Small Things Considered
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A blog for sharing appreciation of the width and depth of microbes and microbial activities on this planet.
Small Things Considered
17h ago
by Roberto
This post's title is taken directly from Arthur Kornberg's 1989 autobiographical chapter in Annual Reviews of Biochemistry. (For the uninitiated, Kornberg shared the 1959 Nobel Prize in Physiology or Medicine with Severo Ochoa "for their discovery of the mechanisms in the biological synthesis of ribonucleic acid and deoxyribonucleic acid." ) Arthur fell in love with enzymes early in his career and remained a devoted enzymologist all his life. To him, all enzymes, regardless of origin or function, were a source of excitement and certainly never ever dull. This memory of Arthu ..read more
Small Things Considered
2d ago
by Christoph
In the first part of this piece on phage–plasmids (P–Ps), I focused on examples that are well known today, and on the fact that they are representatives of larger families with dozens of members, rather than peculiar solitary cases. As a reminder, phage–plasmids transfer horizontally between cells as viruses and vertically within cellular lineages as plasmids. Here now, in the second part, I will introduce some lesser-known examples of phage–plasmids.
Cosmids Barbara Hohn and John Collins introduced the most widely used lab-constructed cosmid, pHC79, in ..read more
Small Things Considered
1w ago
by Christoph
Once you think again about horizontal gene transfer (HGT) and how genomic DNA can pass from one cell to another, you may soon feel quite medieval and ruminate «mille viae ducunt hominem per saecula Romam» (Alain de Lille (1128–1203) in his Liber Parabolarum). One of the main routes of chromosomal and extra‑chromosomal DNA (to Rome) is via transduction by bacteriophages, another via conjugation by plasmids, but there are other main roads too (see the recent post by Mechas and Roberto).
In the ancient Roman road network, there are secondary roads and the mai ..read more
Small Things Considered
1w ago
by Roberto
Fig. 1. Absolute change in Shannon diversity associated with travel to the eight most common travel destinations in the study. All box plots denote the median, interquartile range, and 95% quantiles. Significance was tested by t tests (paired except for between-group comparisons). Source. Frontispiece: International Airline Route Map. Source
Whether it is to attend meetings, carry out collaborative research, visit family, or simply explore exotic locations, scientists tend to do a lot of international travel (myself very much included). And one thing we do not want to exper ..read more
Small Things Considered
1w ago
[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
Small Things Considered
2w ago
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
Small Things Considered
2w ago
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
Small Things Considered
3w ago
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
Small Things Considered
3w ago
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
Small Things Considered
1M ago
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