Category Archives: Bacteria

Going deep with your guts full of microbes: a lesson from Chinese fish

by Piter Kehoma Boll

All around the world, many animal species have adapted to live in cave environments, places that are naturally devoid of light, either partially or entirely, and are, therefore, nutrient-poor habitats. The lack of light makes it impossible for plants and other photosynthetic organisms to survive and, as a result, little food is available for non-photosynthetic creatures. They rely almost entirely on food that enters the cave from the surface by water or animals that move between the surface and the depths.

Due to the lack of light in caves, animals adapted to this environment are usually eyeless, because seeing is not possible anyway, and white, because there is no need for pigmentation on the skin to protect from radiation or to inform anything visually. On the other hand, chemical senses such as smell and taste are often very well developed.

All these limitations make cave environments relatively species-poor when compared to surface environments. Or at least that is what it looks like at first. There are, of course, much less macroscopic species, such as multicellular animals, but those animals are themselves an environment and they may harbor a vast and unknown diversity of microrganisms inside them.

As you may know, most, if not all, animals have mutualistic relationships with microorganisms, especially bacteria, living in their guts. Those microorganisms are essential for many digestive processes and many nutrients that animals get from their food can only be obtained with the aid of those microscopic friends. The types of microorganisms in an animal’s gut are directly related to the animal’s diet. For example, herbivores usually have a high diversity of microorganisms that are able to break down carbohydrates, especially complex ones such as cellulose.

A recent study, conducted in China with fishes of the genus Sinocyclocheilus, compared the gut microbial diversity of different species, including some that live on the surface and some that are adapted to caves. All species of Sinocyclocheilus seem to be primarily omnivores but different species may have preferences for a particular type of food, being more carnivorous or more herbivorous.

The study found that cave species of Sinocyclocheilus have a much higher microbial diversity than surface species. But how can this be possible if there is a limited number of resources available in caves compared to the surface? Well, that seems to be exactly the reason.

Sinocyclocheilus microphthalmus, one of the cave-dwelling species used in this study. Photo extracted from the Cool Goby Blog.

As I mentioned, species of Sinocyclocheilus are omnivores. On the surface, they have plenty of food available and can have the luxury of choosing a preferred food type. As a result, their gut microbiome is composed mainly by species that aid in the digestions of that specific type of food. In caves, on the other hand, food is so scarce that one cannot chose and must eat whatever is available. This includes feeding on small amounts of many different food types, including other animals that live in the cave and many different types of animal and plant debris that reach the cave through the water. Thus, a much more diverse community of gut microorganisms is necessary for digestion to be efficient.

Look how the number of different genera of bacteria is much larger in the cave group (right) than in two groups of surface species (left and center). Image extracted from Chen et al. (2019).

More than only an increased diversity by itself, the gut community of cave fish also showed a larger number of bacteria that are able to neutralize toxic compounds of several types. The reason for this is not clear yet but there are two possible explanations that are not necessarily mutually exclusive. The first states that water in caves is renewed in a much lower rate than surface waters, which promotes the accumulation of all sort of substances, including metabolic residues of the cave species themselves that can be toxic. The second hypothesis is of greater concern and suggests that this increased number of bacteria that are able to degrade harmful substances is a recent phenomenon caused by an increase in water pollutants coming from human activities, which is promoting a selective pressure on cave organisms.

The diverse gut microbiome of cave fish is, therefore, a desperate but clever strategy to survive in such a harsh environment. Nature always finds a way.

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More on cave species:

Think of the worms, not only of the wales, or: how a planarian saved an ecosystem

Don’t let the web bugs bite

Friday Fellow: Hitler’s beetle

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Reference:

Chen H, Li C, Liu T, Chen S, Xiao H (2019) A Metagenomic Study of Intestinal Microbial Diversity in Relation to Feeding Habits of Surface and Cave-Dwelling Sinocyclocheilus Species. Microbial Ecology. doi: 10.1007/s00248-019-01409-4

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Friday Fellow: Bt

by Piter Kehoma Boll

With the current raise in genetically modified crops and all controversies around them, you probably heard about things such as Bt corn and Bt cotton. But do you know what Bt means?

