Difference between revisions of "Kushneria konosiri"

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== Ecological Habitat ==
 
== Ecological Habitat ==
'''''LO: Microorganisms are ubiquitous and live in diverse and dynamic ecosystems.'''''
+
This bacterium was isolated from the liquid portion of the Korean fermented seafood product daemi-jeot. This food product is a variation of the popular Korean dish jeotgal. [https://en.wikipedia.org/wiki/Jeotgal Jeotgal] is a popular Korean dish consumed either as a condiment or as a seasoning to other dishes. In general, all forms of jeotgal are made by heavily salting a particular type of seafood such as fish, shellfish, and squid and can be characterized by their main ingredients (8). Daemi-jeot in particular comes from the adductor muscle, stomach, and intestines of the dotted gizzard shad (9). The liquid environment of ''Kushneria konosiri'' was isolated from was not tested extensively for abiotic physical and chemical factors as it came from a homemade food product bought at a market on the coast of South Korea (3). However, as this type of dish is relatively common in Korean cuisine and is prepared in a traditional manner (8), some assumptions can be made about these factors. Since daemi-jeot is fermented using solar salt rather than traditional purified salt we can assume that within this environment there are a significant amount of micronutrients and minerals such as K, Mg, and Ca (10). The NaCl concentration is also likely significantly high within this environment with as some
 +
forms of jeotgal are prepared in environments around 25% w/v NaCl (8, 11). During the fermentation process occurring within a common jeotgal environment there is an overall decrease in pH consisting of a drop in pH initially followed by a small increase after some time (12). Oxygen concentration and temperature are also unknown for this particular environment but as this product commonly is left to sit out at the market (Fig. 2) we can assume that it was exposed to atmospheric levels of oxygen and varying temperatures that were likely mild at the time as this sample was collected in April (2).
  
'''''LO: The survival and growth of any microorganism in a given environment depends on its metabolic characteristics.'''''
+
'''Environments of other species within the ''Kushneria'' Genus'''
  
* Describe its habitat and contributions to the environment. Note that an organism’s environment might be in or on another organism (e.g. bacteria in insect digestive system)
+
The genus ''Kushneria'' is relatively novel and small, containing only 9 classified species (13). In general, ''Kushneria'' species are located in hypersaline environments. Species have been located in areas such as leaves of the black mangrove in Puerto Rico (14), the Yellow Sea in Korea (7), salt mines in Pakistan (15), and even within traditional Chinese cured meat (6). All members of this genus are also aerobic so they must be in the presence of oxygen to grow (13). Within their environment, they are not known to form spores (5).
*Include a '''link''' to a photo of a representative habitat with a figure caption that explains what kind of habitat this is and where the habitat is found.
 
 
 
* Where the genus is most commonly found 
 
** If it is found in the environment, what macroscopic “field marks” does it have (color, smell, etc…)
 
** If found in clinical samples – what is a diagnostic test?
 
* Describe the physical and chemical abiotic characteristics of the environment
 
** Temperature, pH, oxygen, etc..
 
  
 
== Significance to the Environment ==
 
== Significance to the Environment ==

Revision as of 17:03, 17 March 2021

Introduction

Microbes have been an extremely important part of human history for thousands of years. They assist us in numerous daily functions and allow for life on Earth to run smoothly. One of their most important functions is in the production of food products, especially in those that are fermented. Fermented food products have been a staple in human diets due to their unique tastes, decreased perishability, and possible health benefits. An example of a popular fermented food product is daemi-jeot. This is a salt- fermented dish prepared commonly in Korea from Konosirus punctatus, a species of fish known as the dotted gizzard shad. This fish falls within the same family as sardines and anchovies (1). To make this traditional Korean dish, the fish is heavily salted and left to ferment. Like many other food products that undergo fermentation, daemi-jeot is able to be made due to the microbial interactions within its environment. However, bacterial populations found within this product are still being understood and discovered. Kushneria konosiri is the proposed name of a novel bacterial strain, strain X49T, discovered within this Korean fermented fish product (3). Kushneria konosiri is a halophilic, Gram-negative, and oval or rod-shaped organism. It is motile and contains a single flagellum that branches out from the cell. Metabolically, it is obligately aerobic. The optimum growth conditions for this bacterial strain are at 15–25 degrees Celsius, pH 5.0–7.0 and in the presence of 11–19 % (w/v) NaCl (3). Within its environment, its halophilic properties characteristic of members within its family (4) allow this microbe to survive and outcompete other microorganisms by withstanding the high salt concentrations surrounding it during the preparation of daemi-jeot. This is due to its development of several functional genes and its ability to perform carotenoid biosynthesis (2). With these adaptations this particular strain can survive in environments with salt concentrations up to 26% w/v NaCl (3). This bacterium thrives within this environment and could be a contributor to the fermentation process of daemi-jeot as it produces acids through a majority of its metabolic processes (3).

