Tag: Microorganism

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Bacteria by Dr. Dipika Mishra

Tiny and deadly
the cause of many diseases
and found in breezes.

by Dr. Dipika Mishra

Bacteria are small organisms that can be visualised through a microscope. Most of these tiny microbes are the causative agent of various diseases. Moreover, these organisms are found everywhere, from the surface of our hands to the air encompassing us.

Further reading:

‘Bacteria’, Wikipedia article: https://en.wikipedia.org/wiki/Bacteria

Author bio:

Dipika Mishra has a Ph.D. in Life Sciences and is a SciComm enthusiast. Her articles and poems can be found in “The Wire Science“, PLOS blogs, and Consilience journal. You can find her on X/Twitter here: @dipikamishra16

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Saba, the morning breeze by Dr Jolene Ramsey

We know you were small
Preying on Proteus too
Surprise, DNA!

by Dr Jolene Ramsey

Bacteriophages, or phages, are the viruses that infect bacteria. They come in different shapes and sizes, but are often icosahedral (spherical) and tailed. A tailed phage is structured like a filled lollipop, where the candy represents the phage head, the filling represents the nucleic acid genome, and the stick is like the tail. The overwhelming majority of phages scientists and students have discovered up to this point are tailed with a DNA genome, largely due to bias in our sampling methods. Recent investigations suggest many phages with RNA genomes remain to be isolated, and they were hypothesized to be small and round, similar to the ones that are already known. We want to find them.

In a very focused hunt, we looked for small RNA phages against the human opportunistic pathogen Proteus using a filtration selection method. After a few rounds of selection, there was a prime candidate that was definitely small, but it didn’t pass the other tests that define RNA phages. It was a puzzle. For clues, we looked at the phage shape in the electron microscope. To our astonishment the phage had a tail and a very small head! We immediately verified that it had a DNA genome as well. Though the search was a failure, we put phage Saba in the arsenal for use in other projects. To fully survey the diverse kinds of phage in the environment we will need to develop and refine targeted and general protocols for phage isolation. This will give us the most accurate picture of the phage universe.

Original research: https://doi.org/10.1128/MRA.01094-19

Jolene Ramsey studies bacterial viruses (phage) as a Center for Phage Technology postdoctoral researcher. She tries to understand how phages orchestrate their escape plan at the molecular level. You can catch up with her on Twitter: @jrrmicro

Enjoyed Jolene’s sciku? Check out her excellent sciku ‘Privateer, the phage’, ‘TF gets in on the bud’, ‘Click click go!’ and ‘The Phriendly Phage‘.

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The Phriendly Phage by Dr Jolene Ramsey

Phage are phriends, not phood
Not Phriendly to host, but nice
Plaques phor lab hunters

By Jolene Ramsey

Vibrio natriegens is an environmental microbe that naturally resides in marine habitats, including brackish waters and salty marshes. If you Google this bacterial species, all the top hits will tout its ‘fast’ growth. Unusual among bacteria, but common with other vibrios, V. natriegens has a  >5 Megabase genome split across two chromosomes. It also has a high count of total ribosomes, the cellular machines that make protein. As a non-pathogenic environmental organism, researchers are exploring its use in various biotechnology applications, including as a protein production system. This is one reason some are hoping V. natriegens will become the next lab workhorse in molecular and industrial microbiology that could even rival E. coli.

With an interest in improving the resources available to use in this field of research, we decided to look for bacteriophages that target V. natriegens. Bacteriophages, or phage, are the viruses that infect bacteria. Because phage rely so heavily on their host cell to copy themselves, they turn out to be extremely useful tools for probing how the cell works. As a kind of natural predator, phages can be found everywhere the host lives. The phage this Sciku is about, named Phriendly, was found in a sample collected by a college student brand-new to research on a trip to the beach.