Bt stands for Bacillus thuringiensis, and this is going to be our fellow for today. A Gram-positive bacterium, Bt is found in many environments, including the soil, the surface of several plants and in the gut of several species of caterpillars. Belonging to the large and heterogeneous genus Bacillus, Bt is very closely related to, and sometimes considered as being of the same as, Bacillus cereus, which can can foodborne illness, and Bacillus anthracis, the species that causes anthrax. The main differences between these three species relies on their plasmids (small DNA pieces in a bacterium’s cytoplasm), while the genetic composition of their chromosome is basically the same.

Colonies of Bacillus thuringiensis growing on sheep blood agar.

As all species of Bacillus, Bt can sporulate, i.e., convert itself into a dormant form called endospore (sometimes wrongly named spore) when environmental conditions are not favorable. During sporulation, Bt forms crystals of delta-endotoxins, a proteinaceous inseticide also named crystal proteins or cry proteins. Cry proteins are encoded by cry genes, which are located in plasmids and not in the bacterial chromosome. When insects and nematodes ingest those crystals, they are denatured in the alkaline environment of the animal’s gut and become soluble. In soluble phase, the crystals are digested and liberate their toxins, which then paralyze the digestive tract and make the animal starve to death. The number of different cry proteins in Bt is really large, indicating a yet unknown selective pressure to the development of such a sophisticated defense mechanism.

Gram-stained colony of Bt under a 1000 X magnification. Photo by Wikimedia user Dr. Sahay.*

Due to this strong insecticidal effect, Bt endospores and cry proteins have been used to control insect pests during the last century. The insecticide is usually applied as a spray and can be bought under different trademarks. However, because of natural selection, the pests end up developing resistance to the toxins and new strains of Bt are constantly produced to originate newer varieties of the insecticide.

Since the 1980s, there have been studies on the production of genetically modified organisms that incorporate Bt genes responsible for the production of cry proteins. Currently, the two most widely cultivated genetically modified crops containing Bt genes are Bt corn and Bt cotton. The cry genes of Bt have been introduced in the DNA of these species, allowing them to synthesize cry proteins. When an insect eats the leaves of such plants it ingests the crystals and dies as if it would have eaten the spores of Bt. And in fact, that is what happened. The introduction of Bt corn, for example, strongly reduced the attack of several corn pests, such as the corn borer.

Although the use of Genetically Modified Organisms (GMOs) is still seen as bad by many people, most studies have shown that they are relatively safe compared to many other human-interference activities. Bt corn and Bt cotton were shown to be safe for non-targeted organisms and to the environment as a whole. The main problem with GMOs is the fact that the technology to produce them lies in the hands of giant profit-maker companies.

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References:

Helgason, E.; Økstand, O. A.; Caugant, D. A.; Johansen, H. A.; Fouet, A.; Mock, M.; Hegna, I.; Kolstø, A.-B. (2000) Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis — One species on the basis of genetic evidence. Applied and Environmental Microbiology, 66(6): 2627–2630. doi:
10.1128/AEM.66.6.2627-2630.2000

Schnepf, E.; Crickmore, N.; Van Rie, J.; Lereclus, D.; Baum, J.; Feitelson, J.; Zeigler, D. R.; Dean, D. H. (1998) Bacillus thuringiensis and its pesticidal crystal proteins. Microbiology and Molecular Biology Reviews, 62(3): 775–806.

Wikipedia. Bacillus thuringiensis. Available at < https://en.wikipedia.org/wiki/Bacillus_thuringiensis >. Access on December 28, 2018.

