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| Soybean
| | ==Description of Niche== |
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| The soybean, Glycine max, belongs to the family Leguminosae, which refers to the fruits of the flowering plants, legumes. Historical and geographical evidence indicates that the soybean originated from East Asia, specifically Northern China. Soybean has been cultivated and incorporated as food and medicine into the daily lives of the Chinese for the past 5,000 years. In China, the soybean was regarded as one of the sacred grains, including rice, wheat, barley, and millet.
| | ===Where located?=== |
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| During the process of cultivation, the Chinese has transformed soybean into various types of soy foods. Soy paste (Jiang or Chiang in China and Miso in Japan), soy sauce, stinky tofu, natto, and tempeh are to name a few. These cultivation methods and soy food preparation were progressively introduced to other Asian countries, such as Japan, Vietnam, and Korea. Each country slightly modified the soybean product.
| | ===Physical Conditions?=== |
| | What are the conditions in your niche? Temperature, pressure, pH, moisture, etc. |
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| Soybeans were first introduced to the United States in the 18th century. Only until the 1900s did soybean become an important fruit. Currently globally, production of soybean is estimated at 150 million metric tons, with major producers being the Unites States, Brazil, China, India and Argentina. Demands of soybeans have been significantly increasing due to its nutritious and medicinal values.
| | ===Influence by Adjacent Communities (if any)=== |
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| | Is your niche close to another niche or influenced by another community of organisms? |
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| | ===Conditions under which the environment changes=== |
| | Do any of the physical conditions change? Are there chemicals, other organisms, nutrients, etc. that might change the community of your niche. |
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| ==Classification==
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| ===High Order Taxa=== | | ==Who lives there?== |
| Plantae (Kingdom); Magnoliophyta (Phylum); Magnoliopsida (Class); Fabales (Order); Leguminosae or Fabaceae (Family); Glycine (Genus)
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| ===Species=== | | ===Which microbes are present?=== |
| Glycine max
| | You may refer to organisms by genus or by genus and species, depending upon how detailed the your information might be. If there is already a microbewiki page describing that organism, make a link to it. |
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| ==Description and physical characteristics of soybean seed== | | ===Do the microbes that are present interact with each other?=== |
| Soybean is a hearty plant that can be easily grown. Soybean seeds are spherical to long ovals in shape. Although most soy seeds are yellow, soy seeds come in other various seed coat colors, such as: blue, green, dark brown, purplish black, or black. Soy seed varies in size, too. The seed coat of a mature soy seed is extremely hard and water resistant so that germ that is encased within the soy seed is protected. Damages to the seed coat inhibit the seed from germinating.
| | Describe any negative (competition) or positive (symbiosis) behavior |
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| ==Chemical composition of the soybean seed== | | ===Do the microbes change their environment?=== |
| Soybean seeds are extremely high in protein content. On average, dry soybean contains roughly 40% protein, 35% carbohydrate, 20% soybean oil, and 5% ash (non-aqueous, metal oxides). Therefore, soybean has the highest protein content among legume species. Soy protein is a heat-stable protein, thus allowing soy seeds to undergo high temperature cooking and fermentation, without destroying the entire chemical composition of the soybean.
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| The soluble carbohydrates in soybeans are made up of various saccharine: disaccharide sucrose, trisaccharide raffinose, and tetrasaccharide stachyose. These soluble carbohydrates can easily be broken by microbes down during fermentation to create a distinct flavor, odor and texture in soy products.
| | ===Do the microbes carry out any metabolism that affects their environment?=== |
| | Do they ferment sugars to produce acid, break down large molecules, fix nitrogen, etc. etc. |
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| Other valuable components that are found in soybean include phospholipids, vitamins, minerals, and isoflavones. Asia has referred to soybeans as the “miracle beans” and the “yellow jewel.”
