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Different microbial structures and types of microbial cells have different level of resistance to antimicrobial agents.
Contrast the relative resistance of microbes
- Endospores are considered the most resistant structure of microbes. They are resistant to most agents that would normally kill the vegetative cells they formed from.
- Mycobacterial infections are notoriously difficult to treat. Protozoa cysts are quite hard to eliminate too. Gram negative species have high levels of natural antibiotic resistance. Staphylococcus aureus is one of the major resistant human pathogens.
- Fungal cells as well as spores are more susceptible to treatments. Vegetative bacterial and yeasts cells are some of the easiest to eliminate with different treatment methods. Viruses, especially enveloped ones, are relatively easy to treat successfully with chemicals due to the presence of lipids.
- horizontal gene transfer: The transfer of genetic material from one organism to another one that is not its offspring; especially common among bacteria.
- endospores: An endospore is a dormant, tough, and non-reproductive structure produced by certain bacteria from the Firmicute phylum.
Different microbial structures and types of microbial cells have different level of resistance to antimicrobial agents used to eliminate them.
Endospores are considered the most resistant structure of microbes. They are resistant to most agents that would normally kill the vegetative cells from which they formed. Nearly all household cleaning products, alcohols, quaternary ammonium compounds and detergents have little effect. However, alkylating agents (e.g. ethylene oxide), and 10% bleach are effective against endospores. Endospores are able to survive boiling at 100°C for hours. Prolonged exposure to ionizing radiation, such as x-rays and gamma rays, will also kill most endospores.
Certain bacterial species are more resistant to treatment than others. Mycobacterial infections are notoriously difficult to treat. The organisms are hardy due to their cell wall, which is neither truly Gram negative nor positive. In addition, they are naturally resistant to a number of antibiotics that disrupt cell-wall biosynthesis, such as penicillin. Due to their unique cell wall, they can survive long exposure to acids, alkalis, detergents, oxidative bursts, lysis by complement, and many antibiotics. Most mycobacteria are susceptible to the antibiotics clarithromycin and rifamycin, but antibiotic-resistant strains have emerged.
Protozoa cysts are quite hard to eliminate too. As cysts, protozoa can survive harsh conditions, such as exposure to extreme temperatures or harmful chemicals, or long periods without access to nutrients, water, or oxygen for a period of time. Being a cyst enables parasitic species to survive outside of a host, and allows their transmission from one host to another. Protozoa cells are also hardy to eliminate.
Gram-negative bacteria have high natural resistance to some antibiotics. Examples include Pseudomonas spp. which are naturally resistant to penicillin and the majority of related beta-lactam antibiotics. This ability to thrive in harsh conditions is a result of their hardy cell wall that contains porins. Their resistance to most antibiotics is attributed to efflux pumps, which pump out some antibiotics before the antibiotics are able to act.
Staphylococcus aureus is one of the major resistant pathogens. Found on the mucous membranes and the human skin of around a third of the population, it is extremely adaptable to antibiotic pressure. It was one of the earlier bacteria in which penicillin resistance was found—in 1947, just four years after the drug started being mass-produced. Methicillin-resistant Staphylococcus aureus (MRSA) was first detected in Britain in 1961, and is now “quite common” in hospitals. A recent study demonstrated that the extent of horizontal gene transfer among Staphylococcus is much greater than previously expected—and encompasses genes with functions beyond antibiotic resistance and virulence, and beyond genes residing within the mobile genetic elements.
Fungal cells as well as spores are more susceptible to treatments. Vegetative bacterial and yeasts cells are some of the easiest to eliminate with numerous agents and methods. Viruses, especially enveloped ones, are relatively easy to treat successfully with chemicals due to the presence of lipids.
Systems Biology of Plant-Microbiome Interactions
In natural environments, plants are exposed to diverse microbiota that they interact with in complex ways. While plant-pathogen interactions have been intensely studied to understand defense mechanisms in plants, many microbes and microbial communities can have substantial beneficial effects on their plant host. Such beneficial effects include improved acquisition of nutrients, accelerated growth, resilience against pathogens, and improved resistance against abiotic stress conditions such as heat, drought, and salinity. However, the beneficial effects of bacterial strains or consortia on their host are often cultivar and species specific, posing an obstacle to their general application. Remarkably, many of the signals that trigger plant immune responses are molecularly highly similar and often identical in pathogenic and beneficial microbes. Thus, it is unclear what determines the outcome of a particular microbe-host interaction and which factors enable plants to distinguish beneficials from pathogens. To unravel the complex network of genetic, microbial, and metabolic interactions, including the signaling events mediating microbe-host interactions, comprehensive quantitative systems biology approaches will be needed.
Keywords: SynComs microbe-host interactions microbial communities plant microbiome plant systems biology.