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Friday Fellow: Alder-Root Bacterium

by Piter Kehoma Boll

The success of many plant species wordlwide is the result of their association with different organisms in their root systems, such as fungi and bacteria. Among bacteria, the most widely known group of root-associated species is that of the so-called rhizobia, bacteria that are associated with the root of legumes (plants of the family Fabaceae).

However, this kind of association evolved independently many times in many lineages of plants and many lineages of bacteria. Today I’ll present you a bacterium that is not closely related to the rhizobia, but acts similarly. Known scientifically as Frankia alni, it does not have a common name, but I decided to call it the alder-root bacterium.

As both its scientific name and its brand-new common name imply, the alder-root bacterium is a species associated with the roots of trees in the genus Alnus, commonly known as alder in English. It belongs to the phylum Actinobacteria and the order Actinomycetales, having a filamentous growth that produces a structure similar to the mycelia of fungi.

750px-hypha_and_vesicle_of_franikia

The hyphae that form the mycelium of Frankia alni. Photo by Wikimedia user Kkucho.*

The bacteria do not penetrate the cell membranes of the host plant at first, but remain inside a structure that develops from the plant cell wall. From there, they stimulate cell division and the production of nodules that grow from the rooth and inside of which they migrate, entering the nodule’s cells.

800px-frankia_alni

A nodule caused by Frankia alni on the root of an alder species. Photo by Gerhard Schuster.*

Through a complex biochemical process that I won’t present here in detail, the alder-root bacteria can capture nitrogen from the atmosphere and synthesize aminoacids from it, part of which is shared with the host. As a result, alder trees that contain nodules of alder-root bacteria are able to grow in nitrogen-poor soils and eventually enrich that soil and allow other plants to establish.

750px-sporangium_of_frankia

Sporangia of Frankia alni. Photo by Wikimedia user Kkucho.*

In order to disperse themselves through the environment and find new hosts, the alder-root bacteria produce spores inside sporangia. Once released, the spores may migrate, probably through water, to new localities where they germinate and restart the cycle.

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References:

Benson, D. R.; Silvester, W. B. (1993) Biology of Frankia strains, actinomycete symbionts of actinorhizal plantsMicrobiology and Molecular Biology Reviews 57(2): 293–319.

Wikipedia. Frankia alni. Available at: < https://en.wikipedia.org/wiki/Frankia_alni >. Access on March 13, 2018.

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Friday Fellow: Hay bacillus

by Piter Kehoma Boll

Today we’ll return to the tiny world of the bacteria once more. And I guess it is a good time to introduce another celebrity from the bacterial world, the hay bacillus or grass bacillus, Bacillus subtilis.

579px-bacillus_subtilis_colonies

Several colonies of Bacillus subtilis on agar. Photo by Wikimedia user Debivort.*

As any typical Bacillus, the hay bacillus has rod-shaped cells, hence the name. They measure about 4–10 µm in length and 0.25–1.0 µm in diameter and have many flagella, so they can move quickly in a liquid medium. The natural habitat of the hay bacillus is the soil, but it can also be found in the intestine of mammals, including humans.

As it is common among the members of the phylum Firmicutes, the hay bacillus is able to enter in a dormant form called endospore that is able to tolerate extreme environmental conditions. They can survive in this form for decades, centuries, perhaps even millenia, until the conditions are adequate again.

bacillus_subtilis_spore

Microscopic image showing vegetative (red) and endospores (green) of Bacillus subtilis. Photo by Wikimedia user Y tambe.*

The hay bacillus is one of the most studied and cultivated bacterium in the world, being considered a model organism. In East Asia, one of its varieties is used in the production of the Japanese traditional food nattō. Before the introduction of antibiotics, it was common to use cultures of B. subtilis in treatments to improve immunological responses. Currently, it is used in laboratory studies focused on the formation of endospores and the phenomenon of transformation, a process by which a bacterium can capture DNA from the medium in which it is and incorporate it into its own genetic material. Additionally, it is used to produce a variety of substances, including naturally produced antibiotics.

