Drivers of biodiversity loss - IV - Over-exploitation and V - Climate change

Drivers of biodiversity loss - IV - Over-exploitation or Over- harvesting of Animals and Plants

The five important drivers of biodiversity loss are

1.      Habitat loss and degradation

2.      Pollution

3.      Invasive species

4.      Over-exploitation

5.     Climate change associated with global warming

4.      Over-exploitation or Over- harvesting of Animals and Plants

More than one- third of the world’s endangered birds, fish and mammals are threatened directly by human activities such as fishing, hunting, and trading for meat and other commodities.

Wild animals are captured as pets or for skins or other luxury items while plants are taken for gardens or as ingredients in herbal medicines.

Overfishing

For millennia, the oceans supplied fish and seafood to us without any noticeable decrease in the fish populations due to their high reproductive potential. But the industrialized fishing and exploding human populations increased the demand on fisheries that resulted in overfishing.  

Fishery collapse also affect rest of the ecosystem, such as decrease in seabirds population, increase in sea urchins population, etc.  

Consumers can play a role in reducing overfishing by buying fish and seafood wisely. Information on whether fish and seafood is being harvested sustainably can be found online in lists kept by the Blue Ocean Institute (Guide to Ocean Friendly Seafood), Environmental Defense (Oceans Alive), and the Monterey Bay Aquarium (Seafood Watch Program).

Hunting

Early humans hunted animals for food, warm clothing, and other commodities. As agriculture developed, farmed foods provided people’s diet and Hunting became a sport such as big-game hunting or trophy hunting. Favorite targets are moose, caribou, bear, and elk in North America; reindeer, elk, and wolf in Europe; tiger, leopard, elephant, and wild goat in Asia; and antelope, gazelle, zebra, leopard, lion, giraffe, rhinoceros, and elephant in Africa

Innumerable species have been hunted nearly to extinction, examples are buffalo, passenger pigeon and cheetah.

When Europeans arrived in Colonial America many animals were hunted into extinction or near extinction. The American bison or the buffalo, covered the Great Plains of the United States and Canada, with a population of about 30 million. The railroad companies paid hunters to destroy the herds so that the animals did not interfere with trains by standing on the tracks. Hunting bison was also done to prevent the sustenance of the Native American tribes who were at war with the United States. By 1890, there were fewer than 750 bison left, all in zoos or protected areas.

Passenger pigeons were hunted to the last bird. They were the most abundant bird species on Earth, they lived in enormous flocks; the largest flock, of 2 billion birds even darkened the sky for several days as it flew overhead. Because passenger pigeons lived close together and were slow flyers, they were extremely easy to hunt and their meat was so cheap and was fed to hogs and slaves. The last remaining flock, approximately 250,000 birds, was killed by sport hunters in a single day in 1896. The very last passenger pigeon died in captivity in 1914.

Species of marine mammals primarily whales, dolphins, seals, sea lions, sea otters are also being hunted to extinction or near extinction for their fur, oil, and meat.

The Marine Mammals Protection Act of 1972 bans taking (harvesting, hunting, capturing, or killing, or attempting to do so) or importing any marine mammals or mammal products in United States territorial waters and fisheries. Hunting land animals in developed nations is now highly regulated. These laws save significant populations of game animals and birds.

Professional hunters are sometimes hired to control animals in populated areas, such as bears in parks.

Wildlife Trade

The sale and exchange of wild animals and plants and the products made from them is known as the wildlife trade. Plants are gathered from the wild and sold for gardens or herbal medicines; animals are sold as pets, or for food, exotic leather products, furs, musical instruments, and medicines. Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) by the United Nations prohibits international trade in threatened or endangered organisms, which now include more than 28,000 species of plants and 5,000 species of animals.

Bushmeat

Bushmeat is commercially hunted wild animal meat, often from Africa. Recent studies show that between one and five million tons of wild animal meat are taken annually from the Congo Basin in West Africa.  This is making the wild life there unsustainable.

