Diversity 

of microbial world 
                                                    Three Domains of Life 

The Microbial World

• All three biological domains include microbial organisms (or “microorganisms”)

• Although microorganisms include some of the smallest organisms, they play critical roles
in the evolution of life on our planet and in the ecology of both terrestrial and marine
environments
• Microorganisms are the most important primary producers in many marine environments
• Via photosynthesis and chemosynthesis, they manufacture organic matter from CO2
• As a result, they directly or indirectly feed most marine organisms
• Microorganisms make essential nutrients available to other primary producers

Viruses
• Although they may not technically constitute a living organism (???), viruses are a
critical component of the marine food web
• Viruses are particles made up of nucleic acid (RNA or DNA) protected by a protein coat
• They are parasites that reproduce and develop only with the aid of a living cell
• Viruses are minute, measuring 20-200 nanometers (a nanometer is one-billionth of a
meter)!
You can swim, but you can’t hide
• Viruses are everywhere in the marine environment
• They parasitize bacteria and plankton (and everyone else) releasing organic matter into
the ocean
 – Provides organic compounds to be grazed upon by other members of the
microbial community
– Releases nutrients which may be used by photosynthetic organisms
– May be responsible for half of the bacterial mortality in aquatic ecosystems and
substantial amounts in phytoplankton
– The amount of viruses in a given environment is directly related to the abundance
of the microbial life, which they invade
– Viruses are now recognized as the most abundant ‘biological’ organisms in the
ocean
– For every liter of Long Island Sound water, there are 100,000,000,000 viruses!
Prokaryotes
• Prokaryotes are the smallest and structurally simplest true-living organisms, and the
oldest life forms on Earth
• Prokaryotes are unicellular organisms which lack a nucleus and other membrane-bound
organelles
• Prokaryotes include all members of Domains Archaea and Bacteria

Prokaryotes: Domain Bacteria

• Bacteria (Domain Bacteria) appear to have branched out very early on the tree of life and
are genetically distinct from Archaea and eukaryotes (Domain Eukarya)
• They are abundant in all parts of the ocean
• Bacteria are vital to life on Earth because they ensure the recycling
of essential nutrients in oceanic food webs
• Most organic matter is decomposed by bacteria
• Bacteria constitute a major part of the organic matter that feeds countless bottom-
dwelling animals
• Organic particles sinking in the water column are composed mostly of bacteria!
– Very important food source!

Marine Snow
• Marine snow is a continuous shower of mostly organic detritus falling from the upper
layers of the water column
• Detritus is non-living particulate organic material, and is typically colonized by
communities of microorganisms
• Includes dead or dying animals and plants, phytoplankton, fecal
matter, sand, soot and dust
• A single cell sinks at a rate of ~1-2 meters day-1
• Aggregates sink ~150-200 meters day-1
• Sinking cleanses pollutants from surface waters and brings much-needed nourishment to
deep sea organisms
• Sediment traps capture sinking debris
• Flux of particulate matter mirrors productivity at the surface; peak separated by 2
weeks
Feeling small?
• Particulate matter is defined as anything larger than 0.2µm
• Anything smaller is considered to be dissolved
• Particulate organic matter is only 10% of the total organic material in the ocean;
dissolved organic matter makes up the rest (90%)
– Of all the fish, all the whales, all the bacteria, all the organic debris in the oceans,
90% of it is dissolved
– Viruses are considered to be dissolved organic material
Bac(k) to Bacteria…
• Bacteria feed primarily on dead organic material
• Some bacteria, however, are photosynthetic; the cyanobacteria
• Cyanobacteria have chlorophyll as well as a bluish pigment called phycocyanin
– “blue-green algae”
– Among the first photosynthetic organisms
• Cyanobacteria are widely distributed
• Because of their size, cyanobacteria are believed to be the most abundant photosynthetic
organisms in the ocean
• In addition to being free-living, some bacteria have evolved to live in close association
with other marine organisms
– Symbiotic bacteria
• Many of the organelles found in eukaryotic organisms evolved from symbiotic bacteria
• Examples of symbiotic bacteria include those involved in the digestion of wood by
shipworms, those responsible for bioluminescence and those found in association with
mussels, clams and tubeworms that live around hydrothermal vents
Prokaryotes: Domain Archaea
• Archaea (Domain Archaea) are among the simplest, most primitive forms of life
• Oldest fossils ever found (3.8 billion years old) appear similar to Archaea
• Archaea are prokaryotes, unicellular organisms that lack a nucleus and other membrane-
bound organelles
• Thought to have had an important role in the early evolution of life
Archea – Extremophiles
• Some groups of Archaea were discovered only recently
• First in extreme environments on land – hot sulfur springs, saline lakes, and highly acidic
or alkaline environments
• “Extremophiles”
• Archaea were subsequently found in extreme marine environments, such as in very deep
water, where they survive at pressures of 300-800 atmospheres
• Some archaea live at the high temperatures of hydrothermal vents, and cannot grow in
temperatures under 70-80°C (158-176°F); 1 hydrothermal vent archaeum can live at
121°C (250°F) – the highest of any known organism
Evidence for life on Earth?
• Many of the harsh conditions which extremophiles require to survive were characteristic
of our early Earth
• Likely that Archaea evolved to dwell in such conditions billions of years ago & survive
today in similar (specific) environments
 Eukaryotes: Domain Eukarya
• Eukaryotes (Domain Eukarya) possess a nucleus, a membrane that encloses the DNA, in
each of their cells
• While all prokaryotes (domains Archaea and Bacteria) are uni-cellular, eukaryotes
include both uni-cellular and multi-cellular organisms
– Kingdoms Protista, Fungi, Plantae, and Animalia
Microbial Eukaryotes
• Most microbial marine eukaryotes belong to the Kingdom Protista