Our fellow is indeed a good friend for us.

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References:

Anagnostopoulos, C.; Spizizen, J. (1961) Requirements for transformation in Bacillus subitilisJournal of Bacteriology81(5): 741–746.

Stein, T. (2005) Bacillus subtilis antibiotics: structures, syntheses and specific functions. Molecular Biology56: 845–857. https://dx.doi.org/10.1111/j.1365-2958.2005.04587.x

Wikipedia. Bacillus subtilis. Available at < https://en.wikipedia.org/wiki/Bacillus_subtilis >. Access on November 9, 2017.

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Friday Fellow: H. pylori

by Piter Kehoma Boll

I already introduced three species of bacteria here, all of them free-living and/or friendly little ones. But we all know that many bacteria can be a real annoyance to us humans, and so it’s time to show some of those, right?

I decided to start with one that I thought to have living inside me some time ago (but it happened that I don’t), and this is the ill-tempered Helicobacter pylori, which as usual lacks a common name, but is commonly called H. pylori for short by doctors, so that’s how I’ll call it.

empylori

Electron micrograph of a specimen of H. pylori showing the flagella.

The most common place to find the H. pylori is in the stomach. It is estimated that more than half of the human population has this bacterium living in their gastrointestinal tract, but in most cases it does not affect your life at all. However, sometimes it can mess things up.

H. pylori is a 3-µm long bacterium with the shape of a twisted rod, hence the name Helicobacter, meaning “helix rod”. It also has a set of four to six flagella at one of its ends, which make it a very motile bacterium. The twisted shape, together with the flagella, is thought to be useful for H. pylori to penetrate the mucus lining the stomach. It does so to escape from the strongly acidic environment of the stomach, always penetrating towards a less acidic place, eventually reaching the stomach epithelium and sometimes even living inside the epithelial cells.

In order to avoid even more the acids, H. pylori produces large amounts of urease, an enzyme that digest the urea in the stomach, producing ammonia, which is toxic to humans. The presence of H. pylori in the stomach may lead to inflammation as an imune response of the host, which increases the chances of the mucous membranes of the stomach and the duodenum to be harmed by the strong acids, leading to gastritis and eventually ulcers.

The association between humans and H. pylori seem to be very old, possibly as old as the human species itself, as its origin was traced back to East Africa, the cradle of Homo sapiens. This bacterium is, therefore, an old friend and foe and it will likely continue with us for many many years in the future.

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References:

Linz, B.; Balloux, F.; Moodley, Y. et al. (2007) An African origin for the intimate association between humans and Helicobacter pyloriNature 445: 915–918. https://dx.doi.org/10.1038/nature0556

Wikipedia. Helicobacter pylori. Available at < https://en.wikipedia.org/wiki/Helicobacter_pylori >. Access on August 5, 2017.

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Friday Fellow: Conan the Bacterium

ResearchBlogging.orgby Piter Kehoma Boll

Most people would agree that 2016 was a hard year. So let’s try to make 2017 better by starting this year with a tough Friday Fellow, actually the toughest of them all: Conan the bacterium, or Deinococcus radiodurans.

A relative of Taq, Conan the bacterium is a rather large bacterium, measuring 1.5 to 3.5 µm in diameter and usually forming groups of four organisms sticking together, a formation known as tetrad. It is an extremophilic bacterium, able to resist to very harsh environments. Actually, Conan the bacterium is one of the most radiation-resistant organisms known to date and can also resist extremes of cold, dehydration, vacuum, and acid. Its popular name was based on the character Conan the Barbarian.

deinococcus_radiodurans

A tetrad of Deinococcus radiodurans.

Conan the bacterium was discovered in 1956 during an experiment that tried to sterilize canned food using high doses of radiation. One bacterium survived the high doses of gamma radiation and was identified as a new species.