Of the seven great ape species, only humans are not facing extinction.  The reasons for the decline are habitat loss, pathogens, and the rise in the bushmeat trade.  Besides humans infecting apes with deadly diseases, African apes and monkeys harbor pathogens that can get transmitted into human populations. The introduction of HIV into humans has been traced to the consumption of chimpanzee meat.

China is also involved in wild animal meat. There is high demand for exotic foods such as pangolin, a slow-moving anteater.

Exotic Pet Trade

Exotic pets are animals that have not been domesticated and often do not live well with humans, and yet the trade thrives, especially in the United States, the European Union, and Japan.  Examples are baboons, chimpanzees, rhesus monkeys, tigers, lions, wolves, black bears, three-toed sloths, foxes, raccoons, snakes, tarantulas, scorpions, turtles, lizards, birds and coral reef fish.

Wild animals spread disease to domestic animals and humans.  Salmonella infection from reptiles, Herpes B virus from macaque monkeys, etc are examples

Medicinal Plants

80% of the world’s people use traditional medicine to treat illnesses which require medicinal plants. China and India are the largest markets for medicinal plants.

For more than 3,000 years, the Chinese are using natural ingredients from plants, animals, and minerals to cure everything from the common cold to fevers, arthritis, and sexual dysfunction. These medications are sold throughout China and other Asian countries and to Asians around the world. Traditional Chinese medicines use ingredients from hundreds of species of plants and animals including endangered, threatened, or protected species.  

Most medicinal plants are gathered from the wild and are an important income source.  Wild Asian ginseng cost tens of thousands of dollars per kilogram.  To protect wild medicinal plants, regulations must be enforced and cultivation of medicinal herbs should become more widespread.

5. Climate change associated with global warming

Climate change has been an important factor for evolutionary processes and caused extinctions throughout Earth history. Human activities, such as fossil-fuel and forest burning results in a rapid change in Earth’s climate resulting in global warming. Amphibian species are undergoing extinction since global warming has allowed pathogens increase.

Global Warming

Since the end of the Pleistocene ice ages about 10,000 years ago, 4°C rise in global temperatures have occurred.

Each plant and animal species have an optimal climate condition to which they are adapted. Global warming alters the climatic conditions at regions which becomes intolerable for some species which may either move toward the poles or to higher elevations until it finds conditions where it can grow. Those species that cannot move or adapt to the new conditions will be extinct.

Increasing temperatures are melting glaciers and ice caps which destroys the habitat required for polar bears and northern seals. Melting ice results in rise of sea level which alter the coastal areas that habitat numerous species.

Temperature changes affect the breeding of some animal species, some populations decrease and some populations increase.

The sex of some aquatic animals, such as some turtles and fish, which are determined by water temperature and warmer water leads to all-female turtle hatchlings

Since most pathogens thrive in a warm environment, global warming increase both their survival and transmission rates.  Most disease vectors are now capable of completing their life cycle in a faster rate. About one-third of forests are affected by climate change due to increased risk of pathogen attack and problems associated with drought.

Global warming is occurring at a faster rate so that many plants and animals are not able to adapt before they suffer population decline or even extinction. The most detrimentally affected are the amphibian populations.

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References

• Emerging Consequences of Biotechnology - Biodiversity Loss and IPR Issues, Krishna Dronamraju, World Scientific Publishing Co. Pte. Ltd.
• Biosphere - Ecosystems and Biodiversity Loss, Dana Desonie, Chelsea House

Drivers of biodiversity loss -III - Invasive species

Drivers of biodiversity loss - III - Invasive species 

The five important drivers of biodiversity loss are

1.      Habitat loss and degradation

2.      Pollution

3.      Invasive species

4.      Over-exploitation

5.     Climate change associated with global warming

3.      Invasive species

Invasive species are organisms that enter into an ecosystem where they are not native.  Generally this occurs as the result of human activities.

Many alien species blend into their new habitat and actually increase biodiversity there. A few damage the local ecosystem

Species naturally enter new environments frequently, but the number and rate at which they are introduced has increased dramatically around the world.

When members of an alien species are introduced into a new ecosystem, there are three possible outcomes.

