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Why is GenBank growth slowing down?

Why is GenBank growth slowing down?


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https://www.ncbi.nlm.nih.gov/genbank/statistics/ shows the growth of the GenBank database is slowing since WGS (Whole Genome Shotgun) emerged. Is this happening because sequencing centers are submitting their data unannotated (WGS submissions are allowed to be unannotated assemblies)?


It is not really slowing down. The graph that you see in that link is semi-log. So the exponentiality of the growth has reduced. It is not surprising because we have much more data than what we had 10 years back but the rate is not going to increase at the same rate (10 to 1000 is a great change but 1000 to 5000 is not despite the fact the the number of new sequences is greater in the latter). However, new data is being continuously added and the linear growth has not saturated yet.

See these graphs that I replotted from the data in your link.

Nonetheless, the number of new sequences will also slow down in future because we would be approaching the maximum.


GenBank Overview

GenBank ® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 2013 Jan41(D1):D36-42). GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Nucleotide Archive (ENA), and GenBank at NCBI. These three organizations exchange data on a daily basis.

A GenBank release occurs every two months and is available from the ftp site. The release notes for the current version of GenBank provide detailed information about the release and notifications of upcoming changes to GenBank. Release notes for previous GenBank releases are also available. GenBank growth statistics for both the traditional GenBank divisions and the WGS division are available from each release.

An annotated sample GenBank record for a Saccharomyces cerevisiae gene demonstrates many of the features of the GenBank flat file format.


Assessing Cell Growth

Accurate cell counting is of paramount importance when assessing cell growth in cultures, as faulty counts can lead to mistaken conclusions about cell health. Cell counts can be determined using a hemocytometer. However, automated cell counters that utilize the Coulter principle where cells flow, one by one, through an aperture within an electrical sensor, yield the most precise cell counts.

Figure 2. Scepter™ 2.0 Handheld Automated Cell Counter


Why does human growth slow down so substantially once we leave the womb?

I just read a Stephan Jay Gould essay about this. The other posters are right, development doesn't slow down after birth, but our development is quite slow, compared to other animals. Our childhoods and our periods of dependency are lengthened, which allows us to learn more from our families before pursuing reproduction and independence.

I would say it just picks up speed! I mean, ok, when you're embryonic, a few cell divisions is a massive fraction of your total, but once you're no longer a parasite, running around eating candy and such and not feeding off someone else's blood supply, you're adding on real gains.

I wouldn't say it slows down substantially, I mean babies spend 9 months getting to around 7.5 pounds in the womb, then double their weight in just 6 months once born.

Energy comes from food which is used for: Growth, keeping warm, metabolizing/breaking down food (yes that cost energy too), waste (not all food can be metabolized), and reproduction (maybe not in this case).

In the womp the baby is kept warm so more energy can be diverded to growth. Also getting nutrients directly from the umbilical cord instead from breaking down milk and later solid food.


Why We Refrigerate Fruits and Vegetables

Ever wonder why we keep some foods in the refrigerator while other foods go to the pantry? Spoilage is inevitable, but refrigeration slows it down in two ways.

Cold Is Key

First, cold temperatures interfere with the growth of microorganisms that harm food, such as bacteria, mold, and yeast. In order to grow, any microorganism that could damage fruits or vegetables needs food, a favorable moisture content, and a favorable temperature.

Obviously, it is impossible to eliminate a food source for these microorganisms, so other factors that facilitate their growth must be eliminated.

Fighting Bacteria With Your Fridge

We refrigerate food to keep bacteria, yeasts, and molds from the favorable temperature they need to grow. The moisture-control available in many refrigerators also helps slow the deterioration of foods, so that two of the three favorable situations for microorganism growth are eliminated.

Though the microorganism growth is slowed down at low temperatures, it still can occur at the 38 degrees of an ordinary refrigerator. Hence, the mold that grows on forgotten leftovers in the back of a refrigerator.

Ripen=Rot? Not Quite.

The second benefit of refrigeration is that it slows down the food's own natural processes that lead to ripening and eventual decay.

For fruits and vegetables, the very chemical processes that cause plants to grow and ripen also cause them to rot. In effect, refrigeration helps save the plant tissue from itself. Keeping these foods at low temperatures dramatically slows this aging process.


No way to stop human population growth?

An asteroid impact that wiped out hundreds of millions of people would barely slow down human population growth. That’s one of the surprising results of a new computer model, which still finds that there may be a couple of things we can do to keep our numbers in check.

Every dozen years or so, we add another billion people to the planet. If the trend continued, we’d eventually run out of food and water, and we’d be unable to handle the massive amounts of waste and pollution we produce. Yet we know that population growth is already leveling off due to a combination of family planning programs and education for women. Is it possible to slow population growth even more in the next few decades? Corey Bradshaw decided to find out.

Bradshaw, a population biologist at the University of Adelaide in Australia, studies population ecology in animals. But when he gives talks at scientific meetings on declining biodiversity, audience members increasingly ask, “What about the elephant in the room? What about human population size?” he says. “I’ve modeled changing populations in other species for years,” he says, “but I never applied [those models] to human beings.”

So Bradshaw and University of Adelaide climate biologist Barry Brook decided to see how much momentum the human population has. They also wanted to see how sensitive population growth is to factors like mortality and fertility. The duo obtained data on death rates, average family size (i.e., fertility), and regional population size from the World Health Organization and the U.S. Census Bureau International Data Base. They created a computer model that projects human population growth from 2013 to 2100. They added variables to the model that they could modify to create different scenarios. Their goal was to assess how sensitive human population growth is to changes in mortality, life span, family size, and a mother’s age when she has her first baby.

The team then created 10 scenarios, including a “business-as-usual” scenario in which death and fertility rates stayed the same as they were in 2013. The other scenarios projected the effects of alterations such as longer life spans, mothers having their first children at older ages, the imposition of a global one-child policy, and catastrophic deaths due to war or pandemics. Using the regional data, the researchers also examined the effects of population growth on biodiversity hotspots in different parts of the world.

The business-as-usual model matched U.N. projections of 12 billion people by 2100, giving the researchers confidence in their model. But they also saw booming population growth even when they introduced global catastrophic deaths of up to 5% of the population, the same seen in World War I, World War II, and the Spanish flu. When the computer model population lost half a billion people, the total population was still 9.9 to 10.4 billion people by 2100, the team reports online today in Proceedings of the National Academy of Sciences. “It actually had very little effect on the trajectory of the human population,” Bradshaw says.

Some economists argue that shrinking populations create an unsupportable burden of elderly dependents that leads to economic collapse. But the team’s model showed otherwise. When the population is growing, more of the dependents are children, and when the population is shrinking, more are older adults, the model indicates. A dependent is always supported by 1.5 to two workers. The idea that shrinking populations cannot support older adults is a “fallacy,” Bradshaw says.

