Question for #archaea #microbiology #bioinformatics folks: I'm looking at a specific contig in an Archaeal genome with repeat elements that remain difficult to resolve even with 100~1000x coverage and minimum 10k read length.
Anyone else dealt with something similar? What could I even be looking at?
#ISEPpapers 26: October 2024 to March 2025 https://www.isep-protists.com/post/iseppapers-26
Your twenty-sixth digest of papers and preprints published by members of the International Society for Evolutionary Protistology is here!
The origin of the eukaryotic cell corresponded to the most significant increase in #complexity in the history of #life's evolution on Earth.
The billions of years that have passed since the fusion of an #archaea and a #bacteria have resulted in a lack of evolutionary intermediates in the phylogenetic tree until the emergence of the #eukaryotes.
Now researchers present theoretical and observational evidence that a phase transition in genetic complexity was involved.
https://phys.org/news/2025-04-evolutionary-algorithmic-phase-transition-billion.html
Received invitation to submit a review article to an established academic journal - it'll be on a topic adjacent to long read sequencing analysis and #Archaea
Not too bad for a warehouse worker sequencing out of an artists' studio, IMHO! I'm feeling pretty nervous though.
Any good resources out there for first-time review article writers?
Newly discovered #microbes in Amazon peatlands could affect global carbon balance https://phys.org/news/2025-01-newly-microbes-amazon-peatlands-affect.html
Functional insights of novel #Bathyarchaeia reveal metabolic versatility in their role in peatlands of the Peruvian Amazon https://journals.asm.org/doi/10.1128/spectrum.00387-24
"Under stable conditions, they enable #peatlands to act as vast carbon reservoirs, reducing #climate risks. However, environmental shifts, including drought and warming, can trigger their activity, accelerating #ClimateChange."
#Microbes and #minerals: How microorganisms accelerate calcification https://www.marum.de/en/Microbes-and-minerals.html
Marine #CarbonBurial enhanced by microbial carbonate formation at hydrocarbon seeps https://www.nature.com/articles/s43247-024-01960-0
"#Methane and other hydrocarbons are released from the #ocean floor at so-called cold seeps, forming the basis for ecosystems independent of sunlight. The basic process is methane oxidation without oxygen, which is carried out jointly by #archaea and #bacteria."
Advanced genetic techniques and #microscopy offer new insights into anaerobic ciliate and methanogen #symbiosis https://phys.org/news/2024-10-advanced-genetic-techniques-microscopy-insights.html
Methanogenic #symbionts of anaerobic #ciliates are host and habitat specific https://academic.oup.com/ismej/article/18/1/wrae164/7737421 #ISEPpapers by @joro
"This study provides a clearer understanding of how anaerobic ciliates have evolved a mix transmission mode to both maintain and replace their symbionts over time"
Scientists may have figured out why a potent #greenhousegas is rising.
Though it breaks down faster than #CO2, #methane is over 80 times as potent as carbon dioxide. It suddenly started increasing in atmosphere in 2007 — and in 2020, its growth rate doubled.
While scientists have suspected it was #naturalgas, researchers have new theory methane produced by microbes — mostly single-celled organisms called #archaea, which live in cow stomachs, wetlands & agricultural fields
https://www.msn.com/en-us/weather/topstories/scientists-may-have-figured-out-why-a-potent-greenhouse-gas-is-rising-the-answer-is-scary/ar-AA1ttGxX
Breathing deep: A metabolic secret of ethane-consuming #archaea unraveled https://phys.org/news/2024-10-deep-metabolic-secret-ethane-consuming.html
Ethane-oxidising archaea couple CO2 generation to F420 reduction https://www.nature.com/articles/s41467-024-53338-7
"Seeps on the deep seafloor naturally emit #alkanes, which are pollutants that are potentially dangerous to life. Fortunately, the sediments around the seeps host #microbes that act as a biological filter: They consume most of the alkanes before their release into the oceans and our atmosphere."
New Method Reveals Hidden Activity of Life Below Ground https://www.dri.edu/new-method-reveals-hidden-activity-of-life-below-ground/
Species-resolved, single-cell respiration rates reveal dominance of sulfate reduction in a deep continental subsurface ecosystem: Melody Lindsay et al. https://www.pnas.org/doi/10.1073/pnas.2309636121
"deep wells in the #DeathValley regional flow system provide windows into #subsurface environments... one of them contains several key #microorganisms that are only found in the deepest South African #GoldMines"
The parasitic lifestyle of an archaeal symbiont https://phys.org/news/2024-08-ancient-antarctic-microorganisms-aggressive-predators.html https://www.nature.com/articles/s41467-024-49962-y
The #archaea used in the study were collected from the cold and hypersaline Deep Lake in #Antarctica... #DPANN archaea are much smaller than other archaea, with very small genomes and limited metabolic capabilities... they depend on host #microbes to survive... This is the first time such aggressive behavior has been observed in archaea.