Copyright © 2019 The Author. Published by Elsevier Inc. All rights reserved.
URI scientists discover function of microbes living in oysters
KINGSTON, R.I. - June 3, 2021 - Scientists from the University of Rhode Island have taken the first steps toward understanding the function of microbes that live on and in Eastern oysters, which may have implications for oyster health and the management of oyster reefs and aquaculture facilities.
"Marine invertebrates like oysters, corals and sponges have a very active microbiome that could potentially play a role in the function of the organism itself," said Ying Zhang, URI associate professor of cell and molecular biology. "We know very little about whether there are resident microbes in oysters, and if there are, what their function may be or how they may help or bring harm to the oyster."
Zhang and doctoral student Zachary Pimentel extracted the DNA of microbes living in or on the gut, gill, inner shell, mantle and other tissues of oysters to identify the microbes that live there. They then applied a metagenomics technology to reconstruct the genome of the most abundant microbes to better understand the nature of the oyster microbiome and the function of some of the microbes.
"This was the first overview of what microbes live in certain parts of Eastern oysters," said Pimentel, the lead author on a paper about the study published in May by the American Society for Microbiology. "In humans, we know that the microbes that live in the gut versus the skin are quite different. But we didn't know about the compartmentalization of certain microbes in certain oyster tissues."
The researchers identified one microbe, a bacterium in the class Mollicutes, that gains energy from the consumption of chitin, a substance found throughout the marine environment. It was most abundant in the gut of the oysters and appears to be an indicator of a healthy oyster, but when found in other tissues, it may be correlated with infections.
"When they're abundant in the gut of healthy oysters, that may indicate that the oysters are happy to have them," Zhang said. "But when the microbe gains abundance in other tissues, that may be a sign that the oyster is not doing well, maybe because the immune system is freaked out."
The same microbe was also discovered to consume arginine, an amino acid found in all organisms that is used to create proteins.
"We're really interested in that one because it has potential implications for the immune system of oysters," Pimentel said. "Oysters rely on arginine for its immune response. A pathogen has been found to steal the arginine to hide from the oyster's immune system, so it's really interesting that there's another microbe that uses arginine and has potential implications for oyster immunity."
Once the researchers have identified the function of key beneficial microbes, the next step is to learn when and where the microbes are acquired.
"One microbe was found to be abundant in adult oysters but very rare in larval samples," Zhang said. "So they could be acquired at some point in their growth, but when and how they are acquired is a big question. If we know they are important and we can identify the source of where they came from, then perhaps we can help preserve the population of this specific microbe."
According to Zhang and Pimentel, oysters play an important role in building reefs, filtering water, and providing other ecological functions, in addition to their role in supporting the aquaculture industry. Further research about the microbiome of oysters could be beneficial to understanding more about oyster health and the health of their ecosystem.
"We know for other organisms that the microbiome is a really important factor when considering health and disease, so we're laying the groundwork for future research that might implicate certain microbes in important processes related to health and disease," Pimentel said.
"The more we know about oysters and their interactions with microbes, the more we'll understand about how to conserve them," added Zhang.
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Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth–promoting bacteria and fungi in the rhizosphere prime the whole plant body for enhanced defense against a broad range of pathogens and insect herbivores. A wide variety of root-associated mutualists, including Pseudomonas, Bacillus, Trichoderma, and mycorrhiza species sensitize the plant immune system for enhanced defense without directly activating costly defenses. This review focuses on molecular processes at the interface between plant roots and ISR-eliciting mutualists, and on the progress in our understanding of ISR signaling and systemic defense priming. The central role of the root-specific transcription factor MYB72 in the onset of ISR and the role of phytohormones and defense regulatory proteins in the expression of ISR in aboveground plant parts are highlighted. Finally, the ecological function of ISR-inducing microbes in the root microbiome is discussed.
Resilience of Microbial Composition
Even if microbial composition is sensitive to a disturbance, the community might still be resilient and quickly return to its predisturbance composition. A number of features of microorganisms, and in particular Bacteria and Archaea, suggest that resilience could be common. First, many microorganisms have fast growth rates thus, if their abundance is suppressed by a disturbance, they have the potential to recover quickly. Second, many microbes have a high degree of physiological flexibility. This is famously the case for the purple nonsulfur bacteria, which can be phototrophs under anoxic conditions and heterotrophs under aerobic conditions. Thus, even if the relative abundance of some taxa decreased initially, these taxa might physiologically acclimate to the new abiotic conditions over time and return to their original abundance. Finally, if physiological adaptation is not possible, then the rapid evolution (through mutations or horizontal gene exchange) could allow microbial taxa to adapt to new environmental conditions and recover from disturbance. All of these arguments assume that abundance is reduced by a disturbance, but some microbial taxa may benefit from the new conditions and increase in abundance. Thus, in order for some taxa to recover in abundance, those that responded positively to the disturbance would also need to decrease in abundance to return the community to its original composition.