Kingdom Protista (the Protists)

• Kingdom Protista is the ‘trouble-maker’ of the classification system
• Can be autotrophic or heterotrophic
• Can be unicellular or multi- cellular
• But all are eukaryotic!
(Domain Eukarya)
• Debates over classification persist
• Different groups possess different evolutionary histories
• Some are more plant-like (e.g., multi-cellular seaweeds)
• Some are more animal-like (e.g., heterotrophic and mobile)
• Some are photosynthetic and heterotrophic (what we call “mixotrophic”)
 Algae
• Algae are a diverse group of protists
• Nearly all algae perform photosynthesis using photosynthetic pigments
• As protists, algae are distinct from plants and lack a cell wall, specialized tissues, and
flowers
• They also lack true leaves, stems and roots
• Unicellular or multi-cellular
– Multicellular algae are seaweeds!
Plants evolved from green algae (which is now considered a plant, not a protist!)

Unicellular Algae: The Diatoms

• Diatoms are unicellular, although many species aggregate to form chains
• Diatom cells are enclosed by cell walls made of silica; this glassy shell or frustule
consists of 2-tightly fitting halves
• The glass frustule allows light to pass through so that photosynthetic pigments can
capture light energy for photosynthesis
- UV protection?
- Aid in sinking?
- Protection from predation?
- Diatoms are very important primary producers in temperate and polar regions
- Account for a large share of the organic carbon produced on Earth
- Favorable environmental conditions (light and nutrients) promote periods of rapid
reproduction known as blooms
- The glass frustules of dead diatoms eventually settle to the sea floor; diatomaceous ooze
Dinoflagellates
• Dinoflagellates are another important group of planktonic, unicellular protists
• Two flagella; one wrapped along a groove along the middle of the cell, the other trailing
free
• Dinoflagellates may be autotrophic, heterotrophic or both (mixotrophic)!
• Nearly all dinoflagellates are marine
• Important primary producers, especially in tropical regions
• Some species release toxic substances and can cause harmful “red tides”
– And some are bioluminescent
• In addition to blooms of “red tide”, some dinoflagellates release toxins responsible for
open sores on fish, crustaceans and bivalves

Zooxanthellae
• A group of dinoflagellates called zooxanthellae live in close association with animals
such as coral, sea anenomes, sponges and giant clams
• Symbiotic: zooxanthellae photosynthesize within the body of an animal host, releasing
organic matter and receiving nutrients (in the form of waste products) and shelter in
return
• Loss of the colorful zooxanthallae is behind the phenomenon of coral bleaching

Coccolithophorids
• Coccolithophoridsare unicellular protists covered with ornamental plates made of
calcium carbonate (CaCo3)
• Form seasonal blooms in North Atlantic
• Produce dimethyl sulfide, which alters climate patterns!
– Long considered to be “smell of the sea”
 Foraminiferans
Foraminiferans (“forams”) are marine protists that also have a shell made of CaCo3
• Animal-like; possess pseudopodia – extensions of the cytoplasm used for trapping
diatoms and other suspended material in the water
• Benthic or planktonic
• Important indicators of past climate change
• Radiolarians are planktonic marine protists that secrete elaborate shells made of silica and
other materials
• Cells are typically spherical with radiating spines
• Ciliates are protists with many hair-like cilia used in locomotion and feeding
• Planktonic or benthic
• Tintinnids are common ciliates that build vase-like cases or loricas made up
tiny particles such as sand grains
• Important grazers in the microbial.
• Ciliates are protists with many hair-like cilia used in locomotion and feeding
• Planktonic or benthic
• Tintinnids are common ciliates that build vase-like cases or loricas made up
tiny particles such as sand grains
• Fungi are eukaryotic organisms belonging to the Kingdom Fungi
• All are heterotrophic
• Can be unicellular or multicellular
• 1,500 known species of marine fungi
• Absorb nutrients from their environment. Important decomposers in the marine
environment, but also parasitic (disease-causing)

IMPORTANCE OF MICROBIOLOGY IN PHARMACY

Pharmacy and pharmaceutical companies uses microbiology extensively. It is used

1) for production of medicines like antibiotics, enzymes, vaccines, insulin, vitamins, steroids etc. Some of
the substance are exclusively obtained from microbial cultures.
 Most anti-biotics are obtained only from microbes. Vitamin-B12 (cyanocobalamin) is obtained from
culture of microbes. Similarly human insulin for diabetics is purely obtained from microbial culture
by rDNA technology.
Initially diabetics were given injection of insulin obtained from animals. But due to heavy demand and
also compatibility problems (as it was animal derived) there was need for some other source of human
insulin.
Then rDNA technique involving E.coli bacteria was adopted to produce large amounts of human insulin
which is even safe.
2) For sterilization of manufactured drugs. Microbes are destroyed by sterilization.
3) Also many new drugs are in search by use of microbiology. Since many antibiotics, enzymes etc were
derived from microbes, still the microbes are searched for more new drugs.

