Overview of Rhizopus oryzae
a. Higher order taxa
Domain: Eukarya, Kingdom: Fungi, Phylum: Zygomycota, Class: Zygomycetes, Order: Mucorales, Family: Mucoraceae, Genus: Rhizopus, and Species: oryzae.
2. Description and significance
Describe the appearance, habitat, etc. of the organism, and why you think it is important.
- Include as many headings as are relevant to your microbe. Consider using the headings below, as they will allow readers to quickly locate specific information of major interest*
3. Genome structure
The genome of R. oryzae strain 99-880, which measures 45.3 Mb in length, contains numerous transposable elements (TEs) and coding sequences . These TEs and coding sequences comprise 20% and 39% of the genome, respectively. The TEs of R. oryzae can be categorized into two classes: Class I and Class II. Class I TEs contain retrotransposons, while Class II TEs include DNA TEs . In addition to TEs and coding sequences, the genome of R. oryzae contains expanded gene families involved in several processes such as cell wall synthesis, protein hydrolysis, and cell signaling . The presence of the protease gene family in particular indicates a greater ability of R. oryzae to degrade organic matter. Additionally, the increase of the CHS and CDA gene families to 23 and 34 genes, respectively, accounts for the increase in chitin and chitosan within the microbe’s cell wall . Other gene families found in R. oryzae transcribe proteins such as GTPases, GTPase regulators, chitin synthases (CHS), chitin deacetylases (CDA), secreted aspartic proteases, and subtilases . Compared to other fungal microorganisms, R. oryzae possesses a highly repetitive genetic structure, as it contains ancestral genes similar to those contained in metazoan genomes rather than dikaryotic fungi genomes . Such findings suggest that the genomic structure of R. oryzae observed today occurred as a result of whole genome duplication and subsequent sequence deletions .
4. Cell structure
R. oryzae grows as a result of mycelium accumulation . Such accumulations are composed of tubular filaments known as hyphae. Mycelial cell walls, located in the body of the microbe, are reinforced by polysaccharides such as chitin . Chitin reinforces the hyphae, creates a stronger cell wall, and thus allows for the cell to withstand greater pressures. While chitin provides a source of external, structural support to this microbe’s cells, lipids provide a source of internal, metabolic support as they can act as cellular storage sites .
5. Metabolic Processes
Microbes belonging to the Rhizopus genus are optimal organisms for fumaric acid production . R. oryzae, in particular, produces and accumulates large quantities of fumaric acid under aerobic conditions via the tricarboxylic acid cycle. Such cycling occurs in the cytosol through use of the C3 and C1 mechanism, which works in conjunction with the carbon dioxide fixation pathway, to allow for the biosynthesis of fumaric acid . The process begins when pyruvate is catalyzed by pyruvate carboxylase into oxaloacetate. The catalysis reaction is continued by malate dehydrogenase, and later by fumarase, to break down L-malic acid and ultimately produce fumaric acid . Acidic stress on cells can occur during acid production, which decreases the pH in the fermentation broth . A pH of 4.0 has been reported to be favorable for the synthesis of fumaric acid by R. oryzae. At a pH of 4.0, R. oryzae exhibited rapid glucose consumption and a higher output of both fumaric acid and biomass than at a pH of 3.0 . Glucose was also completely consumed by the end of the process and twice as much fumaric acid was produced than at a pH of 3.0. On the contrary at a pH of 3.0, acid production significantly decreased and some glucose remained in the broth . The decreased acid levels at pH 3.0 demonstrate that low pH inhibits fumaric acid production by R. oryzae. Acid production may be inhibited due to limited availability of carbon sources that are alternatively used for cell survival processes in low pH conditions .
Current knowledge about the reproductive process of R. oryzae is primarily derived from observing and comparing different species under the group Rhizopus. R. oryzae has a heterothallic mating arrangement, meaning that offspring may be produced following reproduction between two compatible spore types . The method by which R. oryzae reproduction occurs is dependent upon the available media type. In high nutrient environments, this microbe can reproduce asexually through mitosis, the most common reproductive method used by the species . In minimal nutrient environments, diploid cells produce spores through meiosis. These spores can grow as azygospores, which are produced through asexual reproduction, or zygospores, which are produced through haploid cell fusion . Mating can occur between different species as well. For instance, R. oryzae and R. delemar can act as mating partners as their zygospores are physically and molecularly similar.  Both microbes contain central vacuoles and produce round, reddish brown zygospores. In order to form spores, both require little to no light and an incubation period of about two to three weeks . The crossing of R. oryzae and R. delemar results in offspring that cannot create zygospores due to the presence of a conserved sex locus, contained in the genome strain RA99-880 .
Habitat; symbiosis; contributions to the environment.
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.
7. Key microorganisms
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8. Current Research
R. oryzae can cause postharvest disease in certain fruits such as apples and bananas . This disease originates from soft rot, a fungal infection that occurs when products are stored at nonoptimal temperatures or extended periods of time at cold temperatures. When such fruits rot, white and cottony R. oryzae colonies will form on their surfaces .
Visible structure of R. oryzae – sporangium is typically visible on decaying food as fuzz. http://www.uq.edu.au/_School_Science_Lessons/9.196.1.GIF
Although R. oryzae is a pathogenic microbe, it can be useful in food production . Commercial R. oryzae cultures can be cooked and used as dry starters to inoculate different fruits and grains. As a fermentative agent, this microbe can enhance sweetness and acidity while producing a white, protective covering on food surfaces . Although such food covers are edible, further research is needed to determine whether these products are safe to incorporate into the food industry completely. The new R. oryzae strain FSIS4 also produces an 𝛼-amylase enzyme that increases the volume and height-to-width ratio of bread . Once purified via a three-phase partitioning technique, the enzyme is added to wheat flour at a concentration of 1.936 U per kg of flour. The increase in volume and height-to-width ratio may occur due to a reduced viscosity of the dough during starch gelatinization . An aerated bread structure also results from the presence of 𝛼-amylase produced by the microbe. Bread utilizing commercial 𝛼-amylase creates a similar aerated structure, however with larger holes . Upon further research, the effects of R. oryzae FSIS4 𝛼-amylase may prove useful in other food products as well.
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