a type of bacteria due to their microscopic size and similar appearance under a microscope, but further research revealed significant differences between the two domains. Here are some key ways in which archaea differ from bacteria:Then there is the 'problem' that the first eukaryote cells may be the result of bacteria and archaea getting together in symbiotic relationship and we are all descended from that association when single-celled organisms evolved multicellularity and evolution took it from there.In summary, while archaea and bacteria share some superficial similarities, they are fundamentally different in terms of cellular structure, genetic makeup, metabolism, ecological niches, and evolutionary history. Studying archaea provides valuable insights into the diversity of life on Earth and the fundamental processes that sustain ecosystems.
- Cellular Structure: While archaea and bacteria are both single-celled organisms, archaea have unique cell membranes composed of branched hydrocarbon chains attached to glycerol by ether linkages, whereas bacteria have unbranched fatty acid chains attached to glycerol by ester linkages. This distinction is crucial and reflects differences in their biochemistry and evolutionary history.
- Cell Wall Composition: Archaeal cell walls are chemically distinct from those of bacteria. While bacteria typically have cell walls made of peptidoglycan, archaeal cell walls lack peptidoglycan and instead may contain pseudopeptidoglycan, S-layers, or other proteins. Some archaea lack a cell wall entirely.
- Genetic Makeup: Archaea have unique genetic characteristics that distinguish them from bacteria. For example, archaeal DNA replication, transcription, and translation machinery are more similar to those of eukaryotes than bacteria. Additionally, archaeal genes often contain introns, similar to eukaryotic genes, whereas bacterial genes generally lack introns.
- Metabolic Diversity: Archaea exhibit a wide range of metabolic capabilities, including methanogenesis (the production of methane), extreme halophily (thriving in high-salt environments), thermophily (thriving in high-temperature environments), and chemolithotrophy (obtaining energy from inorganic compounds). While some bacteria share these metabolic traits, archaea often have unique biochemical pathways.
- Ecological Niches: Archaea inhabit diverse environments, including extreme environments such as hot springs, salt flats, deep-sea hydrothermal vents, and acidic or alkaline environments. Some archaea are also found in more moderate environments like soil, oceans, and the digestive tracts of animals.
- Evolutionary History: Archaea and bacteria are believed to have diverged from a common ancestor over 3.5 billion years ago. Archaea are considered more closely related to eukaryotes than to bacteria based on genetic and biochemical evidence, suggesting a complex evolutionary history.
- Ecological Importance: Archaea play vital roles in various ecosystems, including nutrient cycling, carbon cycling, and symbiotic relationships with other organisms. For example, methanogenic archaea are essential for decomposing organic matter in anaerobic environments, contributing to the global carbon cycle.
And now, scientists have discovered a parasitic archaeon that manipulates its host to produce just the nutrients it needs to build its lipid cell membrane.
The fallback explanation used by creationists to explain parasites as not the malevolent design of their uniquely creative god, but the result of Biblical 'sin' allowing genetic entropy from their god's initial perfect design, causing organisms to 'devolve'. Why a perfect design would diversify, let alone devolve is anyone’s guess, but creationism isn't strong on logical thinking , or any sort of thinking for that matter.
But, in what sense is acquiring the ability to manipulate a host 'devolutionary', anyway? Biologically, anything which increases the fitness of an organism to live and breed in a given environment is evolution towards greater perfection and therefore not 'devolutionary' or a move away from some notional perfection - which creationists defined not biologically but arbitrarily as some assumed starting point at some assumed moment of magic creation out of nothing - when everything was perfectly fitted for its niche (so there was no pressure to change).
The discovery of these manipulative archaea was made by biologists at the Nederlands Instituut voor Onderzoek der Zee (Royal Netherlands Institute for Sea Research - NIOZ) , as described in a NIOZ news release and an open access research paper in the journal Nature Communications:
A parasite that not only feeds of its host, but also makes the host change its own metabolism and thus biology. NIOZ microbiologists Su Ding and Joshua Hamm, Nicole Bale, Jaap Sinninghe Damsté and Anja Spang have shown this for the very first time in a specific group of parasitic microbes, so-called DPANN archea. Their study, published in Nature Communications, shows that these archaea are very ‘picky eaters’, which might drive their hosts to change the menu.
Archaea are a distinct group of microbes, similar to bacteria [see box]. The team of NIOZ microbiologists studies the so-called DPANN-archaea, that have particularly tiny cells and relatively little genetic material. The DPANN archaea are about half of all known archaea and are dependent on other microbes for their livelihood: they attach to their host and take lipids from them as building material for their membrane, their own outer layer.
Picky eaters
So far, it was thought that these parasitic archaea just eat any kind of lipids from their host to construct their membrane. But for the first time, Ding and Hamm were able to show that the parasitic archaeon Candidatus Nanohaloarchaeum antarcticus does not contain all the lipids that his host Halorubrum lacusprofundi contains, but only a selection of them. “In other words: Ca. N. antarcticus is a picky eater”, Hamm concludes.