• The habitat is inhospitable and the invader perishes
• The habitat is suitable for the invader and it develops a population and increase the ecosystem’s biodiversity
• The habitat is suitable for the invader and it outcompetes the native species, its population explodes wiping out the native population – resulting in a decrease in biodiversity.

Invasive species may cause harm to native organisms in three ways

• Predation:  The Australian brown tree snake has eliminated several native bird species by eating them.
• Spreading disease: Birds introduced to Hawaii are less susceptible than the native birds.to the avian malaria parasite (this parasite is also an introduced species)
• Altering the environment: The Australian melaleuca tree is spreading through the Everglades; oil in the tree’s leaves burns easily which results in spreading fires that kill native plants.

Invasions of Aquatic Ecosystems

Alien species have damaged both marine and freshwater ecosystems.  The alien species are introduced into an aquatic ecosystem through the ballast water of a ship. Ships suck water into tanks as counterbalance to heavy loads.  This water contains as many as 300 species of organisms or their larvae.  When the ship dumps the ballast water, these organisms are expelled with it.

An example for such an alien species is the zebra mussel, a small mollusk, from the Caspian Sea which reached United States. The organism is a voracious filter feeder and reproducer and drive out native species and clog drain pipes.

Aquarium dumping is another common path for the invasion of an aquatic system by alien species.

Milfoil, a lovely aquarium plant that was released into the eastern United States formed very dense mats at the surface of a lake.  It interferes with recreational activities and power generation and prevent dissolving of oxygen into the water there by destroying the fish population.

Invasions of Terrestrial Ecosystems

Terrestrial ecosystems are also suffering from invasive species. Island animals are highly susceptible to invasive species.    Example is the dodo, a large, flightless bird lived on the island of Mauritius in the Indian Ocean had no predators to fear. When the Dutch arrived, 400 years ago, their dogs and pigs and the rats that had sneaked on their ships consumed the easy to obtain dodo eggs and in less than 100 years, the Dodo was extinct.

Invasive Species Control

We can control invasive species before they enter a new environment, early during their invasion or after they have become a serious problem.

The most effective way to keep down alien species damage in a location is to stop the aliens from entering

Once they enter a new habitat, most alien species blend into the ecosystem. Mechanical methods such as pulling off weedy plants, chopping of trees, use of herbicides to stop seedlings, etc may be adopted. Animals may be stopped by trapping or hunting.  Chemical controls such as the use poisons such as herbicides and insecticides may be employed.  Biological control, or biocontrol which uses a pathogen or a predator to control invasive species may be used to reduce the alien population density.

After habitat destruction, invasive species is the second greatest cause of biodiversity loss. The best way to avoid destruction by alien species is to stop the organisms from entering the new environment. Once they are integrated into the ecosystem, most invaders are very difficult or impossible to remove.

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References

• Emerging Consequences of Biotechnology - Biodiversity Loss and IPR Issues, Krishna Dronamraju, World Scientific Publishing Co. Pte. Ltd.
• Biosphere - Ecosystems and Biodiversity Loss, Dana Desonie, Chelsea House

Computer applications in fermentation technology

Computer applications in fermentation technology

The use of computers for control of fermentation process has increased significantly in the last decade. It is being used for both industrial fermentation and fermentation research.  A computer can be a vital instrument for process optimization and control. The first project to computerize a fermentation began in 1966 in England when direct digital control for the control of temperature, pH, air flow and form level were done in a production fermentation vessel. 

For a fermentation production plant the primary objective of computer control is to produce a product as economically as possible.  The computer is generally used to provide quality control, to save the operational time, to furnish automatic documentation and to decrease the per loop control cost.

The basis of any system used in monitoring and controlling a fermentation process is instrumentation.  Both computer hardware and software are required for control of fermentation process to measure and control the process variables which may be either environmental parameter or physiological parameter or based on the Biomass.  Common environmental variables are temperature, pH, dissolved oxygen, agitation speed, aeration rate and nutrient concentration.  Physiological variables are the products of metabolism and variables describing the state of metabolism.