#Scientists publish first experimental evidence for new groups of #methane-producing organisms https://phys.org/news/2024-07-scientists-publish-experimental-evidence-groups.html #archaea #microbes
Cultivation and visualization of a methanogen of the phylum #Thermoproteota https://www.nature.com/articles/s41586-024-07631-6
Methyl-reducing #methanogenesis by a thermophilic culture of #Korarchaeia https://www.nature.com/articles/s41586-024-07829-8
Isolation of a methyl-reducing methanogen outside the #Euryarchaeota https://www.nature.com/articles/s41586-024-07728-y
#Microbes Likely Form #Magnetite in the South China Sea
https://eos.org/research-spotlights/microbes-likely-form-magnetite-in-the-south-china-sea
Methanogenic #Archaea as Catalysts for Magnetite Formation in Iron-Rich Marine Sediments https://agupubs.onlinelibrary.wiley.com/doi/10.1029/2023JB028312
"The team suspects that these microbes can reduce iron for energy, which triggers the formation of magnetite."
So sometimes you get these quick wins where suddenly everything works out. By combining my DNA and SQLite tooling, I was able to benefit from the sqlite *spelling* module to fuzzily identify common proteins. This one appears to be present in most #archaea and is only known as "DUF5786 family protein".
#Archaea can be picky eaters: Study shows a group of parasitic #microbes can change host metabolism
https://phys.org/news/2024-05-archaea-picky-eaters-group-parasitic.html
Selective lipid recruitment by an archaeal #DPANN symbiont from its host https://www.nature.com/articles/s41467-024-47750-2
"these parasitic microbes can affect the metabolism of other microbes, which in turn could alter how they can respond to their environment"
Happy to share the latest manuscript from our lab, in which we propose that eukaryotes evolved from a genomic chimera of Asgard archaea and giant viruses.
https://www.biorxiv.org/content/10.1101/2024.04.22.590592v1
This is a controversial topic, but we believe we have strong evidence to suggest a critical viral role in eukaryogenesis.
A Whiff of #Taxonomy – Altiarchaeum hamiconexum
https://schaechter.asmblog.org/schaechter/2024/04/a-whiff-of-taxonomy-altiarchaeum-hamiconexum.html by @STCmicrobeblog
"within its #biofilm... Individual coccoid cells are rather distant from each other. Yet they are connected by thin cellular appendages... the constant structure and size of these appendages define the distance between cells. The three-dimensional reconstruction of the appendage reveals a remarkable hook structure"
#FEMSmicroBlog: The incredible world of archaeal viruses
https://fems-microbiology.org/femsmicroblog-the-incredible-world-of-archaeal-viruses/
Review: Archaeal #virus entry and egress https://academic.oup.com/microlife/article/doi/10.1093/femsml/uqad048/7505774
"Archaeal #viruses have a broad range of morphologies, with many families showing unique shapes. In comparison to other viruses, most aspects of the infection cycles of viruses of #Archaea and their genomic features remain unexplored."
Prokaryotic single-celled organisms, the ancestors of modern-day #bacteria and #archaea, are the most ancient form of #life on our #planet, first appearing roughly 3.5 billion years ago.
The first #eukaryotic cells appeared around 1–1.5 billion years later.
However, eukaryotic cells have since diversified into many complex, #multicellular organisms that we see around us every day—#fungi, #plants and #animals—while prokaryotes have remained decidedly unicellular.
Extreme environments are coded into the #genomes of the organisms that live there https://theconversation.com/extreme-environments-are-coded-into-the-genomes-of-the-organisms-that-live-there-219072
Environment and #taxonomy shape the genomic signature of #prokaryotic extremophiles https://www.nature.com/articles/s41598-023-42518-y
"The expectation was that all the clusters would be along taxonomic lines: #bacteria grouped with bacteria, and #archaea grouped with archaea. To our great surprise, this was not always the case... The only obvious commonality was that they were heat-loving #extremophiles."