Two factors did have an impact on human population growth: eliminating unwanted pregnancies, which make up about 16% of all live births, and adopting a global one-child policy. Eliminating those births year after year resulted in population sizes in 2050 and 2100 that are comparable to those produced with a global one-child policy—about 8 billion and 7 billion, respectively.

The models also confirmed that the worst human impacts on biodiversity hotspots will occur in Southeast Asia and Africa, which by 2100 will likely have the highest human densities in the world. Pressures in those parts of the world, Bradshaw says, will be higher than anywhere else in the world. Elephants, rhinos, and lions will likely disappear faster. “So, will my 7-year-old daughter ever see an elephant in Africa unless I get her there very quickly?” Bradshaw says. “I don’t know.”


Overcoming Density-Dependent Regulation

Humans are unique in their ability to alter their environment with the conscious purpose of increasing its carrying capacity. This ability is a major factor responsible for human population growth and a way of overcoming density-dependent growth regulation. Much of this ability is related to human intelligence, society, and communication. Humans can construct shelter to protect them from the elements and have developed agriculture and domesticated animals to increase their food supplies. In addition, humans use language to communicate this technology to new generations, allowing them to improve upon previous accomplishments.

Other factors in human population growth are migration and public health. Humans originated in Africa, but have since migrated to nearly all inhabitable land on the Earth. Public health, sanitation, and the use of antibiotics and vaccines have decreased the ability of infectious disease to limit human population growth. In the past, diseases such as the bubonic plaque of the fourteenth century killed between 30 and 60 percent of Europe’s population and reduced the overall world population by as many as 100 million people. Today, the threat of infectious disease, while not gone, is certainly less severe. According to the World Health Organization, global death from infectious disease declined from 16.4 million in 1993 to 14.7 million in 1992. To compare to some of the epidemics of the past, the percentage of the world’s population killed between 1993 and 2002 decreased from 0.30 percent of the world’s population to 0.24 percent. Thus, it appears that the influence of infectious disease on human population growth is becoming less significant.


Why is GenBank growth slowing down? - Biology

School biology notes: PHOTOSYNTHESIS - importance and factors affecting rate

Its importance and limiting and interacting factors controlling the rate of plant photosynthesis

The ideas are applied to horticultural operations e.g. a greenhouse

Doc Brown's school biology revision notes: GCSE biology, IGCSE biology, O level biology,

US grades 8, 9 and 10 school science courses or equivalent for

14-16 year old students of biology

Sub-index for this page

Green p lants and algae are producers based on the chemistry of photosynthesis and the start of most food chains and the base of subsequent food webs.

We are highly dependant on crops whether to eat directly, processed food or animal feed - so, we might not be 'green', but we ultimately depend for a lot of our food on photosynthesis!

AND, its not just life on land, all aquatic life e.g. fish, also depend, initially, on photosynthesis in plankton or algae.

A food chain is a means of transferring the energy from photosynthesis in the biomass to support many forms of life, including us!

Even the meat we eat, high in protein and fat, did depend at some point on photosynthesis, so there is no getting away from photosynthesis!

TOP OF PAGE for SUB-INDEX

What is the process of PHOTOSYNTHESIS? A simplified version of the biochemistry of photosynthesis

Plants absorb water through their roots and carbon dioxide through their leaves and covert these into carbohydrate molecules, initially in the form of glucose, the waste product is oxygen! handy for us!

The carbon dioxide in air diffuses into leaves through the stomata, water comes up from the roots via the xylem tubes, oxygen diffuses out and sugars are transported around the plant by the phloem tubes.

For more on plant structure and function including gas exchange and leaf adaptations see below and also .

Carbon dioxide into leaves and oxygen out of the leaves is an example of gas exchange system on the surface pores (stomata) of the leaves.

The biochemical process of photosynthesis takes place in the chloroplasts of plant cells in the green leaves and stems with the help of green molecules called chlorophyll.

It is the green pigment chlorophyll that absorbs the light energy to power photosynthesis.

Photosynthesis is summarised by the equation:

carbon dioxide + water == light + chlorophyll ==> glucose + oxygen

This is overall an endothermic chemical reaction, energy is taken in, i.e. sunlight energy is absorbed in the process of photosynthesis.

Photosynthesis is the process by which plants make food, initially in the form of glucose, for themselves, and for most animal life, including us too via food chains!

The plant will use some of the glucose immediately to fuel all the necessary life maintaining processes.

The plant converts some of the glucose to starch - a chemical potential energy food store for the plant and animals like us too!

Photosynthesis utilises sunlight energy to convert carbon dioxide and water into glucose (basis of food) and oxygen.

Most of the oxygen is a waste gas by-product to plants, but vital for respiration for us and other animals!

The green pigment chlorophyll is in the subcellular structures called chloroplasts, where photosynthesis takes place in green plant cells.

All of the photosynthetic chemistry facilitated by enzymes (biological catalysts).

The chemistry of photosynthesis is very complicated but it takes place in two main stages.

1. Chlorophyll absorbs a photon of light energy. This sunlight energy (visible light photons) splits water (H2O) into hydrogen ions (H + ) and oxygen (O2).

From the plants point of view, the oxygen gas is given out as a waste material.

2. The hydrogen ions combine with carbon dioxide (CO2) to form glucose molecules (C6H12O6).

The carbon dioxide diffuses in through the stomata of the guard cells - effectively pores that can open and close ie CO2 in, and oxygen O2 out in the day and O2 in at night.

In daylight the rate of photosynthesis will exceed the rate of respiration.

At night the rate of respiration will exceed that of photosynthesis.

Both processes are need to keep the plant alive.

During photosynthesis light energy is absorbed by the green chlorophyll, which is found in chloroplasts in some plant cells and algae.

Chlorophyll looks green because it absorbs in the violet-blue and orange-red regions of visible light, so plants can absorb use the energy from visible electromagnetic radiation.

Plant structure and photosynthesis - leaf structure adaptations that help!

Photosynthesis in the context of plant organs including stems, roots and leaves.

Water and minerals are absorbed from the soil through the roots and moved up through the plant by transpiration.

Wherever a plant is green, photosynthesis is taking place, at least in daylight!

One essential green molecule for photosynthesis is chlorophyll.

The broad green leaves of plants exposed to light provide a large surface area for the light absorbing sites of photosynthesis - more than the thinner stem.

The leaves are thin so the absorbed carbon dioxide has only a short distance to diffuse to photosynthesising cells.

Leaves have veins (vascular bundles) that support the leaf and transport water and minerals to the leaf and glucose away from the leaf.

Epidermal tissues are the outer layers which cover the whole plant.