IMPORTANCE OF MICROBIOLOGY IN AGRICULTURE:

 Natural Pesticides: Few microbes like bacteria and virus are exploited against pest attacking farm crops.
Hence they are called natural pesticides. They are so specific to the pests or insects and don’t cause any
harm to the plant or animals and humans.
 Natural manures: Few microbes like algae and bacteria are grown up to enhance soil fertility by fixing
nitrogen and also water retaining capacity of soil. Thus they also maintain soil microbiology suitable for
plant growth. Crop rotation is a technique adopted by farmers to enhance soil fertility by use of microbes
in roots of leguminous plants.
 Decompose the waste: Microbes decompose the synthetic pesticide residues and other toxic material in
agriculture soil and there by protect farms from toxin accumulation.
Importance of environmental microbiology:
 Microbes in environment play an important role in scavenging. This means they clear any dead and
decaying matter on the surface, in air and water.
 without microbes this earth would have been full of corpses i.e. dead bodies. Microbes decay any organic
substance directly and inorganic substances indirectly.
 Role of microorganisms in waste water treatment: Waste water is treated by microbes to free from all
garbage. This is termed as biological oxygen demand. i.e. amount of oxygen required by microbes to
decay on quintal (100kg) of waste.
IMPORTANCE OF SOIL MICROBIOLOGY:
Soil microbiology is very important to maintain soil structure and nature.

 The layers of soil which have microbes support growth of plants due to more water and fertility.
 Microbes in soil keep up water, the soil having microbes has higher water holding capacity.
 The humus is top layer of soil rich in microbes suitable for plant growth. This is because microbes
produce natural organic fertilizers which are compatible and easy to absorb.and also fertility.
 Microbes decay the waste remnants in the soil and make it hard. All the fossil fuels are processed by
microbes.
Other application of microbiology
In Industry microbiology is highly used in manufacturing and processing of drugs, alcohol, food etc.

Introduction

Preservation of foods by fermentation is a widely practiced and ancient technology.

Fermentation ensures not only increased shelf life and microbiological safety of a food but also
may also make some foods more digestible and in the case of cassava fermentation reduces
toxicity of the substrate. Lactic acid bacteria because of their unique metabolic characteristics are
involved in many fermentation processes of milk, meats, cereals and vegetables. Although many
fermentations are traditionally dependent on inoculation from a previous batch starter cultures
are available for many commercial processes such as cheese manufacture thus ensuring
consistency of process and product quality. This review outlines the role of lactic acid bacteria in
many such fermentations and the mechanisms of antibiosis with particular reference to
bacteriocins and gives a brief description of some important fermented foods from various
countries. It is anticipated that the contribution of the advances in lactic acid bacteria research
towards improvement of strains for use in food fermentation will benefit both the consumer and
the producer.
For centuries microbial organisms have been part of nature, assuring a number of naturally
occurring fermentation processes. Today micro-organisms are used in industrial food and feed
production and the interest of the industry is safeguarded through the European Food and Feed
Cultures Association (EFFCA).
Main categories of micro-organisms
Micro-organisms responsible for the majority of food fermentations are classified into 3
categories:
• Yeasts
- Yeasts are fungi, a division of thallophytes - non-vascular plants with little or no mycelium.
They ordinarily reproduce by budding. They live in sugary solutions and ferment sugar. Among
the yeasts used in food production one can mention as examples:
- genus Saccharomyces, common in bread, wine or beer making as well as in the dairy industry
(such as Sereveisae used in blue mould cheeses),
- genus Debaromyces, also used in the dairy industry.
• Moulds

Moulds are also fungi, but contrary to yeasts, they feed on organic matter and reproduce by
means of spores. In this family, Penicilliumroqueforti in Roquefort cheese and P. candidum in
Camembert cheeses are well known.
• Bacteria

Bacteria are typically one-celled and multiply by simple division. They occur in three main
forms: spherical (cocci), rod-shaped (bacilli) and spirilla.
• Among the immense family of bacteria one can give as examples:
- Genus Micrococcus present in the meat industry,
- Genus Oenococcus in the wine industry,
- Genus Lactococcus - also known as lactic bacteria - used in the dairy industry.
Micro-organisms can work alone, but they usually work in associations comprising a large
number of gena, species and strains.
Lactic bacteria

Lactic bacteria include a great variety of micro-organisms used in the food industry. They are
primarily used in the dairy industry but can also be used in a number of other applications.
Although classification remains difficult and some times changes, one can distinguish at least a
dozen of different types such as streptococcus, lactococcus, intrococcus, pediococcus,
leuconostoc, bifido bacterium and lactobacillus.
Applications
Fermentation
• Traditional view: The process for the production of alcohol or lactic acid from glucose
• A broader definition:
An enzymatically controlled transformation of an organic compound.