Classification

Higher Order Taxa

Eubacteria (Kingdom); Bacteria (Domain); Proteobacteria (Phylum); Gammaproteobacteria (Class); Oceanospirillales (Order); Halomonadaceae (Family); Kushneria (Genus)

Species

Kushneria konosiri, type strain X49T (Accession GU198748)


NCBI: Taxonomy

JGI:GOLD


Phylogenetic Relatedness

Kushneria konosiri is a Halomonadaceae that belongs to the genus Kushneria. This genus was discovered previously as a reclassification of a cluster of species from the genus Halomonas (5). To discover Kushneria konosiri, researchers isolated genomic DNA using previous methodology (6) and used 16S and 23S rRNA gene sequencing methods in order to determine the genetic relatedness of this bacterial strain. A phylogenetic tree containing this organism was constructed using the neighbor joining method. It was used by researchers to compare 16S rRNA sequences of this species with others in the Kushneria genus. In the same study, a separate tree was constructed using 23S rRNA sequences but it revealed similar information to the results of 16S rRNA (2). This bacterium is most closely related to the species Kushneria marislavi a halophilic bacteria discovered from a water sample in the Yellow Sea (7). Through average-nucleotide identity tests, their relatedness level was found to be just below 90% (3). This indicated that this strain was in fact a novel species within the Kushneria genus.

Ecological Habitat

This bacterium was isolated from the liquid portion of the Korean fermented seafood product daemi-jeot. This food product is a variation of the popular Korean dish jeotgal. Jeotgal is a popular Korean dish consumed either as a condiment or as a seasoning to other dishes. In general, all forms of jeotgal are made by heavily salting a particular type of seafood such as fish, shellfish, and squid and can be characterized by their main ingredients (8). Daemi-jeot in particular comes from the adductor muscle, stomach, and intestines of the dotted gizzard shad (9). The liquid environment of Kushneria konosiri was isolated from was not tested extensively for abiotic physical and chemical factors as it came from a homemade food product bought at a market on the coast of South Korea (3). However, as this type of dish is relatively common in Korean cuisine and is prepared in a traditional manner (8), some assumptions can be made about these factors. Since daemi-jeot is fermented using solar salt rather than traditional purified salt we can assume that within this environment there are a significant amount of micronutrients and minerals such as K, Mg, and Ca (10). The NaCl concentration is also likely significantly high within this environment with as some forms of jeotgal are prepared in environments around 25% w/v NaCl (8, 11). During the fermentation process occurring within a common jeotgal environment there is an overall decrease in pH consisting of a drop in pH initially followed by a small increase after some time (12). Oxygen concentration and temperature are also unknown for this particular environment but as this product commonly is left to sit out at the market (Fig. 2) we can assume that it was exposed to atmospheric levels of oxygen and varying temperatures that were likely mild at the time as this sample was collected in April (2).

Environments of other species within the Kushneria Genus

The genus Kushneria is relatively novel and small, containing only 9 classified species (13). In general, Kushneria species are located in hypersaline environments. Species have been located in areas such as leaves of the black mangrove in Puerto Rico (14), the Yellow Sea in Korea (7), salt mines in Pakistan (15), and even within traditional Chinese cured meat (6). All members of this genus are also aerobic so they must be in the presence of oxygen to grow (13). Within their environment, they are not known to form spores (5).

Significance to the Environment

LO: “Microbes are essential for life as we know it and the processes that support life” – how does your organism and your organisms’ metabolism support life on planet Earth?