Industrial Microbiology, Second Edition, AH Patel

The variables to be measured may be directly measured using a sensor.  For the variables which are not directly measurable gateway sensors are used.  In this technique the non-measurable parameter is extracted from a combination of measurable parameters.  The use of computer is very useful in making this type of variable measurements.

Three distinct areas of computer function in fermentation are:

1. Logging of process data. Data logging is performed by the data acquisition system which has both hardware and software components. There is an interface between the sensors and the computer. The software should include the computer program for sequential sensor signals and the procedure of data

2. Data analysis (Reduction of logged data) : Data reduction is performed by the data analysis system, which is a computer program based on a series of selected mathematical equations.  The analysed information may then be put on a print out, fed into a data bank or utilized for process control.

3. Process control. Process control is also performed using a computer program. Signals from the  computer are fed to pumps, valves or switches via the interface. In addition the computer proggram may contain instructions to display devices, to indicate alarms, etc.

The interfacing techniques used in coupling the computer with measurement and control  in a fermentation process includes the following basic components.  There will be modules providing analogue inputs, analogue outputs, digital inputs, digital outputs and interrupt inputs.

Industrial Microbiology, Second Edition, AH Patel

The computer applications in fermentation Technology are used in the automation in penicillin fermentation, fermentative production of enzymes, for fault analysis during fermentation to monitor product losses and also for fermentation research.   

There are two distinct fundamental approaches to computer control of fermenters. The first is when the fermenter is under the direct control of the computer software.  This is termed Direct Digital Control (DDC). The second approach involves the use of independent controllers to all control functions of a fermenter and the computer communicates with the controller only to exchange information. This is termed Supervisory Set-Point Control (SSC).

It is possible to analyse data, compare it with model systems and use control programs which will lead to process optimization. However, process optimization by use of computer is not a widely used procedure in the fermentation industries at present.

 

References

1. Industrial Microbiology, Second Edition, AH Patel, Trinity press
2. Principles of fermentation technology, PF Stanbury, A Whittakker, SJ Hall, 1995, Butterworth-Heinemann publications

 

Food Fermentation: Bread

Food Fermentation: Bread

Bread is known to man even from about 4,000 B.C. Today, bread is a major food of the world and it supplies over half of the caloric and Vitamins B and E intake of the world’s population.

The basic ingredients

The basic ingredients in bread-making are flour, water, salt, and yeasts. In modern bread making

Some other additives such as ‘yeast food’, sugar, milk, eggs, shortening (fat) emulsifiers, anti-fungal agents, anti-oxidants, enzymes, flavoring, and enriching ingredients are also used.

Flour, the chief ingredient of bread is produced by milling wheat.  Flour contains starch (70%), protein (7-15%), sugar (1%), and lipids (1%).

Flour proteins are of two types, the first type is soluble in water and dilute salt solutions and is non-dough forming. It forms about 15% of the total protein in flour and include albumins, globulins, peptides, amino acids, and enzymes. The second type is gluten which contributes the 85% of flour protein and they are insoluble in aqueous media and are responsible for dough formation. Gluten form an elastic structure when moistened with water and holds the starch, yeasts, gases and other components of dough.

One third portion of gluten is alcohol soluble fraction known as gladilins and two thirds of gluten is not alcohol-soluble and known as the glutenins. Gladilins are of lower molecules weight than glutenins.

Yeast used for baking is Saccharomyces cerevisiae. The ideal properties of yeasts baking are:

(a) Ability to grow rapidly at room temperature of about 20-25°C;

(b) Easy dispersability in water;

(c) Ability to produce large amounts of CO₂ rather than alcohol in flour dough;

(d) Ability to resist autolysis when stored at 20°C; Good keeping quality

(e) Ability to adapt rapidly to substrates during dough making.

(f) High invertase and other enzyme activity to hydrolyze sucrose to higher glucofructans rapidly;

(g) Ability to grow and synthesize enzymes and coenzymes under the anaerobic conditions of the dough;

(h) Ability to resist the osmotic effect of salts and sugars in the dough;

(i) High competitiveness i.e., high yielding in terms of dry weight per unit of substrate used.