The mesophyll, between two epidermis layers, is where most photosynthesis happens in the chloroplasts - it all looks green due to the green chlorophyll molecules needed for photosynthesis (they don't absorb green light).

Palisade cells in the mesophyll contains lots of chloroplasts containing chlorophyll - so palisade cells are well adapted for photosynthesis.

The palisade cells are near the top of the leaf and exposed to the most light.

'Physics note': Plants look green because the chlorophyll absorbs the blue and red wavelengths of visible light, but not the green. The green light is either reflected or transmitted so the plant tissue looks green which ever angle you view it.

The upper side of a leaf is smoother and greener - richer in chloroplasts to capture the sunlight The under side of a leaf is rougher - more 'porous' for efficient gas exchange and the veins more prominent

Xylem and phloem networks of cells, transport substances around the plant e.g. sugars like sucrose and glucose from photosynthesis, and through the roots minerals (e.g. magnesium) and water for photosynthesis.

The tissues of leaves are adapted for gas exchange.

The lower epidermis contains lots of stomata (plural of stoma, pores) which let carbon dioxide directly diffuse into the leaf for photosynthesis and oxygen to diffuse out of the leaves - the gas exchange system.

The spongy mesophyll tissue also contains air spaces that help increase the rate of diffusion of gases in and out of the leaves.

In the outer epidermis layer guard cells are adapted to open and close the pores of the stomata (stomatal pores) which allows gas exchange and water evaporation eg for photosynthesis carbon dioxide in and oxygen out.

This helps regulate transpiration and respiration and all connected with photosynthesis. See transport in plants

The epidermal tissues are covered with a waxy cuticle which helps reduce the loss of water by evaporation.

All of the above structures mentioned must be 'connected' for the 'system to function' in a healthy plant.

It should be mentioned that a large percentage of the Earth's photosynthesis occurs in oceans in phytoplankton.

For more on plant structure and function including gas exchange and leaf adaptations see also .

Leaf structure, diffusion and photosynthesis

Carbon dioxide diffuses into the leaves through the stomata and is depleted through photosynthesis.

Therefore as photosynthesis proceeds, the internal carbon dioxide concentration in the leaf is much lower than in the surrounding air, so carbon dioxide will diffuse into the leaf down this concentration gradient.

The rate of diffusion of the carbon dioxide (and any other gas) is increased by:

Increasing the surface area of the leaf - always the broadest part of any plant.

The smaller the distance the molecules have to travel as they diffuse - thin leaves with an even thinner mesophyll layer.

What does the plant do with the glucose produced by photosynthesis using sunlight energy?

Glucose provides energy and can be converted into, and help to synthesise, a wide range of molecules in plant cell chemistry (plant biochemistry). This means plants make their own food!

The glucose produced in photosynthesis may be converted into insoluble starch for storage in leaves, roots and stems.

The insoluble nature of starch makes it a very useful concentrated chemical store of energy - if it was soluble, it would dissolve and diffuse all over the place.

Starch is a natural polymer made from linking many glucose molecules together and is the main chemical energy store in a plant.

A plant can't photosynthesise at night, so it needs energy from somewhere to stay alive at night!

When needed, starch is hydrolysed (broken down) into the useful sugar glucose, so the process of starch formation is reversed.

Glucose sugar is soluble and easily transported around a plant and fuels respiration in the mitochondria of plant cells - which in turn provides the energy for all the cellular processes needed by a plant.

If a plant tried to store the soluble glucose, the cells would absorb water by osmosis, swell up and burst!

Plants need energy from sugars (from photosynthesis) to power their own life supporting systems just as we do.

Plant cells use some of the glucose produced during photosynthesis for immediate respiration - release of energy to power the cell functions and particularly at night when no light can shine on the leaves.

Plant respiration in principle is the reverse of photosynthesis.

glucose + oxygen ==> products + chemical energy (to power the plant cell chemistry)

The energy released enables the plant to convert glucose plus other elements/ions like nitrogen/nitrate into other essential useful chemical substances - some are listed below.

At night there be a net loss of glucose/starch in respiration, but in daylight the rate of photosynthesis will exceed that of respiration in a growing plant so excess glucose can be converted into starch for storage.

. noting that starch and glucose are chemical energy stores.

Glucose is consumed in plant respiration, e.g. in aerobic respiration, plants use oxygen to oxidise glucose to carbon dioxide and water.

The released chemical energy to power all the cell chemistry including the conversion of glucose into starch and making protein.

Don't forget that plants respire all the time, just like us!

Glucose can be converted into starch that can be stored in roots (e.g. potato), stems and leaves, this provides energy at night and in winter.

Starch has the advantage of being insoluble in water, so won't dissolve away unnecessarily from vital energy reserve storage areas.

It can be used when sunlight is low e.g. winter, and of course at night when photosynthesis stops completely.

Also, by being insoluble, it won't affect the water concentration in cells by osmosis.

A cell with a high concentration of glucose would swell up by water absorption interfering with its function.

The chemical energy from glucose is needed to build larger more complex molecules.

Through growth and accumulation of these larger molecules biomass is built up in plants and algae.

Biomass means the mass of living material.

The energy built up in a plant's or algal organism's biomass enters the food chain so animals can now feed on it (herbivores) and themselves be fed on by other animals (carnivores).

This is why at the start of this page it was emphasised that photosynthesising organisms are the main producers of food for most of life on Earth.

Examples of the larger molecules in the biomass of plants and algae

Glucose is used to produce fats or oils (lipids) for storage - provides sources of energy via aerobic respiration, seeds contain food stores based on oils and fats (think of cooking oil from olives or sunflower oil for margarine) and waxes.

Glucose is used to make cellulose, which makes up and strengthens the cell walls eg of the xylem and phloem and is particularly needed in larger quantities in rapidly growing plants.

Amino acids are first synthesised from glucose and nitrate ions (absorbed from soil through the roots) and other minerals before conversion to proteins for tissue cell growth and repair.

Note that to produce proteins, plants also use nitrate ions that are absorbed from the soil.

W hat factors affect the rate of photosynthesis?

The rate of photosynthesis is usually limited by three main environmental conditions - factors :

(i) Shortage of light (usually lack of sunlight) slows photosynthesis - since the greater the light intensity, the greater the rate of photosynthesis.

(ii) Low temperature, slows down the rate of photosynthesis - a general rule for all chemical reactions

A combination of both (i) and (ii) will cause very different rates between photosynthesis in winter (less sunlight time, less intense light, slower) compared to summer (more sunlight time, more intense light, faster).

At night, light is the limiting factor, in winter its usually the temperature in daylight.

If the temperature gets too high photosynthesis will slow down due to enzyme damage.

(iii) A shortage of carbon dioxide will also slow down the rate of photosynthesis but you can artificially increase it by pumping CO2 into a greenhouse structure.