LO: Human impact on the environment influences the evolution of microorganisms (e.g., emerging diseases and the selection of antibiotic resistance).

  • Describe how this microbe cycles nutrients in the environment. Note that an organism’s environment might be in or on another organism (e.g. bacteria in insect digestive system)
  • Include links to other MicrobeWiki pages on nutrient cycling or other reputable information on nutrient cycling geared toward the public (podcasts, blogs, gov or professional sites)
  • Are there human-induced changes to the environment that have influenced this microbe’s evolution, population numbers, or spread? (e.g. agriculture, clear-cutting/destruction of natural areas, greenhouse gasses, high nitrogen/phosphorous run-off, oil spills, overuse of antibiotics,...)

Ecological Lifestyle and Interactions

LO: “Microorganisms provide essential models that give us fundamental knowledge about life processes.”

LO: “Microorganisms are ubiquitious and live in diverse and dynamic ecosystems."

LO: “Microorganisms and their environment interact with and modify each other.”

LO: “Most bacterial in nature live in biofilm communities.”

  • Describe the organism’s lifestyle, the organisms it interacts with, and how these interactions influence their environment.
  • Name and describe the kind of lifestyle of the organism (free-living? host-associated? obligate? Facultative? Parasitic? Mutualistic? Saprophytic?)
    • If the organism is mutualistic or pathogenic, state what host it most commonly associates with
    • If parasitic – what disease does it cause and what are the symptoms?
    • If mutualistic – what cost/benefit does it receive from the host and what cost/benefit does it give the host?
    • If saprophytic, what kinds of organisms does it feed upon?
    • Does the lifestyle of the organism changes with the host or context? If so, you might select one type of lifestyle to focus on, but then mention the other associations in a few sentences.
  • Describe key groups of microbes that your microbe interacts or are associated with important processes found in this environment.
    • Link to other MicrobeWiki pages or other reputable resources where possible.
  • Describe biological interactions that might take place in this environment, using as many sections/subsections as you require.
    • Are there important biological interactions that are important in this environment?
    • Do these interactions influence microbial populations and their activities?
    • How do these interactions influence other organisms?

Significance to Humans

LO: “Microorganisms can interact with both human and nonhuman hosts in beneficial, neutral, and detrimental ways.”

LO: “Humans utilize (note: this is the correct way to use utilize!) and harness microorganisms and their products.”

  • Describe how this microbe has influenced human society now or in the past.
    • If your microbe is a pathogen, does the ecology and metabolism of the pathogen suggest how we can interrupt its interactions with the host?
  • If there is technology or product that this microbe is part of or could be a part of:
    • describe the technology
    • how this technology or product influences human lives.

Cell Structure

LO: Microbes have unique cell structures that can be targets for antibiotic, immunity, and phage infection.

LO: Microbes have specialized structures (e.g. flagella, endospores, and pili) that often confer critical capabilities.

Provide a physical and metabolic description of the organism. Are there special diagnostic media or methods to distinguish this microbe from close relatives?

  • Colony morphology (size, shape, texture, pigmentation, smell?, etc…)
  • Cell morphology
  • Gram type, if applicable
  • Motility
  • Any other important structures

Cell Metabolism

LO: “Microbes are essential for life as we know it and the processes that support life.” LO: “Microorganisms provide essential models that give us fundamental knowledge about life processes.” LO: Because the true diversity of microbial life is largely unknown, its effects and potential benefits have not been fully explored.

Provide a physical and metabolic description of the organism. Are there special diagnostic media or methods to distinguish this microbe from close relatives?

  • Optimal abiotic growth conditions (temperature, salinity, oxygen, UV)
  • Carbon growth sources
  • Other metabolic abilities
  • Any other unique abilities (e.g toxin production, antibiotic resistance, etc...)

.

Genome Structure, Content, and/or Gene Expression

LO: Genome structure and content provide insight into a microbe's evolutionary history, ecological niche, and interactions with hosts and other microbes.

LO: Mutations and horizontal gene transfer, with an immense variety of microenvironments, have selected for a huge diversity of microorganisms.

