[da capo] designates older posts that we reblog sporadically because we think they very special. We repost this one on this date with a very special Happy Birthday wish for Elio!   by Elio   There are days when I wish that the Woesian Three Domain scheme were wrong. Not that I would be happier if there were four or five or whatever number of domains. What would please me would be an escape from what I feel is an unnecessarily oppressive way of thinking, the seating of phylogeny (and its acolyte, genomics) alone at the head of the table. Why do I say this? Because as essential as ph ..read more

by Roberto   Altiarchaeum hamiconexum is a relatively recent addition to the growing list of microbial primary producers, i.e. those that fix CO2. Its first sightings date back to only a little more than twenty years and its ability to fix carbon was recognized only the last decade. And, as so many microbes, it has thus far resisted cultivation. Sensu stricto, I should be writing Candidatus Altiarchaeum hamiconexum. But I won't be so strict here, I'll forego the Candidatus business and simply call it A. hamiconexum.   Fig. 1. Biofilm droplets sticking to polyethylene nets. Bar = 0.5 ..read more

by Roberto   Fig. 1. Crew on the Woods Hole Oceanographic Institute research vessel Neil Armstrong prepare to deploy a sediment corer to the seafloor of the Puerto Rico Trench. (Photo by Paul Walczak, Oregon State University). Source Estimates are that, at the global scale, there are more microbial cells – maybe 5 x 1029 – in the seabed than in the water column above. These cells are not just near the seafloor, many of them they lie buried deep in the sediment. Very deep indeed, as deep as 2.5 kilometers. And they've been there for a long time, even millions of years (see here in STC). H ..read more

by Roberto   The three greenhouse gases that contribute most to global warming are carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O). There is, of course, an urgent need to reduce the emissions of all. However, two facts point to methane emission reduction as the most impactful in the near term. First, its half-life in the atmosphere (7−12 years) is much shorter than that of CO2, which can persist for hundreds of years. Second, because of its inherent physical-chemical properties, methane's global warming potential per unit mass is 80 times greater than that of CO2. Because mi ..read more

by Christoph   Last week I had in mind to write a short hommage to a venerable lab instrument, the flatbed chart recorder, but then the solar eclipse got in the way. More precisely, not the eclipse, but the map of the USA that went viral on social media, with the booking numbers for short-term rentals around April 8 as prominently visible markers for the large area where the total solar eclipse should be visible depending on weather conditions (Frontispiece).   Figure 1. Halley, E. & Senex, J. (1715). A description of the passage of the shadow of the moon over England as it was ..read more

by Christoph   When microbiologists describe a previously unknown bacterium, they are mainly interested in its lifestyle, metabolism, morphology and cell cycle (see part 1). For me, "getting to know" a newbie always involves – let's call it an addiction – reading its genome sequence and finding out how it initiates the replication of its chromosome(s) (see here in STC for the Lilliputians – formerly CPR bacteria, now Patescibacteria), here for Plancto­mycetota, here for Borrelia). This is particularly intriguing, of course, if it is the first characterized bacterium of an entire phy ..read more

by Christoph   The image is way too large to show it here, but when you join me and Hug et al. (2016) for "A new view of the tree of life" here in STC (or here in Nature, or in Wikipedia), you can spot a bunch of names of bacterial phyla in the top left corner that sound unfamiliar. One of those, Atribacteria, is at the top of the column with Aquificae, Calescamantes, ... , Fusobacteria. You can also see the phyla Dictyoglomi (now Dictyoglomota) and Thermotogae (now Thermotogota, the "-ota" suffix indicating the taxonomic phylum level) in this column, and Elio had a closer look at the en ..read more

    Contributed by Seth Bordenstein (@Symbionticism) on ? and Bluesky) What is the craziest thing a phage enzyme can do to eukaryotic hosts?       Do you want to comment on this post? We would be happy about it! Please comment on mastodon, Bluesky, or on ? (formerly Twitter ..read more

by Roberto   Fig. 1. Frontispiece of Coley's 1895 publication. Source. Frontispiece: Colorized scanning electron micrograph of Streptococcus pyogenes (yellow) and a human neutrophil (blue). Credit: NIAID. Source In the last few years, immunotherapy has quickly become the emerging "fourth pillar" in cancer treatment, joining surgery, radiation therapy and chemotherapy. The basic concept behind the development of immune checkpoint inhibitors as anti-cancer therapeutics is that activating the immune system can sometimes result in the body ridding itself of malignant cells. Such activation i ..read more

by Roberto   Elaborate mechanisms that protect bacteria against phage are well known, with CRISPR leading the way. Less familiar but equally fascinating is the fact that, somewhat unexpectedly, phages themselves sometimes offer bacteria protection in harsh environments. Filamentous phages do just that. I did quick search of STC posts on these phages and found just passing mentions, so a brief primer is in order because of their uniqueness. Can't really call them lytic or lysogenic. Rather, infected cells harbor the phage genomes (integrated in their chromosome or as plasmids) and continu ..read more