Microbial Fermentation Products

• Pyruvic Acid
• Saccharomyces Lactic acid
• Streptococcus
• Lactobacillus Ethanol,CO2
• Bacillus
• Clostridium Butanol, Acetone
• E. coli
• Salmonella Lactic Acid, Ethanol, Acetic acid
Microbial Growth
• Growth of individual cells
• Increase in size and mass of all components within the cell
• Cells continually grow and divide
• Limitation by nutrient or toxic metabolites
• Growth of the entire population
• Total mass of the entire population
• Population is asynchronous
Fermentation
• Microorganisms convert raw materials into useful products
• Type of microorganisms:
• Wild Type
• Mutants
• Genetically Engineered
• Media components
• Metabolites
Some common products of microorganism activities
• Scotch
• Wine
• Beer
• Yogurt
• Pickles
• Cheese
• Amino acid
• Vitamins
• On October 15, 1980 Genentech shares went from $35 to $ 89 producing Insulin from
microbial fermentation. This was the first recombinant DNA product
Specialty Chemicals
• The chemical industry is a + $ 100 Billion
• US market is $250 Million for amino acids
• 20 amino acid, 10 are essential, must be supplied in the diet
• Animal Food supplement 50% of the market
• Food fortifications 25% of the market
• Pharmaceuticals $30 Million
• Specific therapy:
Glutamic acid in epilepsy
In cosmetics - Serine
In intravenous infusion 1% of the market (18% of the revenues)
Other Fermentation Products
• Vitamins
• Sweeteners
• High fructose corn syrup 3 million tons at 7cents/pound while saccharine costs $4.00/pound
• Beverage industry uses 750,000 tons/year
• Americans consume 130 pound of sugar/ capita/yr
• Enzymes
• World wide sales $300 Million
• US sales $100 Million
Substances of Significant Economic Value Derived from Microorganisms
• Antibiotics
• The Brewing Industry
• The Wine Industry
• Amino Acids
• Vitamins
• Recombinant DNA Products: Insulin
Animal Cell Culture Technology
• Why people grow animal cells in cultures
• Variety of research studies
• Production of biopharmaceutical
• Products derived from Animal cells
• Viral vaccines
• Monoclonal antibodies
• Complex Enzymes and Proteins
• In vitro skin growth-clinical practice
Tissue Engineering
• A collaboration of biologists and engineers
• Biological substitutes to be implanted into the body
• Making of non biologic materials that are compatible with the body
• Development of materials that promote the remodeling of tissue
• Artificial Skin Bioartificial organs
• Blood substitutes Neurological implants
• Tissue engineered vascular grafts
• Various orthopedic devices

Development of Animal Cell Culture

• Organ Culture
• Tissue Culture
• Cell Culture and development of cell lines
• Most widely used presently especially for the production of biopharmaceutical products

Industrial usage
The lactobacilli are present almost everywhere in nature and are widely used in the food industry
where they assure a consistent production of high-quality food products.
a. Dairy industry
In the cheese manufacture, the starter culture plays a crucial role during all phases of the cheese
making and maturing process. As the culture grows in the milk, it converts lactose to lactic acid.
This ensures the correct pH and it also assures the final moisture level and yield in the cheese.
During ripening, the culture assures a balanced aroma, taste, texture and, if required, eye
formation. Depending on the cheese type produced, the selection of the correct mixture of culture
is essential in order to obtain a high quality product.
In yoghurt and other fermented milks the culture assures the development of the taste and texture
of the final product. Depending on the level of pH, the product can be either mild or strong in
taste. Depending on the amount of polysaccharides produced, the product can be more or less
viscous.
Dairy products have long been valued as a source of healthy nutrition. Probiotic cultures in
particular are known for this positive effect. These cultures are carefully selected strains; there
are strong indications that they help improve digestion, balance the intestinal flora and safeguard
the immune system.

b. Meat industry
The primary application for meat starter cultures is dried fermented products such as salami,
pepperoni, chorizo and dried ham. In these products the lactic bacteria provide an optimal
development of flavour and colour hereby ensuring correct drying condition and control of
fermentation.
In addition a wide variety of moulds are used for surface ripening of sausages hereby preserving
the natural quality of the product and assuring a controlled development of flavour.
c. Wine industry
In the wine industry, it is well known that yeasts are responsible for the alcoholic fermentation.
Lactic bacteria also play an important role in wine making. They
are responsible for the malolactic fermentation that converts the unstable malic acid naturally
present in wine into the stable lactic acid. This conversion is necessary in order to assure the
stability that characterises high quality, long-hold wines.
d. Bread industry
In bread making, lactic bacteria are responsible for the fermentation, which is normally known as
"sour-dough". This fermentation offers bakers a number of important benefits such as easily
handled dough, uniformity, a shorter resting time, good aroma and longer freshness.
e. Agricultural industry
Lactic bacteria are used in the agricultural industry for a number of different applications.
In modern live stock production, pigs, cattle and chickens are often exposed to stressful
conditions, which can give rise to imbalances in the intestinal flora with consequent low weight
gains, increased diarrhoea incidence and high mortality rates. Lactic acid bacteria have proven
very effective in restoring and maintaining a balanced intestinal flora in the animals, hereby
ensuring optimal production parameters and improved well being of the animals.
Also in the preservation of silage, which is a fermentation of grass alpha-alpha or corn, lactic
acid bacteria are used to assure an optimal preservation of the nutritive elements in these
products.
f. Health food industry
In addition to the food and feed applications, lactic bacteria are also used in a wide variety of
capsules and tablets specifically targeted at the health food industry. Modern day living often
gives rise to imbalances in the intestinal flora of human beings. This imbalance can also be
caused by travelling or medical treatment, and lactic acid bacteria can help in restoring and
maintaining a balanced intestinal flora, hereby assuring a good quality of life despite changed
conditions.
Production process and quality control
Production of lactic bacteria takes place in highly specialisedfermentors under strict hygienic
conditions. It typically involves a number of different steps:
1. The original strains are preserved in a microbiology laboratory that is responsible for - prior to
each production - preparing the inoculation material. This inoculation material is transferred to
fermentors in which the culture is allowed to multiply and grow within carefully defined and
monitored conditions.
After the fermentation has been finalized, the bio mass is harvested, eg by means of
centrifugation, and the resulting bio mass is conserved either in a liquid, frozen or powder form.
Finally the product is formulated and packed in the finished product according to the customers'
needs.
2. The entire production process is at each individual step carefully monitored by Quality
Control laboratories in order to assure that the product remains of the highest quality and is free
from contamination.