Archaea, bacteria and higher organisms
Archaea are single celled organisms that were long believed to be a specific group of bacteria. Similar to bacteria, they do not have a nucleus with dna, or other organelles within their cells. As of the 1970’s, however, microbiologists no longer consider archaea bacteria, but classify them as a separate domain in all life forms. So, now we have archaea, bacteria, and eukaryotes, the latter including all animals and plants, that have a nucleus with genetic material in their cells.
Host responds to parasite
By analyzing the lipids in the host with or without their parasites, Ding and Hamm were also able to show that the host responds to the presence of their parasites. The hosts change their membrane, not only which types of lipids and the amounts of each type that are used, but also modifying the lipids to change how they behave. The result is an increased metabolism and a more flexible membrane that is also harder for the parasite to get through. That could have some consequences for the host, explains Hamm. ‘If the membrane of the host changes, this could have an impact on how these hosts can respond to environmental changes, in for example temperature or acidity.”
Game-changing new technique
The game-changer in this microbiological research was the design of a new analytical technique by Su Ding at NIOZ. Thus far, to analyze lipids you needed to know what lipid groups you were looking for and target them in the analysis. Ding designed a new technique in which he can look at all lipids simultaneously, also the ones you don’t know yet. “We probably wouldn’t have been able to see the changes in the lipids if we had used a classical approach, but the new approach made it straightforward,” says Hamm.
New insight
The microbiologists are very excited about these new findings.
Not only does it shed a first light on the interactions between different archaea; it gives a totally new insight in the fundamentals of microbial ecology. Especially that we’ve now demonstrated that these parasitic microbes can affect the metabolism of other microbes, which in turn could alter how they can respond to their environment. Future work is needed to determine to what extent this may impact the stability of the microbial community in changing conditions.
Joshua N. Hamm, co-lead author
Department of Marine Microbiology and Biogeochemistry
NIOZ Royal Institute for Sea Research, Texel, The Netherlands.
AbstractOne day, if they don't want to be laughed at any more, creationists at Michael J Behe's and Stephen Mayer's Deception Institute are going to need to produce something better than their unintelligently designed genetic entropy/devolution nonsense to explain away parasites and so keep their dupes believing in intelligent [sic] design by an compassionate, all-loving god.
The symbiont Ca. Nanohaloarchaeum antarcticus is obligately dependent on its host Halorubrum lacusprofundi for lipids and other metabolites due to its lack of certain biosynthetic genes. However, it remains unclear which specific lipids or metabolites are acquired from its host, and how the host responds to infection. Here, we explored the lipidome dynamics of the Ca. Nha. antarcticus – Hrr. lacusprofundi symbiotic relationship during co-cultivation. By using a comprehensive untargeted lipidomic methodology, our study reveals that Ca. Nha. antarcticus selectively recruits 110 lipid species from its host, i.e., nearly two-thirds of the total number of host lipids. Lipid profiles of co-cultures displayed shifts in abundances of bacterioruberins and menaquinones and changes in degree of bilayer-forming glycerolipid unsaturation. This likely results in increased membrane fluidity and improved resistance to membrane disruptions, consistent with compensation for higher metabolic load and mechanical stress on host membranes when in contact with Ca. Nha. antarcticus cells. Notably, our findings differ from previous observations of other DPANN symbiont-host systems, where no differences in lipidome composition were reported. Altogether, our work emphasizes the strength of employing untargeted lipidomics approaches to provide details into the dynamics underlying a DPANN symbiont-host system.
Introduction
Members of the DPANN archaea, originally named after the initials of its first five identified groups (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota), are characterized by small cell and genome sizes1. Since their discovery, additional lineages such as Woesearchaeota2 and Pacearchaeota2, Huberarchaeota3, Micrarchaeota4, Altiarchaeota5, Undinarchaeota6, and Mamarchaeota7 have been identified and incorporated into the DPANN superphylum. These archaea are widely distributed in diverse environments, including hypersaline lakes8,9, marine6,10 and freshwater1,2 bodies, sediments11,12, acid mine drainage sites4, and hot springs13. Apart from Altiarchaeota, most DPANN archaea exhibit limited catabolic capabilities necessary to sustain a free-living lifestyle2,14 and the majority of them are predicted to rely on symbiotic interactions with other organisms14,15. Indeed, the few cultivated DPANN have symbiotic lifestyles, with representatives from three lineages (Nanoarchaeota, Nanohaloarchaeota, and Micrarchaeota) available in co-culture with specific host archaea9,13,16,17,18,19,20,21,22,23,24.
