Retrospective, January to June 2025

by the STC Team
 

In keeping with tradition, here is the list of our posts from the last half year.

 

Odds & Ends

Is there a future for STC?  by Roberto — The short answer to that question is an enthusiastic YES! Of course, there is a future for STC, and I think it is bright. The long answer, well... that's what this post is all about. It requires that I give you the background story first.

Did organs precede organisms in the dawn of life?  by Fernando Baquero — We are commemorating the centennial of the first significant scientific hypothesis aimed at understanding the origin of life, published in 1924 by Alexander Ivánovich Oparin (1894-1980). The implicit message in this wonderful-to-read publication, but not expressed as such in the text, is that life arises in a kind of primordial soup of organic and inorganic molecules dissolved in hot water.

Defining Life with Aristotle  by Chelsi Cassilly and Eric Bodlak — What is life? Initially, it seems like a simple question. The immediate response is often to compare and contrast the many things we encounter daily that are animate and inanimate. Yet this question becomes harder the longer you sit with it. Because life on this planet – that is, life as we know it – includes microbial life.

© H. Imachi, M.K. Nobu, and JAMSTEC. Scan­ning elec­tron microscopy image of P. syntrophicum strain MK-D1. Source

Living Construction Materials  Noteworthy — The production of cement – used as a binder in concrete – has a high carbon footprint, accounting for 5%–8% of anthropogenic CO2 emissions. The search for alternative materials with reduced impact on global warming has come up with some interesting options.

The Remarkable Julian Davies  by Roberto — If I were asked to name scientists who have deeply influenced the evolution of my own thinking along the decades, there's little doubt that Julian Davies would be at the top of the list. Julian died this past February 2nd, shortly after turning 93.

Koyaanisqatsi  Noteworthy — Summer break for us is almost here. We'll post our January – June 2025 Retrospective next Monday and then its Summer Vacation for STC! As we end our first semester of "Noteworthy" post experiment we're straying off topic. We're drawing your attention to a film, and it is not a film about microbes.

Diversity, Diversidad, Diversität...  Noteworthy — We are living through interesting times, to say the least. Not long ago, though now it may feel that it's been eons, we could freely celebrate microbial diversity, biodiversity, structural diversity, diversity of opinions, diversity of interests and, yes, human diversity even!

 

Lost & Found

Lost & Found #3  by Christoph — If you want to leave 𝕏 (formerly Twitter) for any reason, you can deactivate or completely delete your account. That's it then. But if you want to take a few still interesting bookmarks with you when you move out, well, then the 𝕏odus takes a little longer. Here are three more of these salvaged bookmarks, in 'Lost & Found #3'.

Lost & Found #4  by Christoph — When you leave 𝕏 (formerly Twitter), it means that among the “bookmarks” you take with you, you will also come across some that contain images or videos that are mainly nice to look at and even entertaining. Two of these – no, none of the infamous cat pictures – are included today, in 'Lost & Found #4'

Lost & Found #5  by Christoph — When you leave 𝕏, it means that among the “bookmarks” you take with you, you will also come across some that contain images or videos that are mainly nice to look at and even entertaining. As in 'Lost & Found #4', two such are included today in 'Lost & Found #5'.

Lost & Found #6  by Christoph — In this episode, again three bookmarks that came to my attention while cleaning up our account on 𝕏 (formerly Twitter) and that are not at all out of date. Give them a brief look and judge for yourself. Here is Lost & Found #6. 

Lost & Found #7  by Christoph — As in 'Lost & Found #1–6', there are three bookmarks that caught my eye when I was cleaning up our account on 𝕏 (formerly Twitter). And which might still be worth a quick look for you, too, I hope, so here it is 'Lost & Found #7'.

 

Physiology & Genetics

Figure 1. Three rotating polystyrene beads attached to in­dividual flagellar motors on an E. coli cell. By Lucas Le Nagard

Bidirectional Plant–Bacterial Gene Exchange  Noteworthy — Plants interact with a broad range of commensal bacteria and often rely on these microbial partners for proper growth and development. In this study, Haimlich et al. analyzed genomes of the fast-growing plant Arabidopsis thaliana and members of its microbiome.

Bacterium Linked to Depression  Noteworthy — The human microbiome – the collection of microbes associated with our bodies – is variable, adapts to its host, but, most importantly, is increasingly recognized as important for our health and physiology. The sheer number and diversity of microbes, not to mention their interactions and activities, makes the study of the microbiome complex. How, then, can we understand what these microbes are doing?