Few studies explicitly focus on the time course of microbial composition after a disturbance instead, most focus solely on the sensitivity of composition. Consequently, we recorded the length of time between the application of the disturbance and when microbial composition was assessed for the studies in Tables S1–S4. If composition is highly resilient, then one should be less likely to detect a compositional change as time from disturbance increases.
We compared the time from initial disturbance for those studies that found composition to be sensitive versus resistant. Generally, the timing of compositional assessment varied widely, from just a few hours to decades. For C amendments, the studies in which microbial community composition changed were significantly longer than studies that did not detect a change (Table 2). This result implies that there is a lag in the response of microbial communities to C additions and does not support the idea that these communities are resilient. For elevated CO2, mineral fertilization, and temperature, all studies were equally likely to find shifts in community composition, regardless of time since disturbance. On average, the reviewed studies examined composition after several years of the disturbance application. Thus, as a conservative boundary, microbial composition is often not resilient within a few years.
Certainly, the strength of the disturbance and how often it is applied will have an effect on the resilience of microbial composition. Most of the studies we reviewed continued to apply the disturbance throughout the study (as occurs for most global change disturbances), rather than a one-time application at the beginning of the experiment. For instance, Enwall et al. (36) compared fertilized and unfertilized soil plots that have been maintained since 1956. The composition of the general bacteria and ammonia-oxidizing bacteria still differs between the plot types. In contrast, Stark et al. (37) applied organic and inorganic forms of N to soil samples and compared the composition of Actinomycetes, alpha-Proteobacteria, and Pseudomonads. After 10 days composition differed between the soil treatments, but after 91 days composition differed only among the Pseudomonads. Conversely, some of the studies that found no effect of disturbance on composition might have found an effect if the study was carried out longer.
Natural (Biological) Causes
In the presence of an antimicrobial, microbes are either killed or, if they carry resistance genes, survive. These survivors will replicate, and their progeny will quickly become the dominant type throughout the microbial population.
Diagram showing the difference between non-resistant bacteria and drug resistant bacteria. Non-resistant bacteria multiply, and upon drug treatment, the bacteria die. Drug resistant bacteria multiply as well, but upon drug treatment, the bacteria continue to spread.
Most microbes reproduce by dividing every few hours, allowing them to evolve rapidly and adapt quickly to new environmental conditions. During replication, mutations arise and some of these mutations may help an individual microbe survive exposure to an antimicrobial.
Diagram showing that when bacteria mulitply some will mutate. Some of those mutations can make the bacteria resistance to drug treatment. In the presence of the drugs, only the resistant bacteria survive and then multiply and thrive.
Microbes also may get genes from each other, including genes that make the microbe drug resistant. Bacteria multiply by the billions. Bacteria that have drug-resistant DNA may transfer a copy of these genes to other bacteria. Non-resistant bacteria receive the new DNA and become resistant to drugs. In the presence of drugs, only drug-resistant bacteria survive. The drug-resistant bacteria multiply and thrive.
Diagram showing how gene transfer facilitates the spread of drug resistance. Bacteria multiply by the billions. Bacteria that have drug resistant DNA may transfer a copy of these genes to other bacteria. Non-resistant bacteria recieve the new DNA and become resistant to drugs. In the presence of drugs, only drug-resistant bacteria survive. The drug resistant bacteria multiply and thrive.
The use of antimicrobials, even when used appropriately, creates a selective pressure for resistant organisms. However, there are additional societal pressures that act to accelerate the increase of antimicrobial resistance.
Selection of resistant microorganisms is exacerbated by inappropriate use of antimicrobials. Sometimes healthcare providers will prescribe antimicrobials inappropriately, wishing to placate an insistent patient who has a viral infection or an as-yet undiagnosed condition.
More often, healthcare providers must use incomplete or imperfect information to diagnose an infection and thus prescribe an antimicrobial just-in-case or prescribe a broad-spectrum antimicrobial when a specific antibiotic might be better. These situations contribute to selective pressure and accelerate antimicrobial resistance.
Critically ill patients are more susceptible to infections and, thus, often require the aid of antimicrobials. However, the heavier use of antimicrobials in these patients can worsen the problem by selecting for antimicrobial-resistant microorganisms. The extensive use of antimicrobials and close contact among sick patients creates a fertile environment for the spread of antimicrobial-resistant germs.
Scientists also believe that the practice of adding antibiotics to agricultural feed promotes drug resistance. More than half of the antibiotics produced in the United States are used for agricultural purposes. 1, 2 However, there is still much debate about whether drug-resistant microbes in animals pose a significant public health burden.