The phage hunt process involves layering spots of environmental samples on top of growing bacteria, then looking for clear spots where the bacteria did not grow (or died due to infection) called plaques. A few of the beach samples yielded these plaques. One was a hazy, weak plaque that was difficult to propagate. We nicknamed it ‘problem phage’. In contrast, another had large, clear plaques that appeared quickly and consistently. We dubbed it the ‘friendly phage’. Following our cute tradition, we replace all ‘f’ sounds with the ‘ph’ used in the word phage to come up with the name Phriendly. Along with others, Phriendly is in a collection of phages we hope can be tools to better harvest the great potential its host microbe has for advancing biotechnology.

Original research: https://doi.org/10.1128/MRA.01096-19

Jolene Ramsey studies bacterial viruses (phage) as a Center for Phage Technology postdoctoral researcher. She tries to understand how phages orchestrate their escape plan at the molecular level. You can catch up with her on Twitter: @jrrmicro

Enjoyed Jolene’s sciku? Check out her excellent sciku ‘Privateer, the phage’, ‘TF gets in on the bud’, ‘Click click go!’ and ‘Saba, the morning breeze’.

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Click click go! by Dr Jolene Ramsey

Galaxy applied
Eyes scan Apollo data
To annotate phage

By Jolene Ramsey

Studying the genetic makeup of an organism helps us understand how they tick. Scientists often make precise notes about the position and function of important features within a genome, called annotation, akin to marking and reviewing the restaurants on a city map. Viruses tend to have smaller genomes, but they are packed with information. We annotate the genomes of bacteriophages, the viruses that infect and kill bacteria, to reveal their genetic secrets. While there are automated annotation programs, manual review by human eyeballs is necessary to ensure high quality outcomes. With the number of interesting new phage genomes rising daily, the need for user-friendly tools to analyze their genomes has grown as well.

Using our curated toolbox in an open-source, online bioinformatic portal called Galaxy (https://cpt.tamu.edu/galaxy-pub), features common to bacterial and phage genomes can be spotted and cataloged by novices and experts. There are many feature types, each one detected by a different tool. Instead of manually passing the genome through each tool, we are able to speed up and standardize the process using automatic pipelines that run a prescribed list of analyses. We can visualize the results in context using another linked platform called Apollo, and also compare to known genomes. The coupled Center for Phage Technology Galaxy and Apollo suite have allowed us to annotate >130 bacteriophage genomes, and train many students and researchers along the way.

Original research: https://doi.org/10.1371/journal.pcbi.1008214

Jolene Ramsey studies bacterial viruses (phage) as a Center for Phage Technology postdoctoral researcher. She tries to understand how phages orchestrate their escape plan at the molecular level. You can catch up with her on Twitter: @jrrmicro

Enjoyed Jolene’s sciku? Check out her excellent sciku ‘Privateer, the phage’, ‘TF gets in on the bud’, ‘The Phriendly Phage’ and ‘Saba, the morning breeze’.

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Privateer, the phage by Dr. Jolene Ramsey

What’s in the EM?
A crayon? A tailocin?
No, that’s Privateer!

By Jolene Ramsey

Proteus mirabilis is an opportunistic human pathogen, causing a large proportion of urinary tract infections. These infections are particularly severe in the elderly, and their treatment is recalcitrant to many antibiotics. There is great interest in using the natural predators of Proteus, their viruses (bacteriophages), to mitigate this issue. However, not many Proteus bacteriophage have been identified or characterized yet.

In our recent study (Corban & Ramsey, 2021), we describe a new phage called Privateer that infects and kills Proteus mirabilis. We first saw this phage in the electron microscope (EM) and noticed its unusual elongated head shape. Privateer has some interesting genes that seem to be common only among the closest related phages. Studies like these are the foundation for future applications combating multi-drug resistant bacterial problems.

Original research: https://doi.org/10.7717/peerj.10645  

Jolene Ramsey studies bacterial viruses (phage) as a Center for Phage Technology postdoctoral researcher. She focuses on their explosive escape from the host cell after a successful infection. You can catch up with her on Twitter: @jrrmicro

Enjoyed Jolene’s sciku? Check out her other sciku ‘Click click go!’, ‘TF gets in on the bud’, ‘The Phriendly Phage’ and ‘Saba, the morning breeze’.