The yeast amounts vary from 2.0 -  3.0% of flour weight. The amount of yeasts used during baking depends on the flour type, Very ‘strong’ flours i.e., with high protein levels, require more yeast than softer ones.  Also baking systems which involve short periods for dough formation, need more yeast.

The roles of yeasts in bread-making are leavening, flavor development and increased nutritiveness.

Yeast ‘food’ contain a calcium salt, an ammonium salt and an oxidizing agent such as iodates, bromates and peroxide. The bivalent calcium ion strengthens the colloidal structure of the wheat gluten, ammonium is a nitrogen source for the yeast and oxidizing agent strengthens gluten by reacting with the proteins and enhances the ability to hold gas releases during dough formation.

Yeast food has the following composition: calcium sulfate, 30%, ammonium chloride, 9.4%, sodium chloride, 35%, potassium bromate, 0.3%; starch (25.3%).

Sugar is added as sucrose or fructose corn syrups,

(a) to provide additional carbon nourishment for the yeasts

(b) to sweeten the bread;

(c) for more rapid browning of the crust through sugar caramelization.  This allows greater moisture retention within the bread.

Animal and vegetable fats such as Butter, lard (fat from pork) or soy bean oil, are added as shortenings in bread-making at about 3% (w/w) of flour in order to yield

(a) increased loaf size;

(b) a more tender crumb; and

c) enhanced slicing properties.

Emulsifiers are used in conjunction with shortening to ensure a better distribution of shortening in the dough. Emulsifiers contain a fatty acid such as palmitic or stearic acid, which is bound to glycerol, lactic acid, sorbic acid or tartaric acid. Emulsifiers are added at 0.5% flour weight. Commonly used surfactants are calcium stearyl- 2-lactylate, lactylic stearate, sodium stearyl fumarate.

Milk is added to make the bread more nutritious, to help improve the crust color by sugar cearamelization and for its buffering value. Milk is added at a ratio of 1-2 parts per 100 parts of flour.

About 2% sodium chloride is usually added to bread for the following purposes:

(a) It improves taste;

(b) It stabilizes yeast fermentation;

(c) As a toughening effect on gluten;

(d) Helps minimize proteolytic activity;

(e) It participates in the lipid binding of dough.

Since salt has a retarding effect on fermentation, it is added only towards the end of the mixing.

Water is needed to form gluten, to permit swelling of the starch, and to provide a medium for the various reactions that take place in dough formation.

Amylolytic enzymes are required to breakdown the starch from flour into fermentable sugars. Flour is supplemented with malted barley or wheat to provide Alpha amylase or Fungal or bacterial amylase preparations may be added. Bacterial amy1ase from Bacillus subtilis is heat-stable and can survive the baking process. Proteolytic enzymes from Aspergillus oryzae are also used.

Mold-inhibitors (antimycotics) are added and the chief antimycotic agent added to bread to prevent fungal growth is calcium propionate, sodium diacetate, vinegar, mono-calcium phosphate, and lactic acid.

Bread is enriched with various vitamins and minerals including thiamin, riboflavin, niacin and iron.

Process of Bread-making

The processes of yeast-leavened bread-making may be divided into:

1.      Pre-fermentation (or sponge mixing): A portion of the ingredients is mixed with yeast and with or without flour to produce an inoculum. During this the yeast becomes adapted to the growth conditions of the dough and rapidly multiplies.

2.      Dough mixing: The balance of the ingredients is mixed together with the inoculum to form the dough. Maximum gluten development occurs.

3.      Cutting and rounding: The dough formed above is cut into specific weights and rounded by machines.

4.      First (intermediate) proofing: The dough is allowed to rest for about 15 minutes at about   27°C. This is done in equipment known as an overhead proofer.

5.      Molding: The dough is flattened to a sheet and then moulded and placed in a baking pan which will confer shape to the loaf.

6.      Second proofing: This consists of holding the dough for about 1 hour at 35-43°C at high humidity (89-95°C)

7.      Baking: During baking the proofed dough in the final pan is transferred to the oven where it is subjected to an average temperature of 215-235°C for 15-60 minutes. Baking is the final stage and it determines the success of all the previous steps.