Importance and Benefits of Fermented Cereals

Fermented foods contribute to about one-third of the diet worldwide (Campbell-Platt 1994).
Cereals are particularly important substrates for fermented foods in all parts of the world and are
staples in the Indian subcontinent, in Asia, and in Africa. Fermentation causes changes in food
quality indices including texture, flavor, appearance, nutrition and safety. The benefits of
fermentation may include improvement in palatability and acceptability by developing improved
flavours and textures; preservation through formation of acidulants, alcohol, and antibacterial
compounds; enrichment of nutritive content by microbial synthesis of essential nutrients and
improving digestibility of protein and carbohydrates; removal of antinutrients, natural toxicants
and mycotoxins; and decreased cooking times.

Fermentation is the process of controlling microbes (bacteria, yeast, and moulds) to modify
food, producing a desired product.

Often we talk about the negative issues caused by microorganisms in food such as food spoilage.
But they can be used as efficient live factories to produce health beneficial food. Without some
microorganisms, production of certain food items may not be possible or may be costly.
Microbes are cheap resources that consist of numerous enzymes which can convert complex
chemical structures into simple digestible molecules with a high efficiency. These
microorganisms use the nutrients in the food as the substrate to produce energy and other
required precursors for their growth in which a fermented food results. There are numerous
examples for fermented food.

Fish sauce
In production of fish sauce, uneviscerated fish is mixed with salt and placed in fermented tanks
to allow liquefaction for about six months. The collected liquid is further ripened for few more
months.Halophillic microbes are involved in this fermentation process. Streptococcus,
Micrococcus and Bacillus species predominate. This product is dark coloured with a distinct
aroma.

Sauerkraut
This refers to fermented cabbage. Normal microflora in cabbage is involved in the fermentation
process under anaerobic conditions. Leuconostocmesenteroides and Lactobacillus plantarum is
involved. Temperature is a crucial factor in the control of fermentation. If the temperature is
below 21 degrees Celcius, Lactobacilli outgrow. L. mesenteroides require a lower temperature
below 21 0C. Acidity created by Lactobacilli prevent the growth of L. mesenteroides.
Pickels
Pickels consist of vegetables like cucumber, onions, chilies etc. Lactic acid bacteria such
as Leuconostocmesenteroides, P. cerevisiae, L. brevis, L. plantarum are involved in the
fermentation process These bacteria also take part in fermentation of olives.

Soy sauce
In production of soy sauce, a mixture of soybean and wheat flour is inoculated with Aspergillus
oryzae and Aspergillus soyae. These fungi digest complex starch and produce sugars which
facilitate the growth of bacteria. Anaerobic bacteria carry out fermentation to produce soy sauce.

Beer and Ale

Malted beverages are produced by brewing. Mainly the yeasts are involved in the process. Yeasts
convert fermentable sugars to ethanol and carbon dioxide. As yeasts do not produce enough
amylases to hydrolyze starch in barley grains, they are germinated prior to brewing. Hops which
are added for bitterness have an inhibitory effect on gram positive bacteria. Saccharomyces
carlsbergensis is the principle organism used. This species is subjected to various genetic
modifications to increase the efficiency of the fermentation. In addition to ethanol and carbon
dioxide, yeasts produce a small amount of glycerol, acetic acid and aromatic esters. Ale is a top
fermented beverage with Saccharomyces cerevisiae.

Wine
Wine is made from grape juice in large scale. Yests; Saccharomyces cerevisiae var.
ellipsoideus is the culture used in wine fermentation. High temperature is not suitable for this
fermentation as yeasts die while low temperature allows the growth of lactic acid bacteria.

Environmental factors such as acidity, pH, oxygen level, moisture level, temperature, sugar
content are important for this fermentation processes. In most food commodities, acidity is
developed by microorganisms. This developed acidity is important for preserving the
food. Proteolytic action may bring down the pH to a higher value. Some yeasts produce alkaline
by products such as ammonia in their regular metabolism which is encouraged in the production
of limburger cheese.