LO: The regulation of gene expression is influenced by external and internal molecular cues and/or signals.

LO: Cell genomes can be manipulated to alter cell function.

LO: Genetic variations can impact microbial functions (e.g. in biofilm formation, pathogenicity, and drug resistance).

Metrics

  • Genome size
  • % GC
  • number of chromosomes and/or plasmids?
  • Circular or linear?
  • Other interesting features?

Relevance

  • Why was this organism sequenced?
  • Where was this organism sequenced?
  • Provide a direct link to the sequenced genome
  • What does the genome tell us about this organism? Ie. What new insights do we have after it is sequenced?
  • Give an example of an interesting feature found in the genome (LGT, mutations, plasmids, antibiotic resistance, toxins, etc...).
  • Explain why this feature is important for the microbes’ survival or success.

Interesting Feature

LO: Mutations and horizontal gene transfer, with an immense variety of microenvironments, have selected for a huge diversity of microorganisms.

LO: Human impact on the environment influences the evolution of microorganisms (e.g., emerging diseases and the selection of antibiotic resistance).

LO: Because the true diversity of microbial life is largely unknown, its effects and potential benefits have not been fully explored.

Describe in detail one particularly interesting aspect of your organism.

  • Why is this detail interesting?
  • How does it help the organism survive?
  • How does this interesting feature influence the larger environment or other microbes?
  • How can this interesting feature be helpful to humans?
  • In ~3 sentences propose WHY more research and WHAT kind of new research should be done on this organism and others like it. Connect this to the learning objective about the importance of microbial diversity
  • If you have created a graphical abstract, meme, image, etc... about this organism and its interesting feature, include it here. You can put a creative commons copywrite it to control how other people use it: https://creativecommons.org/about/cclicenses/

References

Each section must have at least 2 references to the primary peer-reviewed literature and at least 1 reference to a reference book like Bergey’s Manual or resources available on the NCBI bookshelf. Also, link out to reputable blogs like Small Things Considered (https://schaechter.asmblog.org/schaechter/), MostlyMicrobes (http://www.mostlymicrobes.com/), Sarah’s Little World (https://sarahs-world.blog/), professional websites American Society for Microbiology (https://asm.org/browse-asm), Microbiology Society (https://microbiologysociety.org/), and podcasts like the many by ASM (https://asm.org/podcasts), This Podcast Will Kill You (https://thispodcastwillkillyou.com/), etc… These should also be cited in the reference section.

Is this a peer-reviewed journal? Check this partial list: https://www.openacessjournal.com/peer-reviewed-journals

Convert your References section to Vancouver format: BibGuru (https://www.bibguru.com/), PMID2cite (https://www.pmid2cite.com/)

Example references: Vancouver citation

Journal

Takai, K., Sugai, A., Itoh, T., and Horikoshi, K. "Palaeococcus ferrophilus gen. nov., sp. nov., a barophilic, hyperthermophilic archaeon from a deep-sea hydrothermal vent chimney". International Journal of Systematic and Evolutionary Microbiology. 2000. Volume 50. p. 489-500. https://doi.org/10.1099/00207713-50-2-489

Book

Surname Initials. Book title. Edition - if available: Publisher, place of publication; Year .

Books with Editors

Beers MH, Porter RS, Jones TV, Kaplan JL, Berkwits M, editors. The Merck manual of diagnosis and therapy. 18th ed. Whitehouse Station (NJ): Merck Research Laboratories; 2006.

Authored chapter in edited publication;;

Glennon RA, Dukat M. Serotonin receptors and drugs affecting serotonergic neurotransmission. In: Williams DA, Lemke TL, editors. Foye's principles of medicinal chemistry. 5th ed. Philadelphia: Lippincott Williams & Wilkins; 2002.

Electronic

World Health Organization (WHO). Mortality country fact sheet 2006 [internet]. Geneva: WHO; 2006. Available from: www.who.int/whosis/mort_emro_pak_pakistan.pdf


Edited by <your name>, a @MicrobialTowson student of Dr. Anne M. Estes at Towson University. Template adapted from templates by Angela Kent, University of Illinois at Urbana-Champaign and James W. Brown, Microbiology, NC State University.