If there is sufficient light and the temperature not too low, the ambient carbon dioxide concentration becomes the limiting factor.

So, three factors affecting the rate of photosynthesis that can be investigated in the laboratory - see 7 graphs later!

Graphs further down the page, separately, discuss a single limiting factor i.e. (i) to (iii) mentioned above.

(iv) However, under some circumstances the essential green pigment chlorophyll might be the limiting factor too.

Lack of chlorophyll/chloroplasts in the plant cells reduce the plant's capacity to photosynthesise.

Stressed or damaged plants may turn pale yellow or develop spots from a fungus, bacteria or virus.

Plants maybe affected by disease eg halo blight, tobacco mosaic virus, poor nutrition - lack of vital minerals.

Also (v) lack of water denatures cells and plants droop, reducing photosynthesis, and eventually die.

Any of these factors can cause damage to chloroplasts or the cell cannot make enough chlorophyll.

Therefore the plant cell capacity to absorb sunlight is reduced weakening the plants growth and development.

(v) Strictly speaking, lack of water is another factor, but that does affect the whole plant.

Light intensity, temperature and the availability of carbon dioxide interact and in practice any one of them may be the factor that limits the speed (rate) photosynthesis.

You can relate the principle of limiting factors to the economics of enhancing the following conditions in greenhouses.

You can carry out laboratory experiments to measure the rate of photosynthesis under various conditions i.e. changing any of the three factors and keeping the other two factors constant.

These experiments and graphical data analysis are discussed in detail further down the page.

Factors controlling the rate of photosynthesis - detailed discussion of typical data graphs

The limiting factor is one that controls the maximum possible rate of the photosynthesis reactions for given set of conditions.

Graph 1. Light intensity limitation

Light energy is needed for photosynthesis, so as the light intensity increases, the rate of photosynthesis chemical reactions steadily increases in a linear manner - 1st part of the graph is 'light limiting'.

More light, more molecules 'energised' to react.

BUT, at the point where the graph becomes horizontal, light is no longer the limiting factor.

However, eventually the rate levels off to become constant due to limitation of the carbon dioxide concentration (too low) or the temperature (too low) and any increase in light intensity has no further effect on the rate of photosynthesis for plant growth.

Two points to bear in mind when studying any of the graphs dealing with photosynthesis.

Since the graph line has become horizontal (flattened out, constant rate), this also means that light intensity is no longer the limiting factor - you must increase carbon dioxide concentration or temperature to increase the rate of photosynthesis - in other words you need increase some other factor.

Remember: Whenever the graph line on a photosynthesis graph becomes horizontal, a limiting factor is coming into play.

Light intensity falls to

zero at night and there is much less light in winter, so these place limits on photosynthesis.

Plants have adapted to live in shaded areas by having larger and thinner leaves to increase the number of chlorophyll molecules to absorb light (see graph 8 ).

Greenhouse design/operation and light intensity.

Lots of glass window panes to let light in.

Site the greenhouse in a non-shaded area.

At night artificial light can be supplied.

However, the light level with have its limit (either sunlight or artificial light at night), so for maximum effect you may still need a warm temperature and a fresh supply of carbon dioxide.

Graph 2. Temperature limitation

Photosynthesis chemical reactions cannot happen without the help of enzymes.

Raising the temperature gives the molecules more kinetic energy so more of them react on collision, and initially, you get the expected (exponential) increase in the speed of the photosynthesis reaction - initially an accelerating curve upwards (non-linear) with increase in temperature increasing plant growth..

However, too high a temperature is just as bad as too a low temperature (which would be too slow).

At temperatures over 40 o C enzymes involved in the process are increasingly destroyed, so photosynthesis slows down and eventually stops because the photosynthesis enzymes are destroyed.

The denaturing of the protein structure caused by the higher temperatures affects the active sites on enzymes (x-reference key and lock mechanism) and they can no longer catalyse the photosynthesis reactions.

A graph of rate of photosynthesis versus temperature rises at first (usual rate of chemical reaction factor), goes through a maximum (optimum temperature) and then falls as the enzymes are becoming increasingly denatured and eventually cease to function.

The final shape of the graph is due to the combination of the two graph trends from increasing rate of reaction versus increase denaturing, both coincident with increase in temperature.

Greenhouse design/operation and temperature

Ideally in greenhouses you would want the optimum temperature, a constant adequate supply of carbon dioxide and plenty of light - hence the use of transparent glass!

A greenhouse warms up by trapping the heat radiation from the sun - the 'greenhouse effect'.

BUT take care that the greenhouse does not get too hot eg by opening ventilation systems or putting up shades.

In cold weather, heaters might be employed in a greenhouse because the temperature may be too low for efficient photosynthesis for plant growth - but heaters increase cost of production.

If the heaters are not electric and burn a fuel like paraffin, then lots of carbon dioxide is produced - quite handy, two factors catered for at the same time!

3. CARBON DIOXIDE CONCENTRATION

Graph 3. Carbon dioxide limitation

Carbon dioxide is needed for photosynthesis, so as the carbon dioxide concentration increases, the rate of photosynthesis chemical reactions steadily increases in a linear manner - initially the reaction rate of photosynthesis is directly proportional to CO2 concentration (can be in air or water)..

However, eventually the rate levels off due to limitation of the light intensity (too low) or the temperature (can be too low or too high) no matter what the increase in the CO2 concentration.

Since the graph line has become horizontal (flattened out), this also means that carbon dioxide concentration is no longer the limiting factor - you must increase light intensity or temperature to increase the rate of photosynthesis.

You should note that the concentration of carbon dioxide in air is only

0.04%, and is often the limiting factor, especially on warm bright sunny days ..

BUT, short dull winter days (low light intensity) and low temperature (slows chemical reactions) can also be the limiting factors.

Greenhouse design/operation and carbon dioxide concentration

If the ambient temperature is warm and the plants/greenhouse in bright sunshine, the limiting factor might be the concentration of carbon dioxide in air.

You do need some ventilation or the level of carbon dioxide gas will fall if the air is not replenished as the carbon dioxide is used up by the plants.

BUT, for maximum effect you need a warm temperature, plenty of light and extra CO2 if you can supply it!

For more on photosynthesis graphs see:

How to successfully operate a commercial greenhouse!

So 3 three factors can be manipulated to increase the rate of photosynthesis and hence increase plant growth.

Summary so far to help increase crop yields

Greenhouse design/operation and the photosynthesis light intensity factor

Lots of glass window panes to let light in.

Site the greenhouse in a non-shaded area.

At night artificial light can be supplied.

However, the light level with have its limit (either sunlight or artificial light at night), so for maximum effect you may still need a warm temperature and a fresh supply of carbon dioxide.