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| | ==Current Research== |
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| ==Cultivation of Soybean==
| | Enter summaries of the most recent research. |
| Soybeans are successfully grown in regions with high temperature. Since the soy protein is a heat-stable protein, high temperatures cannot easily destroy the seed itself. The optimum temperatures to cultivate soybeans are 20°C to 30°C (68°F to 86°F). Temperatures below 20°C and above 40°C can inhibit growth of the soybean plants. Soybeans can be grown in soil or sand, however, soil with high content of clay is not an optimal environment to grow soybeans. Soil with high organic contents allows soybeans to perform nitrogen fixation. By establishing a symbiotic relationship with the bacterium, Rhizobium japonicum, soybeans and R. japonicum, an aerobic microbe, can break down nitrogen gas from the atmosphere into ammonia, which is a nitrogen product that is usually low in the soil
| | You may find it more appropriate to include this as a subsection under several of your other sections rather than separately here at the end. |
| | | You should include at least FOUR topics of research and summarize each in terms of the question being asked, the results so far, and the topics for future study. (more will be expected from larger groups than from smaller groups) |
| ==Fermentation of Soybean==
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| ===Stinky Tofu===
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| Stinky tofu, or chaotofu, is a traditional Chinese dish where tofu is fermented in a stinky brine to create a specialized flavor, color and odor. Stinky tofu, along with Chinese soy cheese called sufu, is block-type fermented soy foods. During fermentation of stinky tofu and sufu, sufu is made by utilizing molds, whereas bacteria aid in the fermentation process in stinky tofu.
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| A bacterium is smaller than mold and their functions are significantly different. Molds are capable of multiplying under aerobic conditions. In these aerobic environments, molds produce amylases, proteases, and other hydrolases. Bacteria, on the other hand, utilize and forms proteolytic enzymes made by microorganisms under anaerobic conditions. The proteolytic enzymes that are produced in the anaerobic, stinky brine partially hydrolyze the proteins in the tofu to make the soy proteins more digestible. Intermediate metabolites, such as ammonia, are produced from the proteolytic enzymes, thus yielding an odorous brine or stinky brine.
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| The stinky brine that is used to make this distinct tofu come in different variations. The stinky brine’s ingredients can compose of: various vegetables such as (a) amaranth leaves, bamboo shoots, and winter melon, (b) salted mustard brine with shrimp and salted egg brine, (c) fish, shrimp, and animal organs or (d) strong ammonia, which speeds up the overall fermentation process of tofu. Carried out in an open-fermentation process, the stinky brine allows the tofu that soaked in the brine to undergo a natural zymotic growth by producing a strong, stinky odor. The main bacterium that is involved in the fermentation of stinky tofu is the Bacillus sphaericus.
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| Bacillus sphaericus is an aerobic, mesophillic, spore-forming bacterium that is naturally found in soil. B. sphaericus is part of the Bacillus family. B. sphaericus has a circular chromosome made up of 4,639,821 base pairs, with a 37% GC content and a two-copy plasmid (pBsph) of 177,642 base pairs, with a 33% GC content. There are 85 tRNA genes representing all twenty of the amino acids and 10 rRNA operons in the chromosome. B. sphaericus is a gram-positive bacterium, which contains a thick cell wall composed of peptidoglycan. The cell is rod-shaped and can form endospores. B. sphaericus is incapable of directly breaking down polysaccharide, thus requires an exclusive metabolic pathway that can utilize a wide variety of organic compounds and amino acids. B. sphaericus is capable of growing in the presence of oxygen, therefore utilizing oxygen as part of its aerobic cellular respiration.
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| After the stinky brine is inoculate with B. sphaericus, the ammonia content increases from 100mg/L to 3400 mg/L due the protein in the tofu is hydrolyzed by microbial proteases that forms amino acids, followed by deamination processes to form ammonia. Throughout the fermentation process, the ammonia gradually increases due to the growth of more alkali-tolerant bacteria, which is more favorable over lactic acid bacteria. Due to the favorable growth of alkali-tolerant bacteria B. sphaericus, the cell count of the overall lactic acid bacteria decreases. With initial introduction of the bacterium, the pH drops from 6.5 to about 4.7 due to the production of lactic acid and to the growth of lactic acid bacteria. During the rest of the fermentation process, the pH increases slowly until it has reached pH of 7.5.
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| ===Natto===
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| ===Miso===
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| Miso is Japanese fermented soy bean paste or semisolid that can be served as a soup or used as a seasoning to heighten the flavor of meat and poultry. Miso is mainly made from soybean with addition of enzymes from rice, wheat, or soybean koji and salt. Koji processing utilizes a filamentous mold called Aspergillus oryzae as part of the fermentation process.
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| Miso comes in a variety of colors. Based on their colors, miso can be classified as white miso (butter color), red miso (reddish brown color), and light-color miso (light yellowish/ golden). The different colors of the miso are differentiated by their fermentation process.
