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Da Bom: Best of Microbiology News Winter 2022

Welcome to another segment of the Da Bom, Da Best Of Microbiology. A lot has happened already in the first 90 days of 2022, but here we discuss only the exciting research that caught our eye. So read or listen on to learn about some exciting new research happening in the world!

In this microbiology research round-up we will discuss a new giant microbe, some wine news, what role fire plays in helping microbes get around, how bacteria can evade the immune system, and a sustainability superpower or Pseudomonas.

Extremophiles & Space ‘Crobes

The largest bacterium ever discovered has an unexpectedly complex cell

  • Original Article: A centimeter-long bacterium with DNA compartmentalized in membrane-bound organelles (bioRxiv preprint, Volland et. al.)

  • A new bacterial species have been found in the rotting leaves of Caribbean mangroves. It’s so big it can be seen by the naked eye, growing up to 2 centimeters long!

  • Unlike many other bacteria, it has a genome encased in a membrane instead of free-floating, and its genome has 11,000 genes which are 2-3X bigger than an average bacteria.

  • Some even say it may be a missing link in the evolution of complex cells.

  • The bacteria contains 2 membrane sacs, 1 containing DNA and 1 that is filled with water which may be the reason the bacteria can survive.

  • As an oversimplification, essential compounds for bacteria can diffuse easily in and out of the cell due to their size while bigger cells need organelles to ship compounds across the cell.

  • This water-filled sac encompasses 73% of the cell, pushing all the other contents within it to the edge of the cell. By doing so this diffusion can still easily occur.

  • The proposed name of the bacteria is Thiomargarita magnifica.

Food & Agriculture Microbiology

Improving Wine with a cocktail of microorganisms

  • Original Article: Investigations of the mechanisms of interactions between four non-conventional species with Saccharomyces cerevisiae in oenological conditions (PLoS One, Harlé et al.)

  • Saccharomyces cerevisiae has been used to make wine for a long time because it is good at converting sugar into alcohol.

  • Adding a different genus of yeast has been explored recently to improve the aromatic complexity and control alcohol content, but what are the optimal conditions to mix these?

  • A research team at Montpellier asked this and tested 4 new strains of yeast (2 from the genus Hanseniaspora and 2 from the genus Metchnikowia). Growing these alone and in combination with Saccharomyces cerevisiae.

  • Fermentation lasted 12.5 days and measured consumption of sugars and production of metabolites.

  • Only Saccharomyces cerevisiae finished fermentation with 0.1% of the sugars remaining while the other yeasts left 45-71% of the sugars, but indicators showed that, if left to, could finish fermentation.

  • Also, mixed cultures showed higher mortality in the cells, possibly due to the metabolites of 1 species being detrimental to another.

  • Mixed cultures also produced alcohol levels similar to the Saccharomyces cerevisiae monoculture and made more glycerol giving the wine a smoother texture.

  • In conclusion, Saccharomyces cerevisiae is more efficient at alcohol production, but the use of mixed cultures leads to a more favorable texture.

Environmental & Marine Microbiology

Wildland fire smoke alters the composition, diversity, and potential atmospheric function of microbial life in the aerobiome

  • Fires are a huge and growing problem around the world, especially in the western US. Five of California’s 10 largest wildfires on record happened in the horrific year of 2020. But these fires may be doing more than just burning millions of acres of land, destroying structures, and causing fatalities; they may also be transporting microbes to areas they do not belong.

  • Smoke samples collected from air samples during these fires contained 4x as many cells as smoke-free air and 78% of the cells were estimated to be still alive in the atmosphere.

  • This study estimates that 3.71X10^14 microbial cells per hectare are emitted by fires.

  • The main microbes they found included:

  • Actinobacteria

  • Bacteroidetes

  • Chloroflexi

  • Planctomycetes

  • Acidobacteria

  • Deltaproteobacteria

  • Archaea: Thaumarchaeota

  • Unsurprisingly, yet interesting, authors note that many of the microbes they found enriched in smoke are all associated with soil and plant microbiomes, with some being plant pathogens.