Greenhouse design/operation and the photosynthesis temperature factor

Ideally in greenhouses you would want the optimum temperature, a constant adequate supply of carbon dioxide and plenty of light - hence the use of transparent glass!

A greenhouse warms up by trapping the heat radiation from the sun - the 'greenhouse effect'.

BUT take care that the greenhouse does not get too hot eg by opening ventilation systems or putting up shades.

In cold weather, heaters might be employed in a greenhouse because the temperature may be too low for efficient photosynthesis for plant growth - but heaters increase cost of production.

If the heaters are not electric and burn a fuel like paraffin, then lots of carbon dioxide is produced - quite handy, two factors catered for at the same time!

Greenhouse design/operation and the photosynthesis carbon dioxide level factor

If the ambient temperature is warm and the plants/greenhouse in bright sunshine, the limiting factor might be the concentration of carbon dioxide in air.

You do need some ventilation or the level of carbon dioxide gas will fall if the air is not replenished as the carbon dioxide is used up by the plants.

BUT, for maximum effect you need a warm temperature, plenty of light and extra CO2 if you can supply it!

Overview of operating a successful greenhouse - commercial or amateur grower!

A greenhouse used is to artificially create the best environment for growing plants and increase photosynthesis efficiency.

ventilation - need to keep the air fresh and ensure the carbon dioxide level doesn't fall below that in the air outside.

glass (or transparent plastic) panels - allows the transmission of visible light for photosynthesis and infrared radiation to be absorbed and raise the temperature.

carbon dioxide supply - can artificially increase CO2 available to plants to increase rate of photosynthesis.

water supply - plants need a constant supply of water, the soil or compost may get to dry for optimum plant growth and the higher temperatures in a greenhouse increase the rate of transpiration.

heater - electric to raise temperature on colder days, preferably from renewable source, if paraffin, the combustion produces CO2 so that helps increase the rate of photosynthesis.

artificial lighting - enables photosynthesis to be continuous 24/7 and independent of the weather, BUT you need periods of darkness (use a timer) to allow the plant to transport and store glucose as starch.

humidifier - if the atmosphere becomes too dry the rate of transpiration increases and plants may droop from lack of water

blinds - can be used to control the light if necessary.

thermostat - not sure if this is used in greenhouses?

Growing crops in greenhouses can significantly increase the crop yield for a given area.

Greenhouse horticulture (agricultural growing of flowers, fruit and vegetables) is an intensive farming method using various technological developments - this particularly applies to hydroponics (described on my food production page).

ideally farmers-horticulturalists want optimum yields of crops without excessive leaf or root production.

A greenhouse traps the sunlight energy raising the internal temperature to make it less of a limiting factor but heating may be required in winter.

However, the extra costs of heating, artificial lighting or adding CO2 to the air, must be off-set by selling an acceptable quality product at a sustainable market price that the consumer is prepared to pay!

You can increase the temperature and carbon dioxide levels at the same time by using a paraffin heater - one of the better uses of a fossil fuel when burned to form carbon dioxide!

In summer it might get too hot so extra shade and ventilation may be needed to create cooler conditions.

Using artificial light extends the growing period beyond normal daylight hours - but an extra cost.

You should also note that plants enclosed in a greenhouse are less susceptible to pests and diseases.

Fertilisers may be added to the soil to provide the minerals the plant need's and absorbed from the soil by the root system.

Using greenhouses enables market gardeners to produce more good crops per year and if you can control the conditions and efficiently produce a reasonable quality crop - then your business can be commercially successful.

Large scale greenhouse complexes are proving successful in using artificial growing conditions and employ light and heat controls.

More complex graphs demonstrating more than one limiting factor controlling the rate of photosynthesis

Reminder: The limiting factor is one that controls the maximum possible rate of the photosynthesis reactions for given set of conditions.

For these experiments a suitable temperature must be chosen and kept constant! (eg lab. temp. of

Graph 8 Chlorophyll as a limiting factor

Graph 8 shows the rate of photosynthesis for two plants A and B.

We have looked at the way in which light, temperature or carbon dioxide can be limiting factor.

A shortage of chlorophyll can also be the 4th limiting factor.

Assume the graph for plant A is typical of most plants which are not adapted to live in shaded areas and receive an sample of sunlight i.e. do not live in a very shaded area.

In this case the rate of photosynthesis is limited by temperature or carbon dioxide concentration in the air.

Some plants, like plant B, live in continuous shade i.e. a low level of light intensity.

These plants have adapted to these conditions by evolving to grow a higher ratio of leaves to roots compared to other plants.

The leaves are larger and thinner with a greater surface area so more chlorophyll in chloroplasts is available to absorb light, so increasing the plant's photosynthesis efficiency.

The graph for B show a faster initial rate of photosynthesis because of the higher concentration of chlorophyll, but the rate of photosynthesis levels off before that of plant A as a limiting factor comes into play.

The limiting factor might a low temperature in a shaded area,

or carbon dioxide level if there is no air movement.

Possible practical work you may have encountered - methods of measuring the rate of photosynthesis

You can investigate the need for chlorophyll for photosynthesis with variegated leaves

Taking thin slices of potato and apple and adding iodine to observe under the microscope - test for starch.

Investigating the effects of light, temperature and carbon dioxide levels (using Canadian pondweed, Cabomba, algal balls or leaf discs from brassicas) on the rate of photosynthesis.

You can use computer simulations to model the rate of photosynthesis in different conditions

You can use sensors to investigate the effect of carbon dioxide and light levels on the rate of photosynthesis and the release of oxygen.

You may have done/seen experiments on the rate of photosynthesis in which the volume of oxygen formed is measured with a gas syringe connected to a flask of sodium hydrogen carbonate solution (to supply the carbon dioxide) and Canadian pondweed immersed in it.

All experimental methods depend on measuring the rate of oxygen production as a measure of the rate of photosynthesis.

The faster the oxygen production the faster the photosynthesis.

It is assumed that the rate of oxygen production is proportional to the rate of photosynthesis.

So, how can we measure the rate of photosynthesis?

Next, methods of measuring the rate of photosynthesis

Measuring the r ate of photosynthesis - experimental method 1 measuring the volume of oxygen produced with a gas syringe

You can use this gas syringe system to measure the effects of changing temperature, light intensity and carbon dioxide level (via a sodium hydrogencarbonate solution).

Method 1. Gas syringe system

A lamp and thermostated water bath are not shown in this diagram, but they are in the apparatus diagram for method 2 .

There are several aquatic plants you can use, the most popular seems to Canadian pondweed (elodea canadensis), but this is regarded as an invasive species, so perhaps some other oxygenated aquatic plant should be used!

In this 'set-up' you measure the rate of photosynthesis by measuring the rate of oxygen production as the gas is collected in the gas syringe.