Due to incomplete biosynthetic pathways for nucleotides, amino acids, and lipids, most DPANN representatives are predicted to be dependent on metabolites from their hosts. Our current knowledge regarding the identity of those metabolites and the molecular basis for the exchange and/or uptake of these compounds is limited. Two DPANN representatives (i.e., Nanoarchaeum equitans and Ca. Micrarchaeum harzensis) are thought to acquire lipids from their hosts (Ignicoccus hospitalis25 and Ca. Scheffleriplasma hospitalis21, respectively). Lipid analyses of pure host and symbionts as well as symbiont-host co-cultures have revealed no significant qualitative difference in the lipid composition profiles between those cultures, indicating that the process of lipid uptake from the host is non-selective. However, it remains unclear whether non-selective lipid uptake from host organisms is a common feature among the various DPANN representatives.
In this study, we conducted a comprehensive analysis of the lipidome of the DPANN symbiont-host system consisting of Ca. Nanohaloarchaeum antarcticus – Halorubrum lacusprofundi9,26. Ca. Nha. antarcticus has so far not been obtained in a stable pure co-culture with Hrr. lacusprofundi (long term co-cultivation results in loss of Ca. Nha. antarcticus or death of the culture) and must be maintained in an enrichment culture (CLAC2B) containing multiple Hrr. lacusprofundi strains along with a Natrinema sp9. Recent work has shown that the instability of pure co-cultures may be due to Ca. Nha. antarcticus being a parasite that invades the host cytoplasm leading to host cell lysis26. Ca. Nha. antarcticus lacks identifiable genes encoding proteins involved in lipid biosynthesis and metabolism and is thus hypothesized to rely on lipids of its host for survival9. Through the investigation of the lipidome of Ca. Nha. antarcticus and its host, we aimed to (1) determine whether the lipids of Ca. Nha. antarcticus closely resemble those of the host or exhibit differences; and (2) assess potential changes in the host’s membrane lipid composition upon infection by Ca. Nha. antarcticus. Notably, our analyses reveal that Ca. Nha. antarcticus selectively takes up a specific set of lipids from its host. Moreover, in co-cultures, the lipidome composition undergoes changes that are likely compensating for an elevated metabolic load as well as enhanced mechanical stress on the host membrane.
Ding, S., Hamm, J.N., Bale, N.J. et al. Selective lipid recruitment by an archaeal DPANN symbiont from its host. Nat Commun 15, 3405 (2024). https://doi.org/10.1038/s41467-024-47750-2
Copyright: © 2024 The authors.
Published by Springer Nature. Open access.
Reprinted under a Creative Commons Attribution 4.0 International license (CC BY 4.0)
Examples such as this parasitic archaeon either evolving or being intelligently designed to exploit and control its hosts, give the lie to those creationist claims. Anything that could design such a thing is malevolent, not benevolent, and any process that could produce it is not 'devolutionary' or a move away from perfection in its environment, caused by 'genetic entropy', it is evolutionary, plain and simple, in classic Darwinian style.
The Unintelligent Designer: Refuting The Intelligent Design Hoax
ID is not a problem for science; rather science is a problem for ID. This book shows why. It exposes the fallacy of Intelligent Design by showing that, when examined in detail, biological systems are anything but intelligently designed. They show no signs of a plan and are quite ludicrously complex for whatever can be described as a purpose. The Intelligent Design movement relies on almost total ignorance of biological science and seemingly limitless credulity in its target marks. Its only real appeal appears to be to those who find science too difficult or too much trouble to learn yet want their opinions to be regarded as at least as important as those of scientists and experts in their fields.
Available in Hardcover, Paperback or ebook for Kindle
The Malevolent Designer: Why Nature's God is Not Good
This book presents the reader with multiple examples of why, even if we accept Creationism's putative intelligent designer, any such entity can only be regarded as malevolent, designing ever-more ingenious ways to make life difficult for living things, including humans, for no other reason than the sheer pleasure of doing so. This putative creator has also given other creatures much better things like immune systems, eyesight and ability to regenerate limbs that it could have given to all its creation, including humans, but chose not to. This book will leave creationists with the dilemma of explaining why evolution by natural selection is the only plausible explanation for so many nasty little parasites that doesn't leave their creator looking like an ingenious, sadistic, misanthropic, malevolence finding ever more ways to increase pain and suffering in the world, and not the omnibenevolent, maximally good god that Creationists of all Abrahamic religions believe created everything. As with a previous book by this author, "The Unintelligent Designer: Refuting the Intelligent Design Hoax", this book comprehensively refutes any notion of intelligent design by anything resembling a loving, intelligent and maximally good god. Such evil could not exist in a universe created by such a god. Evil exists, therefore a maximally good, all-knowing, all-loving god does not.
Illustrated by Catherine Webber-Hounslow.
Available in Hardcover, Paperback or ebook for Kindle
Illustrated by Catherine Webber-Hounslow.
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