  • So, in the end, the authors have shown that smoke is a viable source of microbial dispersion. As wildfires continue to increase, we can expect these fires to move microbial populations to new territories which may have a detrimental effect on native wildlife and our crops.

Pathogen Profiles & Medical Microbiology

Intracellular bacteria use sophisticated ‘hack’ to evade a host’s immune system

Original Article: Virulence factors perforate the pathogen containing vacuoles to signal efferocytosis (Cell Host Microbe, Hiyoshi et al.)

  • UC Davis has discovered a signaling mechanism allowing species of Salmonella to evade death by the immune system.

  • Salmonella can infect macrophages and, in turn, trigger the death of the cell. Next, Salmonella tricks the immune system to deliver the bacteria to another macrophage.

  • But first, let's dive into a little background.

  • The complement system is part of the innate immune system, more specifically, it is a class of proteins that act on pathogens in a variety of manners depending on the pathway utilized.

  • Neutrophils - immune cells recruited by complement to go after bacteria.

  • Macrophages- actively engulf microbes, also part of the innate immune system.

  • Salmonella can survive in macrophages, living in a compartment within the cell. This allows the microbe to evade the rest of the immune system.

  • However, macrophages only live for 30 days, so Salmonella needs to find a new place to live.

  • To find a new home, Salmonella has virulence factors that create holes in both the membrane they live in and in the macrophage, causing the macrophage to die.

  • The holes activate the complement system which, in turn, attracts neutrophils that engulf the dead macrophage (a process called efferocytosis).

  • The macrophage corpse then protects the bacteria from the antimicrobial mechanisms (ROS) of the neutrophils.

  • This type of mechanism has also been seen in Brucella species.

  • This is interesting because science already knows of a method Salmonella kills macrophages, called pyroptosis, by secreting components of the flagella into the cytoplasm of the macrophages. Unfortunately for the bacteria, this ejects the microbe outside the cell, causing them to be attacked by the immune system.

  • To respond to this, Salmonella limits flagellar production and, instead, develops a survival mechanism utilizing efferocytosis.

Biotech & Microbial Products

Transcriptome Analysis Of Environmental Pseudomonas Isolates Reveals mechanisms of Biodegradation of Naphthenic Acid Fraction Compounds (NAFCs) in Oil Sands Tailings

  • Mining practices require copious amounts of water and, in turn, create large quantities of toxic wastewater. In this article, the toxins of interest were Naphthenic Acid Fraction Compounds or NAFCs. It is estimated there are some 700 billion liters of this toxic water floating around.

  • Treating this wastewater is difficult, but certain microbes have evolved to degrade this waste. Some of these microbes are Pseudomonas putida and Pseudomonas protegens. When the microbes worked together they were found to completely detoxify the water after 30 days!

  • The paper went beyond just profiling the genes or identifying the microbes in the wastewater. The researchers combined Genomics (understanding what the microbes are capable of) with transcriptomics (which is understanding what the microbes are doing in the environment) and metabolomics (what the microbes are producing in the environment). By combining all of these methods they are able to better understand what is the mechanism behind this superpower.

  • Researchers looked at each pseudomonas on their own and compared this behavior to how the microbe behaved when it was in the presence of the other. They found that the microbes behaved differently alone than together and how effective they were at detoxifying the wastewater was different for each situation.

  • Researchers found 17 pathways in Pseudomonas protegens but only 2 pathways in Pseudomonas putida that played a role in this degradation of the toxins when they were both placed in the toxic water together. Pseudomonas putida might be a bit of a freeloader, but they did do enough work to make the group project more successful than Pseudomonas protegens working on this task alone.

  • When researchers understand the mechanism, then they can start microbial engineering. In microbial engineering, scientists can harness this power of bioremediation and amplify it so that more wastewater can be detoxified faster!

Those were our picks! What do you think is the greatest microbiology discovery so far for 2021? Tell us in a comment below!

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