From the graph of volume of oxygen versus time you measure the initial gradient to calculate the rate of production of oxygen as a measure of the rate of photosynthesis.

The graph should be reasonably linear at first e.g. rate of photosynthesis in cm 3 /min .

You can use sodium hydrogencarbonate (NaHCO3) as source of carbon dioxide and vary its concentration to vary the carbon dioxide concentration. You can use from 0.1% to 5% of NaHCO3 ie 0.1g to 5g per 100 cm 3 of water.

With increasing concentration you should see an increase in the rate of oxygen bubbles (eg cm 3 /min), but you must keep the temperature constant eg lab. temp. 20-25 o C, and the light intensity constant by keeping the lamp (not shown in the diagram) the same distance from the flask.

The light from the laboratory itself will contribute, but the total light should be constant.

You need to use the same quantity and batch of pondweed (or other oxygenating aquatic plant).

You use the same volume of water/sodium hydrogencarbonate solution.

Using the set-up described in the diagram, at constant temperature, constant light intensity - by using same lamp at the same distance from the flask, you can investigate the effect of the concentration of carbonate/carbon dioxide on the rate of photosynthesis.

To vary temperature you need to immerse the conical flask in a water bath (not shown) of different, but carefully controlled constant temperatures.

You should be able to demonstrate a maximum

35-40 o C i.e. the rate should be significantly lower at

The concentration of NaHCO3 and the light intensity should be both kept constant.

Varying the light intensity is quite difficult, you need to position a lamp at different measured distances away from the flask, but for accurate results you must take a light meter reading by the flask in the direction of the lamp - but you can still use the basic set-up of apparatus described in method 1. above.

A lamp in position is shown in method 2. and see the discussion on the inverse square law further down the page.

This simple experiment can readily show in principle the effect of changing the three controlling factors of the rate of photosynthesis.

Problems and errors with the method

Ideally the experiments should be done in the dark, with the lamp the only source of light, not very convenient in a classroom situation but it is particularly important when varying the light intensity - I don't see how you can get accurate results for light intensity though using a light meter might just ok?

Do you swirl the flask so the NaHCO3 concentration remains reasonably constant?, but will the same leaf area be exposed to the light in the direction of the lamp?

When varying the temperature it is not easy to maintain a constant temperature - if it falls a little, you could use the average temperature, not as accurate, but better than nothing! A thermostated water bath would be ideal.

The above apparatus is typical of that used in rate of reaction experiments in chemistry.

You can use other experiment designs to look more conveniently, and hopefully more accurately at the three factors that influence the rate of photosynthesis.

Measuring the r ate of photosynthesis - experimental method 2 - timing the movement of a bubbles of gas

You can use this gas syringe system to measure the effects of changing temperature, light intensity and carbon dioxide level (via a sodium hydrogencarbonate solution).

At the end of method 2 the inverse square low of light intensity is explained.

Method2.

Method 2. Following the gas evolution from a gas bubble in a capillary tube

I've seen this sort of set-up in textbooks and on the internet and it seems ok in principle, but I have doubts about its use in practice?

In this the Canadian pondweed (elodea) is enclosed in a boiling tube and placed in a large beaker of water that acts as a simple thermostated bath to keep the temperature constant. Again a thermostated water bath would be ideal.

A lamp is positioned at suitable distances with a ruler.

The oxygen bubbles are channelled into a capillary tube.

From the rate of movement of the bubbles you get an estimate of the rate of production of oxygen as a measure of the rate of photosynthesis.

It might ok just to measure the speed of a bubble down the capillary tube, BUT what happens if it fills with oxygen gas - you won't see any movement.

The general points about investigating the three variables were described in method 1. should be no need to repeat them.

How do you measure the rate?

You can measure the speed of an air bubble by the scale,

If you used a gas syringe here you would get a mixture of gas and liquid in the syringe - not very satisfactory, liquid in the syringe might make it quite stiff in movement and difficult to measure an accurate volume of oxygen gas formed.

Further thoughts on the experimental methods described in methods 1. and 2. above for determining the rate of photosynthesis in Canadian pondweed experiment.

The 'set-up' probably the best system I can devise sitting at home in front of the computer screen!

In method 2 the pondweed tube could be enclosed in a large beaker of water that acts as a simple thermostated bath to keep the temperature constant - ideally a thermostated water bath.

The tube of pondweed is immersed in NaHCO3 solution is subjected to a lamp emitting bright white light at a specific distance from tube of pondweed.

You can again use sodium hydrogencarbonate (NaHCO3) as source of carbon dioxide and vary its concentration to vary the carbon dioxide concentration.

You can use from 0.1% to 5% of NaHCO3 ie 0.1g to 5g per 100 cm 3 of water.

(i) The oxygen bubbles are still channelled into a capillary tube but the gases and liquids allowed to freely exit from the capillary tube - no problem with liquid in the syringe which might quite stiff anyway and difficult to measure an accurate volume.

(ii) A T junction in the tubing allows the 'injection' of water into the gas stream to make bubbles of gas visible.

You need to use the same quantity and batch of pondweed (or other oxygenating aquatic plant).

You use the same volume of water/sodium hydrogencarbonate solution.

What can you measure and vary?

Measuring the rate of photosynthesis by measuring the rate of oxygen gas production in the gas syringe is more accurate but requires more time to get a set of readings to plot a graph.

Measuring the speed of the horizontal movement of the gas bubbles is quite easy via the accurate linear scale and stopwatch.

You can use quite a long uniform capillary tube to increase the sensitivity and hence accuracy of the experiment.

For each set of experimental conditions get at least three reasonably consistent readings and compute an average for the best accuracy.

The speed of bubbles in cm/s gives you a relative measure of the rate of the overall reaction of photosynthesis to produce oxygen.

With increasing concentration (of NaHCO3) you should see an increase in the rate of oxygen bubbles, but you must keep the temperature constant eg lab. temp. 20-25 o C, and the light intensity constant by keeping the lamp a fixed distance from the flask. The light from the laboratory itself will contribute, but the total light should be constant and you can use a light meter to ensure the same light intensity.

Try to use a range of concentrations eg 1% to 5% solutions (1g - 5g NaHCO3 per 100 cm 3 of water).

To vary temperature you need to immerse the boiling tube in water baths of different carefully controlled and constant temperatures - ideally using a thermostated water bath.

You should be able to get enough results eg 5 o increments from 15 o C to 50 o C to show maximum the maximum rate of photosynthesis expected to be around 35-40 o C.

The concentration of NaHCO3 and the light intensity should be both kept constant.

Varying the light intensity is quite difficult, you need to position a lamp at different measured distances away from the pondweed tube.

You can calculate the relative intensity using the inverse square law, see light intensity section on this page.