Alcohol, which is a byproduct of many fermentation pathways also have a preservative action.
Alcohol content produced will depend on the sugar content, type of yeast involved in
fermentation, temperature and the oxygen level. Most yeast can’t tolerate high alcohol levels.
Temperature has a direct effect on microbial fermentation which in turn affects the final quality
of the product. Sauerkraut production is an ideal example to show the importance of temperature
in fermentation process.
Microorganisms have different oxygen requirements for their growth and fermentation. In wine
production, yeasts grow best under aerobic conditions. In baking, anaerobic conditions favour
the quality of the final product. Vinegar production involves anaerobic as well as aerobic
fermentation.

BIOWARFARE
Biological warfare (BW)—also known as germ warfare—is the use of biological
toxins or infectious agents such as bacteria, viruses, and fungi with the intent to kill or
incapacitate humans, animals or plants as an act of war. Biological weapons (often termed "bio-
weapons", "biological threat agents", or "bio-agents") are living organisms or replicating entities
(viruses, which are not universally considered "alive") that reproduce or replicate within
their host victims. Entomological (insect) warfare is also considered a type of biological weapon.
This type of warfare is distinct from nuclear warfare and chemical warfare, which together with
biological warfare make up NBC, the military acronym for nuclear, biological, and chemical
warfare using weapons of mass destruction (WMDs). None of these are conventional weapons,
which are primarily effective due to their explosive, kinetic, or incendiary potential.
Biological weapons may be employed in various ways to gain a strategic or tactical advantage
over the enemy, either by threats or by actual deployments. Like some of the chemical weapons,
biological weapons may also be useful as area denial weapons. These agents may be lethal
or non-lethal, and may be targeted against a single individual, a group of people, or even an
entire population. They may be developed, acquired, stockpiled or deployed by nation states or
by non-national groups. In the latter case, or if a nation-state uses it clandestinely, it may also be
considered bioterrorism.[1]
There is an overlap between biological warfare and chemical warfare, as the use
of toxins produced by living organisms is considered under the provisions of both the Biological
Weapons Convention and the Chemical Weapons Convention. Toxins andpsychochemical
weapons are often referred to as midspectrum agents. Unlike bioweapons, these midspectrum
agents do not reproduce in their host and are typically characterized by shorter incubation
periods.[2]
Overview
Offensive biological warfare, including mass production, stockpiling and use of biological
weapons, was outlawed by the 1972 Biological Weapons Convention (BWC). The
rationale behind this treaty, which has been ratified or acceded to by 170 countries as of April
2013,[3] is to prevent a biological attack which could conceivably result in large numbers
of civilian casualties and cause severe disruption to economic and societal infrastructure. Many
countries, including signatories of the BWC, currently pursue research into the defense or
protection against BW, which is not prohibited by the BWC.
A nation or group that can pose a credible threat of mass casualty has the ability to alter the
terms on which other nations or groups interact with it. Biological weapons allow for the
potential to create a level of destruction and loss of life far in excess of nuclear, chemical or
conventional weapons, relative to their mass and cost of development and storage. Therefore,
biological agents may be useful as strategic deterrents in addition to their utility as offensive
weapons on the battlefield.
As a tactical weapon for military use, a significant problem with a BW attack is that it would
take days to be effective, and therefore might not immediately stop an opposing force. Some
biological agents (smallpox, pneumonic plague, mycoplasma fermentanincognitus) have the
capability of person-to-person transmission via aerosolized respiratory droplets. This feature can
be undesirable, as the agent(s) may be transmitted by this mechanism to unintended populations,
including neutral or even friendly forces. While containment of BW is less of a concern for
certain criminal or terrorist organizations, it remains a significant concern for the military and
civilian populations of virtually all nations.