8.      Cooling, slicing, and wrapping: The bread is depanned, cooled to 4-5°C, sliced (optional) and wrapped.

Baking

Bread is baked at a temperature of about 235°C for 45–60 minutes. During baking, temperature of the outside of the bread is about 195°C but the internal temperature never exceeds 100°C. The higher outside temperature leads to browning of the crust, a result of reactions between the reducing sugars and the free amino acids in the dough.  As the baking progresses and temperature rises gas production rises and various events occur as below:

•         At about 45°C the undamaged starch granules begin to gelatinize and are attacked by alpha-amylase, yielding fermentable sugars;

•         Between 50 and 60°C the yeast is killed;

•         At about 65°C the beta-amylase is thermally inactivated;

•         At about 75°C the fungal amylase is inactivated;

•         At about 87°C the cereal alpha-amylase is inactivated;

•         Finally, the gluten is denatured and coagulates, stabilizing the shape and size of the loaf.

The Three Basic Systems of Bread-making

There are three basic systems of baking that differ in the presence or absence of pre-fermentation.

(i) Sponge doughs: This is the most widely used. In the sponge-dough, a portion (60-70%) of the flour is mixed with water, yeast and yeast food in a slurry tank (or ‘ingridator’) during the pre-fermentation.  A spongy material develops due to bubbles caused by alcohol and CO₂ (hence the name). The sponge is allowed to rest at about 27°C and a relative humidity of 75-80% for 3.5 to 5 hours. During this period the sponges rises five to six times and collapses spontaneously. During the next (or dough) stage the sponge is mixed with the other ingredients. Then it is processed and baked.  

(ii) The liquid ferment system. In this system water, yeast, food, malt, sugar, salt and milk are mixed during the pre-fermentation at about 30°C and left for about 6 hours. After that, flour and other ingredients are added in mixed to form a dough. The rest is as described above.

(iii) The straight dough system: In this system, all the components are mixed at the same time until a dough is formed. The dough is then allowed to ferment at about 28-30°C for 2-4 hours and then the same process already describedfollows. The straight dough is usually used for home bread making.

The Chorleywood Bread Process is a modification of the straight dough process, which is used in most bakeries in the United Kingdom and Australia. The process is also known as CBP (Chorleywood Bread Process) where All the components are mixed together in 3-5 minutes, with added Fast-acting oxidizing agents and higher level of yeast added and no pre-fermentation time.

Role of Yeast in Bread-making

Leavening is the increase in the size of the dough induced by gases during bread-making. Leavening may be brought about in a number of ways such as Air or carbon dioxide forced into the dough, Water vapor or steam which develops during baking, Hydrogen peroxide added to release oxygen, Carbon-dioxide released by the use of decarboxylase enzymes or by the use of baking powder. Baking powder consists of 30% sodium bicarbonate mixed with leavening acids such as sodium acid pyrophosphate, monocalcium phosphate, sodium aluminum phosphate, monocalcium phosphate generate CO₂ on contact with water and this is suitable for cakes and other high-sugar leavened foods, whose osmotic pressure is too high for yeasts.

But generally bread is Leavened by yeasts.  During bread making, yeasts ferment hexose sugars mainly into alcohol and carbon dioxide and various other alcohols, esters aldehydes, and organic acids. The CO2 dissolves in the dough and the excess CO2 in the gaseous state begins to form bubbles in the dough. This formation of bubbles causes the dough to rise or to leaven. The total time taken for the yeast to act upon the dough varies from 2-6 hours.

Factors which effect the leavening action of yeasts

(i)                 The nature of the sugar available: When glucose, fructose, or sucrose are added these are utilized and when no sugar is added to the dough, the yeast utilizes the maltose in the flour. Thr most rapid leavening is achievable by using glucose.

(ii)              Osmotic pressure: High osmotic pressures inhibit yeast action. Salt is therefore added as late as possible during the dough formation process.