BUT, for accurate results you should take a light meter reading by the flask in the direction of the lamp (see the discussion on the inverse square law further down the page).

You must choose, and keep constant, both the temperature and sodium hydrogencarbonate concentration of appropriate values eg a 2% solution of NaHCO3 and 25 o C.

Although I think this is an improvement on method 2, its still quite difficult to get accurate results.

I think a light meter is essential for accurate results - changing the lamp distance is relevant to changing the light intensity, BUT, intensity is NOT a simple function of distance.

You need to use the same sample of pondweed, but is it always the same leaf area towards the light?

The experimental runs should not take too long as the NaHCO3/CO2 concentration is falling all the time.

Graphs of experimental data and their interpretation

Seven graphs have already been fully described on this page.

The relative intensity of the light from a fixed power is governed by an inverse square law.

When investigating the influence of light intensity on the rate of photosynthesis you must appreciate the inverse square law applied to light intensity for a fixed lamp power and light emission.

As you move the lamp further away, the light intensity falls, and so should the rate of photosynthesis.

BUT the light intensity is inversely proportional to the distance between the light source and the experiment tube squared.

From a specific light source .

relative light intensity = 1 / d 2

. the light intensity is in arbitrary units, d = distance of the lamp from experiment.

The effect of the law can be demonstrated by some simple calculations .

. treating this idea as both predictions and ideal theoretical results!

The inverse square law for relative light intensity means that the relative brightness that the plant experiences falls away quite dramatically as the lamp is move further and further from the experiment tube.

Graphs of rate of photosynthesis versus distance of the lamp from experiments such as method 3.

These graphs are plots of the theoretical data used in the table above assuming a constant light source (a lamp!).

Graph (a) shows how rapidly the light intensity decreases as you move the experiment tube/flask away from the light source, shown by the equally rapid decline in the rate of photosynthesis. This is a consequence of the inverse square law of light intensity. You can show by experiment the rate of photosynthesis is proportional to the light intensity where it is the limiting factor. The graph also shows that the relationship between rate of photosynthesis and lamp distance is not linear.

Graph (b) shows that the rate photosynthesis is not proportional to reciprocal of the lamp distance, but it is a more linear graph than (a).

Graph (c) shows (for ideal results) that the rate of photosynthesis is proportional to the reciprocal of the lamp distance squared (and the lamp light intensity is proportional to 1 / d 2 ). Therefore in graph (c) the horizontal axis could be also labelled relative light intensity, a proportional linear relationship with the rate of photosynthesis.

Some simple experiments to investigate aspects of photosynthesis

Some demonstrations of involving photosynthesis

Demonstrating the presence of starch in plant leaves

Simple experiments on starch production in plants

Experiment 1. To test for starch in leaves

A leaf, held with tongs/tweezers is 'dunked' into boiling water - to stop all its chemical reactions.

The leaf is placed in a boiling tube of alcohol and gently heated in an electric water bath - this dissolves the green chlorophyll and turns the leaf a very pale colour - no longer green!

Take care, ethanol is highly flammable - bunsen burners not recommended!

The almost white leaf is rinsed with cold water and laid out on a filter paper.

With a teat pipette, spot a few drops of iodine solution onto the leaf.

If starch is present , a blue-black colour will appear - the simple standard food test for starch molecules .

Preparation of plants and set-up for experiments 2. and 3.

You can do simple experiments with a small plants in plant pots, if necessary keep them enclosed in a bell jar.

You have to 'de-starch' the plants by leaving them in the dark for at least 48 hours.

The plant will use up its starch energy store to keep itself alive!

You can use this set-up to do a couple of simple experiments, and, finally using the starch test described above, to show what is required for photosynthesis, or indeed, if photosynthesis was taking place.

Experiment 2. To show that light is needed for photosynthesis

From your stock of 'de-starched' plants, you keep one in the dark and one into bright sunlight or artificial light.

After 24 hours you test a sample leaf from each plant for the presence of starch.

The leaf from the plant in the dark should not give the blue-black colour with iodine solution - photosynthesis had not taken place.

The leaf from the plant in the light should have produced starch from photosynthesis, and after testing should give a blue-black colour with iodine solution showing the presence of starch.

This shows light is need for photosynthesis.

The plants should not be enclosed in the bell jar, so that each plant has access to carbon dioxide in the atmosphere.

Ideally, the plants should be identical and kept at the same temperature for a fair test.

Experiment 3. To show that carbon dioxide is needed

From your stock of 'de-starched' plants, two plants are left out in daylight or artificial light.

BUT, one of the plants is put in a bell jar with a small petri dish of soda lime.

(a) This isolates one of the plants from the surrounding 'normal' atmosphere.

(b) Soda lime absorbs and chemically reacts with carbon dioxide to give a solid product - thus removing carbon dioxide from the atmosphere around the plant.

The plants are then left out for 24 hours.

After 24 hours you test a sample leaf from each plant for the presence of starch.

The leaf from the plant left out in the laboratory (not in the bell jar) with access to the atmosphere should have produced starch from photosynthesis - after testing should give a blue-black colour with iodine solution showing the presence of starch.

However, the leaf from the plant in the bell jar should not give the blue-black colour with iodine solution - showing photosynthesis to form starch had not taken place despite having access to light.

This shows carbon dioxide is need for photosynthesis.

Ideally, the plants should be identical and kept at the same temperature for a fair test.

Experiment 4. To show that carbon dioxide is involved in the gas exchange of photosynthesis

This is a simple photosynthesis gas exchange experiment using hydrogencarbonate indicator and plant leaves.

Three test tubes are set up as in the diagram and described below.

All three test tubes are exposed to the same intensity of bright light - sunlight or lamp.

A test tube is set up just containing a few cm 3 of the orange hydrogencarbonate indicator.

This acts as a control and shouldn't change from its original orange colour, since there are no plant leaves in it and it is sealed to the atmosphere, there should be just the normal background level of carbon dioxide above the indicator.

If the indicator solution becomes more acidic, it becomes yellow.

If the indicator solution becomes less acidic, it becomes red.

Now remember, carbon dioxide gas is acidic when dissolved in water.

Observations and interpretation

2. Leaves exposed to bright light

When exposed to light the leaves can photosynthesise and absorb carbon dioxide.

6H2O + 6CO2 ====> C6H12O6 + 6O2

Therefore carbon dioxide will be absorbed by the plant and the reduction of carbon dioxide means conditions are less acidic.

So the hydrogencarbonate indicator changes to red - solution less acidic.

In bright light the rate of photosynthesis will be greater than the rate of respiration.

(Oxygen will replace the carbon dioxide, but that is not detected in this experiment, but you could set up a system to collect it and test the gas with a glowing splint - which should be reignited.)