Modern BW operations

Offensive

It has been argued that rational people would never use biological weapons offensively. The
argument is that biological weapons cannot be controlled: the weapon could backfire and harm
the army on the offensive, perhaps having even worse effects than on the target. An agent
like smallpox or other airborne viruses would almost certainly spread worldwide and ultimately
infect the user's home country. However, this argument does not necessarily apply to bacteria.
For example, anthrax can easily be controlled and even created in a garden shed; the FBI
suspects it can be done for as little as $2,500 using readily available laboratory equipment.Also,
using microbial methods, bacteria can be suitably modified to be effective in only a narrow
environmental range, the range of the target that distinctly differs from the army on the
offensive. Thus only the target might be affected adversely. The weapon may be further used to
bog down an advancing army making them more vulnerable to counterattack by the defending
force.
Anti-personnel
Ideal characteristics of a biological agent to be used as a weapon against humans are
high infectivity, high virulence, non-availability ofvaccines, and availability of an effective and
efficient delivery system. Stability of the weaponized agent (ability of the agent to retain its
infectivity and virulence after a prolonged period of storage) may also be desirable, particularly
for military applications, and the ease of creating one is often considered. Control of the spread
of the agent may be another desired characteristic.
The primary difficulty is not the production of the biological agent, as many biological agents
used in weapons can often be manufactured relatively quickly, cheaply and easily. Rather, it is
the weaponization, storage and delivery in an effective vehicle to a vulnerable target that pose
significant problems.
For example, Bacillus anthracis is considered an effective agent for several reasons. First, it
forms hardy spores, perfect for dispersal aerosols. Second, this organism is not considered
transmissible from person to person, and thus rarely if ever causes secondary infections. A
pulmonary anthrax infection starts with ordinary influenza-like symptoms and progresses to a
lethal hemorrhagic mediastinitiswithin 3–7 days, with a fatality rate that is 90% or higher in
untreated patients.[30] Finally, friendly personnel can be protected with suitableantibiotics.
A large-scale attack using anthrax would require the creation of aerosol particles of 1.5 to 5 µm:
larger particles would not reach the lower respiratory tract, while smaller particles would be
exhaled back out into the atmosphere. At this size, conductive powders tend to aggregate because
of electrostatic charges, hindering dispersion. So the material must be treated to insulate and
neutralize the charges. The weaponized agent must be resistant to degradation by rain and
ultraviolet radiation from sunlight, while retaining the ability to efficiently infect the human
lung. There are other technological difficulties as well, chiefly relating to storage of the
weaponized agent.
Agents considered for weaponization, or known to be weaponized, include bacteria such
as Bacillus anthracis, Brucella spp., Burkholderia
mallei, Burkholderiapseudomallei,Chlamydophilapsittaci, Coxiellaburnetii, Francisellatularensi
s, some of the Rickettsiaceae (especially Rickettsia prowazekii and Rickettsia
rickettsii), Shigella spp., Vibrio cholerae, and Yersinia pestis. Many viral agents have been
studied and/or weaponized, including some of the Bunyaviridae (especially Rift Valley fever
virus), Ebolavirus, many of the Flaviviridae (especially Japanese encephalitis virus), Machupo
virus, Marburg virus, Variola virus, and Yellow fever virus. Fungal agents that have been studied
includeCoccidioides spp.
Toxins that can be used as weapons include ricin, staphylococcal enterotoxin B, botulinum
toxin, saxitoxin, and many mycotoxins. These toxins and the organisms that produce them are
sometimes referred to as select agents. In the United States, their possession, use, and transfer are
regulated by the Centers for Disease Control and Prevention's Select Agent Program.
The former US biological warfare program categorized its weaponized anti-personnel bio-agents
as either Lethal Agents (Bacillus anthracis, Francisellatularensis, Botulinum toxin)
or Incapacitating Agents (Brucella suis, Coxiellaburnetii, Venezuelan equine encephalitis virus,
Staphylococcal enterotoxin B).
Anti-agriculture
Anti-crop/anti-vegetation/anti-fisheries
The United States developed an anti-crop capability during the Cold War that used plant diseases
(bioherbicides, or mycoherbicides) for destroying enemy agriculture. Biological weapons also
target fisheries as well as water-based vegetation. It was believed that destruction of enemy
agriculture on a strategic scale could thwart Sino-Soviet aggression in a general war. Diseases
such as wheat blast and rice blast were weaponized in aerial spray tanks and cluster bombs for
delivery to enemy watersheds in agricultural regions to initiate epiphytotics (epidemics among
plants). When the United States renounced its offensive biological warfare program in 1969 and
1970, the vast majority of its biological arsenal was composed of these plant
diseases. Enterotoxins and Mycotoxins were not affected by Nixon's order.
Though herbicides are chemicals, they are often grouped with biological warfare and chemical
warfare because they may work in a similar manner as biotoxins or bioregulators. The Army
Biological Laboratory tested each agent and the Army's Technical Escort Unit was responsible
for transport of all chemical, biological, radiological (nuclear) materials. Scorched earth tactics
or destroying livestock and farmland were carried out in the Vietnam war (cf. Agent
Orange)[33] and Eelam War in Sri Lanka.
Biological warfare can also specifically target plants to destroy crops or defoliate vegetation. The
United States and Britain discovered plant growth regulators (i.e., herbicides) during the Second
World War, and initiated a herbicidal warfare program that was eventually used
in Malaya and Vietnam in counterinsurgency operations.

Anti-livestock
In 1980s Soviet Ministry of Agriculture had successfully developed variants of foot-and-mouth
disease, and rinderpest against cows, African swine fever for pigs, and psittacosisto kill chicken.
These agents were prepared to spray them down from tanks attached to airplanes over hundreds
of miles. The secret program was code-named "Ecology".
Attacking animals is another area of biological warfare intended to eliminate animal resources
for transportation and food. In the First World War, German agents were arrested attempting to
inoculate draft animals with anthrax, and they were believed to be responsible for outbreaks
of glanders in horses and mules. The British tainted small feed cakes with anthrax in the Second
World War as a potential means of attacking German cattle for food denial, but never employed
the weapon. In the 1950s, the United States had a field trial with hog cholera.[citation needed] During
the Mau Mau Uprising in 1952, the poisonous latex of the African milk bush was used to kill
cattle.[34]
Unconnected with inter-human wars, humans have deliberately introduced the rabbit
disease Myxomatosis, originating in South America, to Australia and Europe, with the intention
of reducing the rabbit population – which had devastating but temporary results, with wild rabbit
populations reduced to a fraction of their former size but survivors developing immunity and
increasing again.
Entomological warfare
Main article: Entomological warfare
Entomological warfare (EW) is a type of biological warfare that uses insects to attack the enemy.
The concept has existed for centuries and research and development have continued into the
modern era. EW has been used in battle by Japan and several other nations have developed and
been accused of using an entomological warfare program. EW may employ insects in a direct
attack or as vectors to deliver a biological agent, such as plague. Essentially, EW exists in three
varieties. One type of EW involves infecting insects with a pathogen and then dispersing the
insects over target areas.[35] The insects then act as a vector, infecting any person or animal they
might bite. Another type of EW is a direct insect attack against crops; the insect may not be
infected with any pathogen but instead represents a threat to agriculture. The final method uses
uninfected insects, such as bees, wasps, etc., to directly attack the enemy.