(iii)            Effect of nitrogen and other nutrients: The addition of minerals and a nitrogen source increases gas production. Ammonium, amino acids and peptides and thiamine act as nitrogen source.

(iv)             Effect on fungal inhibitors: Anti-mycotics added to bread are inhibitory to yeast. So the minimum level inhibitory to yeasts is used.

(v)               Yeast concentration:

Flavor development in bread

The aroma of bread is distinct from all other fermented foods because of the baking process. During baking the lower boiling point molecules escape and new compounds result from the chemical reactions taking place at the high temperature. The flavor compound found in bread are organic acids, esters, alcohols, aldehydes, ketones and other carbonyl compounds.

  

Rye bread and San Francisco sourdough are two distinct artisan bread styles.

Rye Bread

Rye bread is a dense, flavorful type of bread made with various proportions of flour from rye grain. Because rye flour naturally contains less gluten than standard wheat flour, the resulting loaves are typically closer in texture, darker in color, and carry a distinctively earthy, robust flavor profile. It is highly appreciated for its health benefits, offering significantly more dietary fiber and a lower glycemic index than white bread.

Next to wheat, rye is the second most common cereal grain used to make bread. Rye has properties that pose particular challenges when used in bread making.   Unlike wheat (Triticum aestivum), rye (Secale cereale) lacks the protein structure required to form a cohesive, viscoelastic gluten network. The proteins gliadin and glutenin are present in rye, but water-soluble and water-insoluble non-starch polysaccharides called arabinoxylans (pentosans) prevent them from linking effectively.

Rye contains a high concentration of pentosans.  Pentosans are a heterogeneous mixture of pentose-containing polysaccharides consisting mostly of xylose and arabinose.  They constitute as much as 10% of rye flour, which is four to five times more than that found in wheat.  Pentosans have high water-binding capacity and pentosans may interfere with gluten formation, giving an inelastic dough that retains gas poorly.   As a result, breads made with rye as the main grain typically have a small loaf volume and a dense crumb texture. In addition, rye flour contains more amylase than is present in wheat, and this amylase is particularly active at the temperature at which starch gelatinizes. This results in excessive starch hydrolysis in the dough and bread, giving a poor texture and further reducing loaf volume.

The addition of sourdough cultures to rye doughs can compensate for these complications. First, as the pH decreases due to the lactic fermentation, the pentosans become more soluble.   They begin to swell and form a gluten-like network that enhances dough elasticity and gas retention. In other words, at low pH, the pentosans do the role normally performed by gluten. In addition, the sourdough starter culture is stimulated by the availability of free sugars liberated from starch via the amylase. Also, this enzyme begins to lose activity at the low pHs during the sourdough fermentation, so excessive hydrolysis is prevented. Some sourdough bacteria also can ferment pentoses released from pentosans, producing heterofermentative end products, including acetic acid.

San Francisco Sourdough

San Francisco (SF) sourdough fermentation relies on a symbiotic culture of wild yeast (Saccharomyces exiguus) and lactic acid bacteria (Lactobacillus sanfranciscensis). This specific pairing, favoured by cooler local temperatures, produces high levels of acetic and lactic acids, resulting in the bread's signature chewy crumb and tangy flavour.  

San Francisco Sourdough is a world-renowned style of bread defined by its uniquely tangy flavour profile, chewy interior crumb, and deeply caramelised, blistered crust.  This famous bread gets its distinctiveness from local Lactobacillus bacteria (Lactobacillus sanfranciscensis or Fructilactobacillus sanfranciscensis) and wild yeast strains.  A sharp, sour tang characterises its flavour profile, and it has a perfectly crispy, crackly crust with a soft, chewy, and airy texture.

This is traditionally made using unbleached wheat flour, water, salt, and active sourdough starter.  This culinary tradition dates back to the 1849 California Gold Rush, when French immigrant bakers blended European baking techniques with the wild starters.