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Wildfire’s Secrets

Hidden harm of smoke.
Microbial long-haul flights.
Lurking, infecting.

Wildfires cause huge amounts of long-term harm, including human, other animal and plant deaths, habitat loss, property and infrastructure destruction, the loss of carbon reservoirs and increased chances of flooding and landslides. Small airborne particles in smoke can be inhaled and cause fatal problems within the respiratory system, whilst the high levels of carbon monoxide produced can result in long-term brain damage, heart problems and even suffocation.

Yet researchers are revealing a new potential health threat as a result of wildfires – some microbes and fungi known to cause human infections are able to survive in the smoke plumes. Wildfires disturb soils causing these microbes to become airborne. Within the smoke the microbes ‘travel’ on particulate matter which is likely to protect them from ultraviolet radiation.

Kobziar & Thompson (2020) argue that the ability of microbes to survive in smoke plumes means that wildfires could play a role in geographical patterns of infection and that more research is needed to understand this threat. Particulate matter from wildfire smoke has been found to travel inter-continental distances. Those living close to wildfires, and even more so those firefighters working on the front lines are likely to be most at risk to such microbes – the US Centre for Disease Control has already stated that firefighting is an at-risk profession for coccidioidomycosis, a fungal infection also known as Valley fever.

The researchers argue that too little is currently known about microbe survival and spread in wildfire smoke. Essential questions remain, the answers to which will only be more important as the likelihood of wildfires increases as a result of climate change.

Original research: Kobziar & Thompson, 2020, Science, ‘Wildfire smoke, a potential infectious agent’ https://science.sciencemag.org/cgi/doi/10.1126/science.abe8116

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The year’s best species

Mystery protist.

Apes, snailfish and amphipods.

The year’s best species.

 

Every year since 2008 the College of Environmental Science and Forestry has released a Top 10 New Species list. 2018’s selection include single celled organisms, plants and animals (including two species of beetle) as well as a prehistoric marsupial lion identified from fossils. All 10 species are fascinating but those highlighted in the sciku are:

Protist – Ancoracysta twista, a single celled predatory Eukaryote with harpoon-like organelles that it uses to immobilise its prey. Intriguingly its evolutionary origins are unclear and it doesn’t fit neatly within any known groups.

Ape – Orangutans now come in three flavours: Bornean, Sumatran and now a newly identified Southern Sumatran species of orangutans. It is the most endangered great ape in the world.

Snailfish – Whilst snailfish are found at all depths, 2018’s species is the deepest fish in the sea, found in the Mariana Trench at 7,966 meters below the surface. It appears to be the top predator in its benthic community and is tadpole-like and around 4 inches long.

Amphipod – Epimeria quasimodo is found in the Antarctic Ocean. The 2 inch long crustacean takes its name from the hunchback of Notre Dame and has beautiful vivid colours.

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Patches on Venus

Patches on Venus:

Atmosphere harbouring the

conditions for life?

 

In the hunt for extra-terrestrial life, Venus is rarely considered due to the high surface temperatures (~465 °C) and the intense atmospheric pressure (92 times that on Earth). Yet a new study by Limaye et al (2018) suggests that life off the surface of the planet may be possible since the lower cloud layer harbours conditions suitable for microbial life: water, solutes, ~60 °C and an atmospheric pressure roughly equivalent to Earth.

What’s more, observations of Venus have revealed dark patches in the atmosphere that change shape, size and position over time. These are made up of particles roughly the same size as common Earth bacteria and also absorb light of at a similar spectrum. The changes in patch patterns could therefore be the equivalent of algae blooms.

Venus is thought to have once had water on its surface, potentially for as long as 2 billion years providing enough time for life to evolve. As the surface water evaporated the microorganisms could have been transported to the clouds, in similar ways to how bacteria have been found in the atmosphere of Earth (although on Earth aerial microbes do not appear to remain aloft indefinitely). Life on the second planet from the sun therefore remains a possibility and only further observations and potentially even atmospheric sampling will reveal whether the changing dark patches are indeed patterns of microbial life.

Original research: https://doi.org/10.1089/ast.2017.1783