Later, a group of scientists suggested that the high degree of radioresistence was an adaptation to the Martian environment, so this could be an alien bacterium! But that’s actually bullshit. Conan the bacterium has nothing significantly different from other lifeforms on Earth, but how did such a resistance to radiation evolve? Background radiation on Earth is very weak, so it could not appear by natural selection.

The results of some experiments published in 1996 revealed that strains of D. radiodurans that are susceptible to desiccation are also susceptible to radiation. Thus, the most likely explanation is that the high resistance to radiation is simply a side-effect to the resistance to desiccation, a condition much more common in the bacterium’s environment.

The mechanism that allows Conan the bacterium to withstand radiation is very complex, but includes an ability to rebuild DNA strains from fragments, which is helped by the fact that each cells contains four copies of the bacterial chromosome, so that a partially-damaged strain can serve as a model to repair another partially-damaged strain.

Our tiny fellows are always full of amazing surprises!

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References:

Mattimore, V., & Battista, J. (1996). Radioresistance of Deinococcus radiodurans: functions necessary to survive ionizing radiation are also necessary to survive prolonged desiccation. Journal of Bacteriology, 178 (3), 633-637 DOI: 10.1128/jb.178.3.633-637.1996

Wikipedia. Deinococcus radiodurans. Available at <https://en.wikipedia.org/wiki/Deinococcus_radiodurans&gt;. Access on January 2, 2017.

Zahradka, K., Slade, D., Bailone, A., Sommer, S., Averbeck, D., Petranovic, M., Lindner, A., & Radman, M. (2006). Reassembly of shattered chromosomes in Deinococcus radiodurans Nature DOI: 10.1038/nature05160

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Friday Fellow: Witch’s Jelly

ResearchBlogging.orgby Piter Kehoma Boll

I wonder how many people can say they have a bacterium that reminds them of their childhood. Well, at least I can say that I have.

When I was a boy and started to know about the amazing world of living beings that fill our planet, I spent most of my time outdoors looking at every small corner of the backyard and nearby woods in search for interesting lifeforms. And one that always caught my attention was a strange brownish green gelatinous mass that appeared on the ground in the rainy season.

nostoc_commune

Have you ever found something like that on the ground? Photo by flickr user gailhampshire.*

At first I thought it was some species of green alga, but was unable to identify the species. Many years later I finally found out what it is, a colony of cyanobacteria called Nostoc commune and commonly known as star jelly, witch’s butter, witch’s jelly and many other names. It is found worldwide, from the tropics to the polar regions.

As in other cyanobacteria, the witch’s jelly is formed by a colony of unicellular organisms connected in chains. Those are embedded in a gelatinous matrix of polysaccharides that gives the colony its jelly appearance.

nostoc_commune

Chains of Nostoc commune in the matrix of polysaccharides seen under the miscroscope. Photo by Kristian Peters.**

During dry periods, the colonies of witch’s jelly dessiccate and become an inconspicuous thin layer on the ground. They may remain in this state for decades, maybe centuries, until the ideal conditions come back.

In some places, especially Southeast Asia, the witch’s jelly is consumed as food, being a traditional food in the Chinese Lunar New Year.

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References:

Lipman, C. (1941). The Successful Revival of Nostoc commune from a Herbarium Specimen Eighty- Seven Years Old Bulletin of the Torrey Botanical Club, 68 (9) DOI: 10.2307/2481755

Tamaru, Y., Takani, Y., Yoshida, T., & Sakamoto, T. (2005). Crucial Role of Extracellular Polysaccharides in Desiccation and Freezing Tolerance in the Terrestrial Cyanobacterium Nostoc commune Applied and Environmental Microbiology, 71 (11), 7327-7333 DOI: 10.1128/AEM.71.11.7327-7333.2005

Wikipedia. Nostoc commune. Available at: < https://en.wikipedia.org/wiki/Nostoc_commune >. Access on September 19, 2016.

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