Defensive

Biodefense
Research and development into medical counter-measures
In 2010 at The Meeting of the States Parties to the Convention on the Prohibition of the
Development, Production and Stockpiling of Bacteriological (Biological) and Toxin Weapons
and Their Destruction in Geneva[37] the sanitary epidemiological reconnaissance was suggested
as well-tested means for enhancing the monitoring of infections and parasitic agents, for practical
implementation of the International Health Regulations (2005). The aim was to prevent and
minimize the consequences of natural outbreaks of dangerous infectious diseases as well as the
threat of alleged use of biological weapons against BTWC States Parties.
Common epidemiological clues that may signal biological attack
From most specific to least specific:
1. Single cause of a certain disease caused by an uncommon agent, with lack of an
epidemiological explanation.
2. Unusual, rare, genetically engineered strain of an agent.
3. High morbidity and mortality rates in regards to patients with the same or similar symptoms.
4. Unusual presentation of the disease.
5. Unusual geographic or seasonal distribution.
6. Stable endemic disease, but with an unexplained increase in relevance.
7. Rare transmission (aerosols, food, water).
8. No illness presented in people who were/are not exposed to "common ventilation systems
(have separate closed ventilation systems) when illness is seen in persons in close proximity who
have a common ventilation system."
9. Different and unexplained diseases coexisting in the same patient without any other
explanation.
10. Rare illness that affects a large, disparate population (respiratory disease might suggest the
pathogen or agent was inhaled).
11. Illness is unusual for a certain population or age-group in which it takes presence.
12. Unusual trends of death and/or illness in animal populations, previous to or accompanying
illness in humans.
13. Many effected reaching out for treatment at the same time.
14. Similar genetic makeup of agents in effected individuals.
15. Simultaneous collections of similar illness in non-contiguous areas, domestic, or foreign.
16. An abundance of cases of unexplained diseases and deaths.
Identification of bioweapons
The goal of biodefense is to integrate the sustained efforts of the national and homeland security,
medical, public health, intelligence, diplomatic, and law enforcement communities. Health care
providers and public health officers are among the first lines of defense. In some countries
private, local, and provincial (state) capabilities are being augmented by and coordinated with
federal assets, to provide layered defenses against biological weapon attacks. During the first
Gulf War the United Nations activated a biological and chemical response team, Task Force
Scorpio, to respond to any potential use of weapons of mass destruction on civilians.
The traditional approach toward protecting agriculture, food, and water: focusing on the natural
or unintentional introduction of a disease is being strengthened by focused efforts to address
current and anticipated future biological weapons threats that may be deliberate, multiple, and
repetitive.
The growing threat of biowarfare agents and bioterrorism has led to the development of specific
field tools that perform on-the-spot analysis and identification of encountered suspect materials.
One such technology, being developed by researchers from the Lawrence Livermore National
Laboratory (LLNL), employs a "sandwich immunoassay", in which fluorescent dye-labeled
antibodies aimed at specific pathogens are attached to silver and gold nanowires.[43]
In the Netherlands, the company TNO has designed Bioaerosol Single Particle Recognition
eQuipment (BiosparQ). This system would be implemented into the national response plan for
bioweapon attacks in the Netherlands.
Researchers at Ben Gurion University in Israel are developing a different device called the
BioPen, essentially a "Lab-in-a-Pen", which can detect known biological agents in under 20
minutes using an adaptation of the ELISA, a similar widely employed immunological technique,
that in this case incorporates fiber optics.

Genetic Warfare

Theoretically, novel approaches in biotechnology, such as synthetic biology could be used in the
future to design novel types of biological warfare agents.[46][47][48][49] Special attention has to be
laid on future experiments (of concern) that:[50]

1. Would demonstrate how to render a vaccine ineffective;

2. Would confer resistance to therapeutically useful antibiotics or antiviral agents;
3. Would enhance the virulence of a pathogen or render a nonpathogen virulent;
4. Would increase transmissibility of a pathogen;
5. Would alter the host range of a pathogen;
6. Would enable the evasion of diagnostic/detection tools;
7. Would enable the weaponization of a biological agent or toxin
Most of the biosecurity concerns in synthetic biology, however, focused on the role of DNA
synthesis and the risk of producing genetic material of lethal viruses (e.g. 1918 Spanish flu,
polio) in the lab.