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| The main components of miso are soybean, rice, or wheat, salt and water. The secondary components are koji, seasoning and nutritional enrichment ingredients, preservatives and ethanol. The soybean is rich in protein and lipids, which is suitable for miso processing. Rice is can be used miso processing because it has a high moisture uptake, low viscosity, and high rice koji enzymatic activity, which is needed to yield a strong sweet taste and aroma after the saccharization of saccharides that are abundant in soybean. Wheat is another alternative ingredient in miso processing because wheat is rich on glutamic acid, which results in stronger umami flavor, aroma and bolder miso color. Koji, or Aspergillus oryzae, is used as a starter mold, which contains medium-length hyphae with sporangiophores. Short hyphae produce stronger proteases while short hyphae produce stronger amylases. As a result, sweeter miso uses A. oryzae with high amylase activity, while salty miso uses A. oryzae with high protease activity. The optimum temperature for A. oryzae growth is 30°C to 35°C, with a relative humidity of 95%. However, the optimal temperature for the digestion of protein and saccharides by the enzymes from miso koji are 45°C to 50°C for protease and 55°C to 60°C for amylase. The optimal pH for A. oryzae is pH 6.0. As the pH decreases, the protease activity increases.
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| Steaming the soybean is required to prevent the growth of Bacillus subtilis contamination. B. subtilis can inhibit the growth of A. oryzae. After the soybean has been streamed to remove microorganisms that adhere to the surface of the soybean, salt and a brine, which is composed with yeast (Saccharomyces rouzii and Torulopsis versatilis) and a bacterium called Pediococcus halophilus, is mixed with the streamed soybean. P. halophilus is a essential in the miso processing.
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| Pediococcus halophilus is an anaerobic, coccus-shaped, salt-tolerant bacterium.
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| P. halophilus has a circular chromosome made up of 29,924 base pairs, with a 35% GC content. P. halophilus is gram-positive, non-motile, and non-spore forming. It is categorized as lactic acid bacteria, which are a group of bacteria that produces lactic acid as a metabolic end product of saccharide fermentation. P. halophilus can break down sugars, which are abundant in soybeans, by utilizing the enzyme glucose dehydrogenase. P. halophilus cannot grow in the presence of oxygen.
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| During the fermentation, the environment becomes suitable for salt-tolerant organisms, such as p. halophilus. The optimal temperature for bacterial growth is at 30°C. P. halophilus stops growing at 40°C. With introduction of the yeast and P. halophilus, the pH drops from 5.7 to 4.9-5.1. Throughout the fermentation process, the nitrogen concentration also increases. The desirable nitrogen concentration should be 1.51. It has been reported that yeast and P. halopohilus produced non-volatile amines, such as tyramine, histamine, and phenethlamine, which are not detected from the ingredients used to make miso. The interactions between the various molds, yeast and bacteria results in acids reacting with alcohols to produce esters, which contributes to the miso’s aroma. Another interaction that occurs is that the color is produced by the interaction of the amino acids and sugars. Amino acids play the dual role of enhancing flavor and darkening the color of miso.
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| [Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 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.] | | [Sample reference] [http://ijs.sgmjournals.org/cgi/reprint/50/2/489 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.] |
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| ==Photo Credits==
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| Edited by [Amelia Cline and Mimi Van Dang], students of [mailto:ralarsen@ucsd.edu Rachel Larsen] | | Edited by [your name here], students of [mailto:ralarsen@ucsd.edu Rachel Larsen] |
Description of Niche
Where located?
Physical Conditions?
What are the conditions in your niche? Temperature, pressure, pH, moisture, etc.
Influence by Adjacent Communities (if any)
Is your niche close to another niche or influenced by another community of organisms?
Conditions under which the environment changes
Do any of the physical conditions change? Are there chemicals, other organisms, nutrients, etc. that might change the community of your niche.
Who lives there?
Which microbes are present?
You may refer to organisms by genus or by genus and species, depending upon how detailed the your information might be. If there is already a microbewiki page describing that organism, make a link to it.
Do the microbes that are present interact with each other?
Describe any negative (competition) or positive (symbiosis) behavior
Do the microbes change their environment?
Do they alter pH, attach to surfaces, secrete anything, etc. etc.
Do the microbes carry out any metabolism that affects their environment?
Do they ferment sugars to produce acid, break down large molecules, fix nitrogen, etc. etc.
Current Research
Enter summaries of the most recent research.
You may find it more appropriate to include this as a subsection under several of your other sections rather than separately here at the end.
You should include at least FOUR topics of research and summarize each in terms of the question being asked, the results so far, and the topics for future study. (more will be expected from larger groups than from smaller groups)
References
[Sample reference] 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.
Edited by [your name here], students of Rachel Larsen