Watching the flagellar motor at work  by Lucas Le Nagard — Swimming E. coli typically cover a distance equivalent to the radius of a human hair each second. It might not seem very impressive… But for a 2 µm bacterium, it corresponds to 10 body lengths per second! Much better than the swimming speed of our best athletes, which barely exceeds one body length per second. So, how does E. coli achieve this?

Wait, What? extracurricular DNA (eDNA)  by Christoph — Among biologists, DNA is a household term, the acronym for desoxyribonucleic acid, which hardly anyone pronounces in full. But can you find your way around the zoo of prefixes that are in use and in most cases are not separated from 'DNA' by a hyphen, as for example in Z-DNA? cccDNA, rcDNA (ocDNA), mtDNA, ecDNA, cDNA, bDNA, gDNA (chrDNA), kDNA, xDNA, rDNA, tDNA, ssDNA,… and eDNA.

Promising New Antimicrobials  Noteworthy — Amid the turmoil and uncertainty of our times, one fact is undeniable: microbes continue to evolve.

Pseudouridine Stabilizes tRNA  Noteworthy — The modified nucleoside pseudouridine has many reasons to be considered a star among post-transcriptional RNA modifications. It was the first to be identified, in 1960. Incorporating it into mRNA vaccines was a big reason for their success. And it also shows up in numerous antibiotics. Now there's more. 

Gene Location Matters  Noteworthy — Bacterial genomes are not a laundry list of genes, but dynamic structures intimately connected with cellular function. As a result, natural selection has a heavy hand in shaping chromosomal architecture – the position of genes within chromosomes – into configurations that best coordinate gene expression.

 

Symbioses

An Unusual Symbiosome  Noteworthy — This paper describes the highly evolved interactions between anaerobic protists and their syntrophic sulfate-reducing symbionts. Remarkably, the symbionts reside in an elaborate symbiosomal membrane network that places them adjacent to both the host's hydrogenosome and the extracellular milieu, where they can access sulfate. The physical properties of the symbiosome ensures the efficiency of this syntrophy.

Protections and Interactions in the Beewolf Nursery  by Tobias Engl — Beewolves, their larvae, and their Streptomyces symbionts not only use multiple, largely different classes of chemical compounds to protect themselves against detrimental microbial competitors. To be most effective, these compounds are produced and deployed in a precisely timed sequence. Beewolves are solitary digger wasps that hunt on bees, paralyze them and provision single eggs with...

Novel Fungus-Cyanobacterium Symbiosis  Noteworthy — Fungi are wonderfully diverse and versatile microorganisms. And it is perhaps this versatility that makes them so adept at forming symbiotic relationships with other organisms. Mycorrhizae or endophytic fungi, for example, inhabit plant tissues where they reside within or between plant cells.

 

Ecology

Timelapse light microscopy (LM) images show an Aureispira filament approaching V. campbellii  prey cells followed by rapid lysis of the prey. Scale bar, 5 µm. Source

Bdellovibrio–Prey Interactions  Noteworthy — The environmental bacterium Bdellovibrio bacteriovorus is unique in its capacity to prey and feed on other bacteria. This predatory behavior involves attaching and entering prey cells to consume and grow on cytoplasmic macromolecules, eventually lysing the host. But how do these bacterial predators recognize and invade their prey?

Enter the Pirates  by Christoph — Microbiologists know of only a small number of genuine rapacious bacterial species. In scientific terms, they are referred to as "predatory bacteria". Well-known examples are Myxococcus xanthus and its ilk, which practice "wolf pack" swarm hunting, and the more solitary vampires from the Bdellovibrio tribe. Enter the pirates with Captain Aureispira.

Our Built Environment Microbiomes  by Mechas — There is no doubt that our understanding of microbiomes – those microbial communities in practically any environment – has increased in recent years. Research now covers almost any conceivable niches, from cow rumen or the human gut, to numerous human-made ecosystems.

Anticipating Seasons  Noteworthy — While plants and animals can measure differences in the length of days and nights bacteria, with their short life spans, would not be expected to do so.

Of Aerobes and Anaerobes  Noteworthy — When first introduced to microbes, we quickly learn to divide them into aerobes and anaerobes. Then we qualify those titles with modifiers to yield such classes as facultative anaerobes, obligate aerobes and strict anaerobes.

CRISPR-Based Metabarcoding  Noteworthy — Microbes are abundant and very diverse. But acknowledging their significance in our biosphere has taken time and relied on curiosity, hard work, and the development of technologies to access, identify, and study microbial communities.

A Most Useful Light Switch  Noteworthy — Phytoplankton, photosynthetic microbes that inhabit surface ocean waters, form the base of marine food webs. These keystone microbes are the oceans' primary producers. Importantly, their ability to carry out photosynthesis depends on their ability to make chlorophyll.