The evolutionary success of the Kazachstania humilis + Fructilactobacillus sanfranciscensis partnership comes down to a perfect division of food resources, ensuring they never compete with one another. Flour lacks simple sugars but is loaded with maltose. Fructilactobacillus sanfranciscensis aggressively consumes maltose via an enzyme called maltose phosphorylase. Kazachstania humilis is maltose-negative; it completely lacks the metabolic machinery to break down maltose. In a normal ecosystem, this yeast would starve. The bacterium breaks maltose down into glucose and releases the excess glucose into the dough. K. humilis utilises this free glucose to produce carbon dioxide and ethanol. the bacterial and yeast population stabilizes at a perfect 100:1 ratio (bacteria to yeast), allowing the starter to remain viable for centuries.

Property	San Francisco Sourdough	Conventional Bread
Primary Inoculum	Symbiotic wild culture (Lactobacillus sanfranciscensis + Kazachstania humilis)	Saccharomyces cerevisiae
Fermentation time	Long duration (12 to 24+ hours)	Short duration (1 to 3 hours)
pH Range	Acidic environment (pH 3.8 to 4.5)	Near-neutral environment (pH 5.3 to 5.8)

 Conventional bread uses intense mechanical energy (high-speed mixing) or chemical oxidizers (e.g., ascorbic acid) to force glutenin and gliadin proteins into disulfide bonds.  The matrix builds strength quickly but retains a uniform, elastic tension that traps gas in small, identical cells, creating a tight crumb structure. Sourdough dough development relies on biochemical time. Long autolysis windows allow native proteases to gently relax the protein chains. As L. sanfranciscensis generates organic acids, the drop in pH reaches the isoelectric point of wheat gluten. This alters the surface charges on the proteins, reducing their water solubility, increasing dough extensibility, and allowing the crumb to stretch into a wild, open, uneven hole structure.  

Conventional Mixing──► Forced Mechanical Shear ──► Rigid, Uniform Gluten ──► Uniform Closed Crumb

Sourdough Ferment    ──► Acid-Induced Relaxation ──► Extensible Matrix    ──► Irregular Open Crumb

In Sourdough, Phytic Acid (an anti-nutrient that binds tightly to essential minerals like Fe²⁺, Zn²⁺, and Mg²⁺, preventing human absorption) degradation occurs in an acidic environment with a pH of 4.5 to 5.5.  Conventional dough remains at high pH (~5.5) and leaves the phytic acid intact.

The Baking Protocol for San Francisco Sourdough

1. Mix and Autolyse - Mix flour and water and cover and let rest for 45 minutes. This allows enzymes to break down starches into maltose, priming the environment for F. sanfranciscensis.

2. Incorporate Starter and Salt  - add  stiff starter and salt  into the dough, squeeze and knead the dough for 5–7 minutes until it becomes smooth and holds its shape.

3. Temperature-Controlled Bulk Fermentation - Place the dough in a container and maintain a dough temperature of 24°C–26°C which allows K. humilis and F. sanfranciscensis growth. The dough increases in volume by roughly 30% to 50%.

4. Preshape and Bench Rest - Gently work the dough into a loose round shape and let it rest uncovered for 20 minutes to allow the gluten to set.

5. Final Shape and Structural Tension - Dust the top of the dough with flour, flip it over, and shape it, place inside proofing basket

6. Extended Cold Retard (The Flavor Window) - Seal the basket inside a plastic bag to prevent the dough from drying out and immediately transfer to a refrigerator kept at 3°C–5°C and allow to proof for 24 to 36 hours. At this low temperature, the yeast completely stops producing gas, but the bacteria continue to slowly convert maltose into acetic acid, creating the sharp sourdough tang.

7. Score and Bake - Pre-heat a heavy cast-iron oven at 245°C (475°F), take the dough directly out of the refrigerator, drop the cold dough into the hot oven, cover with the lid, and lower the oven temperature to 230°C . Bake covered for 20 minutes to trap steam, and them remove the lid and bake uncovered for an additional 20–25 minutes until the crust develops a deep mahogany color and blistered exterior.

References

1. Industrial Microbiology: An Introduction, M J. Waites, N L. Morgan, J S. Rockey, G Higton
2. Modern Industrial Microbiology and Biotechnology, Nduka Okafor, Science Publishers