About Acidithiobacilli taxonomy

As part of my visit/internship you could say? I don’t know, but I will be reading some papers regarding Acidithiobacilli taxonomy and classification. This is because I’ll be working on this for the next 6 months.

So, for starters, I do know about extremophiles, but this will be my first time working with them and their genomics. This is of course an exciting opportunity for doing some astrobiology after years of just babbling about it.

As a way to start doing some academia-related posts in this personal page, I’ll be doing my first post on these readings. And I’ll probably keep writing this stuff since it is a great way to remember and just get into the topic.

Ok, here come the papers:

A new view of the tree of life (Hug et. al. 2016)

Problem and Solution

So, this one is attempting to incorporate new criteria for the reconstruction of the tree of life. Why? Well, apparently with the current most beloved method (the small subunit ribosomal RNA), certain perspectives are lost to the untrained eye (like mine). Some questions regarding the diversity and structure of the tree remained (which makes me think what is a structre of a tree exactly? Are we only talking about the topology of it?). What the paper is arguing for is that the genome has a lot more to offer than we might think of, so it is natural to just step out of the standard approach with 16S.

The group has built a new tree of life making use of all genomes recovered from public repositories and 1011 newly reconstructed genomes that they recovered. From these genomes, they aligned and concatenated 16 ribosomal protein sequences from each organism. This is advantegous because these genes actually have a function, which means that there would be no artifacts from untranslated genes that might be under different evolutionary forces. I guess this is advantegous in the sense that evolution mainly affects the phenotype rather than the genotype. I mean, selection mainly works on the phenotype, right? Genotype is a derivatve of this pressure on the phenotype.

Another advantage is that they tend to be syntenic (which would allow it to be easily identifiable, right? Since it can be easily aligned, right? Idk, I’m trying to think over here) and they can be co-located (?) in a small genomic region in Bacteria and Archaea, reducing binning errors (?) that could perturb the geometry of the tree.

For the eukarya domain, it is still in dispute where to place it. The paper doesn’t attempt to do it, neither, but uses sequence-based approaches, based on nuclear-encoded ribosomal proteins. This basically classifies them based on their information-heritance rather than other more phenotypic approaches. This because the main attempt of the paper is to classify organisms that are difficult to approach via sight or physical descriptions, like archaea an bacteria.

Remarks

• The best support is found from the species to the class groups. A moderate-to-strong support is found in the Phyla group. The weaskest support is found in the deeper branches.
• Ineterestingly, the ribosomal tree has a deeper approach, since it includes organisms with incomplete or unavailable SSU rRNA gene and more strongly resolves the deeper branching. This gives a better resolution of the tree of life.
• Some compositional bias might be introduced because of the lifestyle of certain ribosomes, like halophilic, thermophilic and mesophilic lifestyles will present a different ribosomal composition.
• There is a new phyla that basically divides the Bacteria domain in 2. The phyla-group is denomined CPR (Candidate Phyla Radiation). It contains symbionts that have small genomes and restricted metabolic capacities in diverse degress. It is not clear if this is something that was lost in time or if it hints at an earlier version of metabolism.
• CPR presents a wide diversity, not seen in the Eukarya groups, for example, since it has a recent divergence from the other domains.

Questions here:

• What is a tree structure exactly? Are we talking about the topology?
• Is it beneficial for the genetic marker to be functional, since the phenotype is the one under the influence of selective pressure?
• What does it mean to be syntenic and co-located in a small genomic region?
• Exact difference on Figure 1 and 2.
• Do we currently consider this phyla?

Genomic evolution of the class Acidithiobacillia: deep-branching Proteobacteria living in extreme acidic conditions (Moya-Beltrán et. al. 2021)

Problem and Solution

Genus Acidithiobacillus now belongs to class Acidithiobacillia. However, since this reform of the clase, there has been no exploration of the class, in general. This paper presents a comparative genomic analysis of 100 genomes, thus trying to research further on the distinctions and important reminders about this class.

Remarks

Questions here: