DA BOM: Best of Microbiology: Spring 2021

Extremophiles & Space Microbes

A bacterium and an archaeon hand in hand: Microbites Contributing Author: Anais Biclot

Original Article: Flagellum Mediates Symbiosis - Takefumi Shimoyama, Souichiro Kato, Shuni’ichi ishii, Kazuya Watanabe

ThArtist: Alice van Helden (personal work, 15-04-2021), with kind permission from the author

Definition of Flagellum - it’s like a microscopic appendage. It's very slender and hair-like. It's predominantly used by protozoa, bacteria, and sperm to swim!

Definition of Archaea - like bacteria, archaea are single-celled microorganisms without a nucleus. So also like bacteria, they are what we call prokaryotes. There are three domains of life, Archaea, Bacteria, and everything else. They differ from bacteria in their cell walls and all in their DNA replication and translation machinery. In the tree of life, they are between Bacteria and Eukaryotes.

• Archaea can survive in very salty brines or breathe methane instead of oxygen; therefore, they are often referred to as “extremophiles”.

• In these extreme environments where archaea live, we can also find some species of extremophilic bacteria. Sometimes, they live in syntrophy: they cooperate at the level of nutrition to mutually benefit each other.

• In their study, Shimoyama and collaborators investigated the syntrophy between a bacterium called Pelotomaculum thermopropionicum (PT) and an archaeon named Methanothermobacter thermautotrophicus (MT).

• The bacterium PT is a fermenter: like yeasts we use it to produce beer or wine, it produces its energy by transforming sugar into alcohol in the absence of oxygen. On the other hand, the archaeon MT is a “methanogen”: it breathes carbon dioxide (as we breathe oxygen) to produce its energy and turns it into methane (as we turn oxygen into carbon dioxide).

• In this case, PT’s fermentation results in the production of carbon dioxide which is directly used by MT for his respiration.

• This is not uncommon, but here, it appears that PT attaches to MT via… its flagellum! Using its flagellum seems to have two roles: first to ensure proximity with its partner MT, and second to synchronize their metabolism.

• This synchronization is necessary because when PT is fermenting, it produces carbon dioxide which MT needs to use in a short matter of time, risking losing access to it.

• In conclusion, this situation between our bacteria and archaea is a good example of what biologists call “co-evolution”: on one side, evolution “shaped” PT’s flagellin to specifically attach to MT; on the other side, evolution “shaped” MT’s genes to be triggered by the adherence of PT’s flagellin present on the flagellum.

Food & Agriculture Microbiology

Scientists evolve a fungus to battle deadly honey bee parasite - Erik Stokstad

• Bees carry mites, called Varroa destructor, that can spread viruses throughout the colony. These mites have also been developing increasing resistance to pesticides.

• A new fungal strain, called Metarhizium brunneum, has been developed by researchers from the University of Washington to combat this mite. (This method of using microbes to treat insects is called biopesticide).

• The way this microbe works is that it lands on the mite and bores through its exoskeleton, growing throughout the mite's body and killing it.

• There was an initial problem though, the fungus could not grow in the temperatures of the beehive so the researchers had to put the fungus under different stressors (starve or hydrogen peroxide) to increase the microbes mutation rate. The fungal spores were then placed in an incubator that slowly raised the temperature to select for more heat-tolerant species (35C).

• Next, the researchers had to select fungi that were deadly to the mites. When you keep anything in captivity including microbes they can become less aggressive. In microbiology, we call this less virulent. The best way to increase virulence is to challenge the microbe to defend itself. They infected mites in a hive and harvested the fungus from the dead mites, repeating the process until the mite mortality went from 4% to over 60%! The fungus became more virulent!

• The overall efficacy still needs to be tested and the research team wants to develop more effective strains, but this is a step toward a safer treatment for bees.

Pathogen Profiles & Medical Microbiology

The Skin’s “frenemy” - Microbites Contributing Author: Tanine Daryoush

Original Article: Staphylococcus epidermidis protease EcpA can be a deleterious component of the skin microbiome in atopic dermatitis - Laura Cau, Michael R. Williams, Anna Butcher, Tissa Hata, Alexander Horswill and Richard Gallo

• Atopic dermatitis, commonly known as eczema, is a ubiquitous inflammatory skin disease. The root causes of eczema are unclear, and likely a consequence of the complex interplay between our genetics, environment, immune function, and skin microbes.

• S. epidermidis is commonly regarded as a crucial resident of healthy skin, acting as a symbiont- protective against severe skin infection. However, it has the potential to cause skin irritation as well. Thus a persistent challenge in the field is pinpointing the environments that favor S. epidermidis commensalism versus S. epidermidis pathogenicity.

• Researchers suspected that S. epidermidis was synthesizing molecules that were detrimental to skin integrity. Specifically, they examined the role of proteases, extracellular enzymes that chew up proteins. They identified the protease EcpA, which could degrade an essential skin barrier protein and skin-produced anti-microbial.

• To test the capacity of EcpA to disrupt the epidermal barrier, researchers colonized mouse skin with two distinct strains of S. epidermidis: one that makes EcpA, and one that does not. Only the S. epidermidis strain that produced EcpA could penetrate the skin barrier, driving skin damage.

• Interestingly, the gene that codes for EcpA is present in both commensal and pathogenic S. epidermidis strains, suggesting that there could be specific conditions that enable EcpA-mediated virulence.

• Our skin microbiome operates on a delicate system of checks and balances. Tipping the scales in one direction (i.e., too much of one bacterial species, too little of another, a decline in species diversity) could wreck havoc on normal skin functions and stoke immune responses.

Environmental & Marine Microbiology

A new letter in the genetic alphabet- Microbites Contributing Author: Anais Biclot

Original Articles: A widespread pathway for substitution of adenine by diaminopurine in phage genomes- Yan Zhou1,, Xuexia Xu, Yifeng Wei, Yu Cheng, Yu Guo, Ivan Khudyakov, Fuli Liu,Ping He, Zhangyue Song, Zhi Li1, Yan Gao1, Ee Lui Ang, Huimin Zhao,Yan Zhang1, Suwen Zhao

A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes-Dona Sleiman, Pierre Simon Garcia, Marion Lagune1, Jerome Loc’h, Ahmed Haouz, Najwa Taib, Pascal Röthlisberger, Simonetta Gribaldo, Philippe Marlière, Pierre Alexandre Kaminski

Noncanonical DNA polymerization by aminoadenine-based siphoviruses- Valerie Pezo, Faten Jaziri, Pierre-Yves Bourguignon, Dominique Louis, Deborah Jacobs-Sera, Jef Rozenski, Sylvie Pochet, Piet Herdewijn, Graham F. Hatfull, Pierre-Alexandre Kaminski, Philippe Marliere

• All DNA is made using the same alphabet, the four-letter code: A, C, T, G. These four nucleotides (Adenine, Cytosine, Thymine, and Guanine) make up the genetic code of all organisms.

• But in 1977, an anomaly was found. A bacteriophage (S-2L) that infects cyanobacteria were found to not have the letter A but a chemically-related nucleotide: diaminopurine or Z. DNA modifications are not uncommon, but here, the new letter completely replaced A in the phage DNA pairing with its complementary base T, while C still paired with G.

• However, it wasn’t until April 2021 that several scientific groups from France and China found the same “anomaly” in other bacteriophages, and were able to better characterize the mechanisms of the new biosynthesis pathway as well, as its implications (REF1, REF2, REF3).

• By studying how the new nucleotide is used in the different organisms, both Zhou and Sleiman’s groups looked at the synthetic pathways involved in the synthesis of Z and in more detail.

• Using several mutants, Sleiman and colleagues showed which enzymes were essential to synthesize the new nucleotide. They showed that purB* mutants had a lower infection efficiency, while ndk* mutants did not infect cells at all. These results highlight that these genes are needed for dZTP synthesis, and without them, phages cannot replicate.

• The latest study of Valerie Pezo and colleagues focused more on the DNA replication machinery. The question is: do these phages have a different DNA polymerase to incorporate ZTP when replicating their DNA? The study showed that the DNA polymerase found in organisms that use ZTPs were from 30 to 90 times more efficient at using ZTPs instead of ATPs. Conversely, E. coli’s DNA polymerase was about twice more efficient in inserting ATP when both ATP and ZTP were put in the cell. Therefore, it seems that these organisms do have a DNA polymerase optimized to use the new alphabet.

• What are the implications? Why did these viruses evolve this way? Zhou and colleagues believe it gives an evolutionary advantage to the phages by letting them evade host defenses, carried out by restriction enzyme attacks. Understanding this new alphabet could have a major impact on different fields such as making nanostructures from DNA, also called DNA origami, or in DNA-based data storage.

Biotech & Microbial Products

Researchers create a quantum microscope that can see the impossible - ScienceDaily Staff

• In a major scientific leap, University of Queensland researchers have created a quantum microscope that can reveal biological structures that would otherwise be impossible to see.

• The microscope is powered by the science of quantum entanglement, an effect Einstein described as "spooky interactions at a distance."

• "The best light microscopes use bright lasers that are billions of times brighter than the sun," Professor Bowen said, "Fragile biological systems like a human cell can only survive a short time in them and this is a major roadblock."

• "The quantum entanglement in our microscope provides 35 percent improved clarity without destroying the cell, allowing us to see minute biological structures that would otherwise be invisible.

• Australia's Quantum Technologies Roadmap sees quantum sensors spurring a new wave of technological innovation in healthcare, engineering, transport, and resources.

• "This breakthrough will spark all sorts of new technologies -- from better navigation systems to better MRI machines, you name it," Professor Bowen said.

Those were our picks! What do you think is the greatest microbiology News for this month? Let us know in a comment below!