 

Viruses

(click to enlarge)
Cryo-electron tomography and segmentation of phage 7-7-1 attached to Agrobacterium flagellum. (b) Example of long flexible fibers (white arrow) of a full-capsid phage 7-7-1, originating from the capsid vertices. (c) Occasionally, it can be observed that the flexible capsid fibers are connecting two phages (white arrow). (d) The interaction of two phage capsid fibers with the host flagellum (red arrows). (e) Two phages attached to the same flagellum (green arrows), further emphasizing the strong interaction between phage 7-7-1 and the host flagellum. (f) A volumetric representation of the tomo­gram subregion shown in e, with manual segmentation performed using IMOD. Scale bar: 50 nm. Source

Not a bad hair day for Phage 7-7-1  Noteworthy — While the phages χ and PBS1 attach to the flagella of their hosts via the tail fibers, phage 7-7-1 of Agrobacterium sp. H13-3 has another trick up its sleeve – or better: on its head (capsid). Noteborn et al. Found that phage 7-7-1 sports a bunch of dreadlocks on its head, proteinaceous fibers with which it attaches to host flagella.

Deep-Sea Viruses Wreak Havoc  Noteworthy — Absorbed in our daily activities and concerns, personal, local or global, we remain largely unaware of how life unfolds on this planet. Viruses, and especially those in our vast oceans, play a major life-defining role.

 

Evolution

Ancient Peptides to Combat Pathogens  Noteworthy — While many of our interactions with microbes are essential for our health, microbes are also well-known causes of diseases, such as the bubonic plague, that have decimated populations. We are, therefore, fortunate to count on antimicrobial drugs to eliminate harmful pathogens.

Cultivating the Ancestors… (1|4)  by Christoph — ...is a metaphysical affair across all human cultures. For experimental biologists, it is the more prosaic, physical task of cultivating extant prokaryotic relatives of the an­cestors of the eukaryotes in the lab. Or the 'most likely' ancestors of the eukaryotes, to be cautious when leaping back ~2 billion years in time. Now, meet the archaeon Promethearchaeum syntrophicum MK-D1, and its syntrophic companions.

Cultivating the Ancestors… (2|4)  by Christoph — Based on their knowledge of the morphology of P. syntrophicum MK-D1 from electron micro­scopy and their knowledge of its physiology from growth assays and genome analysis, Imachi, Nobu et al. (2020) propose a hypothetical model, the E3 model, of how the first evolution­ary steps towards eukaryogenesis might have occurred in an ancestral archaeon living ~2 billion years ago.

Cultivating the Ancestors (3|4)  by Christoph — There was joy, even excitement among archaeologists when the first images of Promethearchaeum syntrophicum MK‑D1 made the rounds. This sense of joy deepend still when images of its cousin Lokiarchaeon ossiferum Loki-B35 were added a little later. The ancestors suddenly got their own faces, literally, and were no longer only vaguely recognizable from genome sequences!

Cultivating the Ancestors (4|4)  by Christoph — Having one or two 'Asgard' archaea under the microscope – after having cultivated them with great effort and even more patience – and looking them in the face is exciting, but a bit unsatisfying if they are cousins. Are they mavericks or rather typical for "Lokis"? Here are the portraits of two more distant re­la­tives, both also cousins: Margulisarchaeum peptidophila HC1 and Flexarchae­um multipro­tru­sionis SC1.

Example of a phenol-red assay plate used to measure VHPO activity in supernatant samples from cultures of Curvularia and other fungal genera after 14 d growth. Wells E1–4 were blank while E5 contained buffer only. Well C3 shows VHPO activity from culture supernatant of fungal isolate 4388. Reactions were incubated for 24 h at 28°C. Source

Evolution of Ant-Fungus Farming  by Mechas — Agriculture has triggered enormous changes in human society. But it is not unique to humans.

Zombie Ants and the Evolution of Mind Control  by Clio Morata de Jong and Nico Morales — In the realm of natural mind control, few phenomena are as gripping – literally – as the death grip of the parasitic fungus in the genus Ophiocordyceps. This fungus doesn't just kill its carpenter ant hosts; it transforms them into instruments of fungal propagation.

 

Fungi

A Fungus that Reduces Methane Emissions  Noteworthy — We face unprecedented rising global temperatures, a crisis driven largely by the burning of fossil fuels. But other sectors, like the livestock industry, also contribute by producing large amounts of greenhouse gases.

 

Pathogens

Making a Living in the Nucleus  Noteworthy — When it comes to intracellular pathogens, we usually think of those that remain inside a membrane-enclosed vacuole and those that escape into the cytoplasm. Much rarer are cases of parasite that make a living inside the nucleus.