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#archaea

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Public
naturepoker

I've been reviewing state of ONT & PacBio #Archaea raw data availability in public repos (preprint coming soon). It's not fantastic.

Once we upload current reads, our warehouse & partner lab might be THE top uploader in the world in terms of diversity of Archaeal species contribution.

We're also covering both #ONT and #PacBio for each species - so 2x the count.

I'll also upload all ONT raws in blow5 format as well! Down with vendor lock-in.

#microbiology#bioinformatics
Public
naturepoker

Registration and booking done for #ASMicrobe2025 woot!

I'll be presenting a poster on methylation patterns of an Archaeal genus members with focus on their MGE & rrn operons. It's something I've been tinkering with at the warehouse lab in Queens, hopefully building up to something interesting

#microbiology #asmicrobe2025 #archaea #amateurscience

If anyone wants to talk shop on archaea, evolutionary microbiology, long-read sequencing and etc, drop me a note whenever!

Screenshot of ASMicrobe conference registration and booking confirmation for 2025
Public
Lukas VFN 🇪🇺

Newly discovered #microbes in Amazon peatlands could affect global carbon balance phys.org/news/2025-01-newly-mi

Functional insights of novel #Bathyarchaeia reveal metabolic versatility in their role in peatlands of the Peruvian Amazon journals.asm.org/doi/10.1128/s

"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."

Photo of a researcher in dirty shirt taking samples of mud in a lush tropical rainforest
#Archaea
Public
Lukas VFN 🇪🇺

#Microbes and #minerals: How microorganisms accelerate calcification marum.de/en/Microbes-and-miner

Marine #CarbonBurial enhanced by microbial carbonate formation at hydrocarbon seeps nature.com/articles/s43247-024

"#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."

underwater photo of mussels and pale crustaceans on the sea floor
Public
naturepoker

Morning train read for background on the ongoing project. This passage caught my attention:

"In other words, the r-protein counterpart of the last archaeal common ancestor was likely more complex than that of most of its descendent lineages"

Is this really a common agreement? I guess it makes sense, but extrapolation of the idea could lead to curious places.

#archaea #microbiology

pmc.ncbi.nlm.nih.gov/articles/

PubMed Central (PMC)Ribosome Biogenesis in ArchaeaMaking ribosomes is a major cellular process essential for the maintenance of functional ribosome homeostasis and to ensure appropriate gene expression. Strikingly, although ribosomes are universally conserved ribonucleoprotein complexes decoding ...
Public
Lukas VFN 🇪🇺

Advanced genetic techniques and #microscopy offer new insights into anaerobic ciliate and methanogen #symbiosis phys.org/news/2024-10-advanced

Methanogenic #symbionts of anaerobic #ciliates are host and habitat specific academic.oup.com/ismej/article #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"

electron and fluorescence microscopy pictures of complex microbial cells
#microbes#protists#bacteria
Public
Benjamin Carr, Ph.D. 👨🏻‍💻🧬

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
msn.com/en-us/weather/topstori

www.msn.comMSN
Public *
Nina Davtian

Over the past few years, I substantially contributed to the OH-isoGDGT #literature (Davtian et al., 2019 PALO; 2021 PALO; Davtian & Bard, 2023 PNAS), so I am overjoyed to highlight this new OH-isoGDGT #scientific #publication by Devika Varma et al. in #Biogeosciences @EuroGeosciences!
doi.org/10.5194/bg-21-4875-202
Disclaimer: I am not a co-author and I did not review this #paper either.
#Science
#ScienceMastodon #AcademicMastodon
#Archaea #Microbiology #Cultures
#Biomarkers #GDGTs #isoGDGTs

bg.copernicus.orgControls on the composition of hydroxylated isoprenoidal glycerol dialkyl glycerol tetraethers (isoGDGTs) in cultivated ammonia-oxidizing ThaumarchaeotaAbstract. Membrane lipids of ammonia-oxidizing Thaumarchaeota, in particular isoprenoidal glycerol dialkyl glycerol tetraethers (isoGDGTs) and hydroxylated isoGDGTs (OH-isoGDGTs), have been used as biomarkers and as proxies in various environments. Controlled growth experiments have been used to investigate the factors that influence the composition of these lipids, in particular on how these factors affect the TEX86 temperature proxy, which is based on the degree of cyclization of isoGDGTs. Recently, the ring index of OH-isoGDGTs (RI-OH′), based on cyclization patterns of OH-isoGDGTs, and the abundance of OH-isoGDGTs relative to summed abundances of OH-isoGDGTs and regular isoGDGTs (% OH) have emerged as promising temperature proxies. Here, we examined the impact of growth temperature and growth phase on the distribution of OH-isoGDGTs and their associated proxies using cultures of two thaumarchaeotal strains. Analysis of core lipids and headgroup compositions of isoGDGTs and OH-isoGDGTs showed no consistent differences between the mid-exponential and stationary phases for both strains. Nitrosopumilus adriaticus NF5 shows a substantially higher relative abundance of OH-isoGDGTs (∼ 49 %) compared to Nitrosopumilus piranensis D3C (∼ 5 %) and also relative to observations reported for core lipids in the marine environment (< 17 %), indicating large variations in % OH values even among closely related species. Unlike in the marine environment, the % OH did not decrease with increasing temperatures in either of the strains, possibly reflecting a threshold below 15 °C for this response in the natural environment. The RI-OH′ increases with increasing temperature in cultures of both strains, similar to the ring index of regular isoGDGTs. The relative abundances of the headgroups varied between strains and did not respond to changes in temperature or growth phase. The % OH and RI-OH′ calculated from intact polar lipids with different headgroups revealed large differences between the distinct intact polar lipids, similar to that previously observed for regular isoGDGTs. Together, our findings suggest that growth temperature has a pronounced effect on the degree of cyclization in isoGDGTs and OH-isoGDGTs, in contrast to the relative abundance of OH-isoGDGTs, which mainly exhibits interspecies variability.
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