3. Leaves shaded from light

If little light can reach the surface of the leaves, then photosynthesis cannot take place efficiently.

In order for the leaves (plant) to survive they must be a switch from less photosynthesis to more respiration.

C6H12O6 + 6O2 ====> 6H2O + 6CO2

The respiring plant leaves give out carbon dioxide which makes the condition more acidic.

Therefore the hydrogencarbonate indicator turns yellow - solution more acidic.

In shade the rate of photosynthesis will be less than the rate of respiration.

Experiment 5. Simple demonstration of the effect of light on the rate of photosynthesis

You can use this simple investigation experiment to help you design more sophisticated and more accurate quantitative experiments described in method 1. gas syringe system and method 2. moving gas bubble system .

You set up a beaker filled with water or sodium hydrogen carbonate solution.

In the beaker you place an oxygenating plant like a pondweed inside an inverted filter funnel.

You fill a test tube with water and invert it, still filled with water, and place it over the exit from the filter funnel.

When you shine bright light (sunlight or lamp) on the system, you should see bubbles of oxygen gas rising and collecting in the inverted test tube.

6H2O + 6 CO2 == light ==> C6H12O6 + 6 O2

If you collect enough gas, it should ignite a glowing splint - a simple chemical test for oxygen.

You can play around with a lamp distance to increase or decrease the light intensity and note any difference in the rate of bubble formation.

You should find adding sodium hydrogencarbonate speeds up photosynthesis because it supplies more carbon dioxide - there is only small amount dissolved in tap/deionised water.

Again, you could compare water with sodium hydrogencarbonate solution at the same light intensity.

BUT, this set-up is no good for looking at temperature.

In fact the whole experiment isn't very accurate at all.

The bubbles tend to form randomly, no way of accurately measuring gas volume or the rate at which the gas is evolved, no thermostated bath to control and vary temperature.

Hence the need for method 1. gas syringe system and method 2. moving gas bubble system .

Three year old granddaughter Niamh doing a bit of garden science!

General PLANT BIOLOGY revision notes

and a section on Stem cells and uses - meristems in plants (at the end of the page!)

Section on plants on Cloning - tissue culture of plants gcse biology revision notes

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What are the four Phases of Bacterial Growth

Anyone who has left sour cream or cottage cheese in the refrigerator too long can attest to the speed with which bacteria can grow. It seems that a colony of green, fuzzy gunk can appear overnight, spoiling your attempt to make your favorite dip at the Saturday afternoon football game. Bacteria can certainly grow quickly, but did you know that they have a distinct pattern of growth. Because they are single celled organisms, bacteria must literally split themselves in half to replicate. There are four phases to this growth cycle. Let’s take a look at each of the four phases of bacterial growth.

The first of the four phases of bacterial growth is called the “lag phase”. This is the longest of the four phases. During this phase, there is little or no cell growth. Instead of growing, the bacterial cells are busy replicating various proteins and DNA in preparation for the next phase. The cells are not shut down during the lag phase. They are very metabolically active, but are not getting any bigger.

The lag phase can go on for several hours, or many days, depending on the particular bacteria, and the conditions it is living in.

The second phase of bacterial growth is called the “log phase”. In this phase the bacteria become extremely active and begin the process of dividing. Every chemical in the cell is being replicated in anticipation of the cell dividing. The log phase gets its name from “logarithmic”, which roughly means that there is massive growth (this is not an exact definition, just what is implied).

The log phase is generally quite rapid and puts the bacterial cells in a vulnerable position. During the log phase, the size of the bacterial colony increases dramatically. The log phase is what’s happening when your sour cream goes from white to green overnight.

The third phase of bacterial cell growth is called the “stationary phase”. As you can probably guess, this phase involves a slow-down in the growth of the cells and the colony. As resources are used, the rate of cell death begins to match the rate of cell division. Thus, the entire colony slows it’s growth. There’s only so much sour cream to go around, right?

The stationary phase is often referred to as a being in a state of equilibrium. This simply means that the colony of bacteria is not getting any bigger or smaller, it is simply living. In addition to limited resources, the build-up of bacterial waste products (yes, bacteria have virtual “poop”) can limit the growth of a bacterial colony.

When conditions around the bacteria get really bad, the colony can enter the fourth and final phase. This is called the “death phase”. I’ll give you one guess as to what’s happening during this phase.

During the death phase, the number of dead or dying bacterial cells begins to outnumber the new ones. Again, this can be because of limited resources (food), because of waste production, or because of other changes in the environment around the bacteria. Cells in the bacterial colony will die off until there are few enough of them to survive on what’s nearby, at which point they will start to cycle back to the first phase and begin the process all over again.

The four phases of bacterial growth may seem rather obvious and not important. In reality, scientists and doctors use the basic knowledge of the metabolic events which are taking place in these phases to develop ways to combat bacterial growth. For example, because bacterial cells are more vulnerable during the log phase, many antibiotics target metabolic processes in that phase in an attempt to stop the bacteria from growing.

The next time you open an old jar of food which is growing fuzzy colonies of goo, you’ll have an idea what phases of growth they took to get there. Yummy thought, eh?


Growth Curve

Since bacteria are easy to grow in the lab, their growth has been studied extensively. It has been determined that in a closed system or batch culture (no food added, no wastes removed) bacteria will grow in a predictable pattern, resulting in a growth curve composed of four distinct phases of growth: the lag phase, the exponential or log phase, the stationary phase, and the death or decline phase. Additionally, this growth curve can yield generation time for a particular organism &ndash the amount of time it takes for the population to double.

Bacterial Growth Curve. By Michał Komorniczak. If you use on your website or in your publication my images (either original or modified), you are requested to give me details: Michał Komorniczak (Poland) or Michal Komorniczak (Poland). For more information, write to my e-mail address: [email protected]m [CC BY-SA 3.0], via Wikimedia Commons

The details associated with each growth curve (number of cells, length of each phase, rapidness of growth or death, overall amount of time) will vary from organism to organism or even with different conditions for the same organism. But the pattern of four distinct phases of growth will typically remain.

Lag phase

The lag phase is an adaptation period, where the bacteria are adjusting to their new conditions. The length of the lag phase can vary considerably, based on how different the conditions are from the conditions that the bacteria came from, as well as the condition of the bacterial cells themselves. Actively growing cells transferred from one type of media into the same type of media, with the same environmental conditions, will have the shortest lag period. Damaged cells will have a long lag period, since they must repair themselves before they can engage in reproduction.

Typically cells in the lag period are synthesizing RNA, enzymes, and essential metabolites that might be missing from their new environment (such as growth factors or macromolecules), as well as adjusting to environmental changes such as changes in temperature, pH, or oxygen availability. They can also be undertaking any necessary repair of injured cells.

Exponential or Log phase

Once cells have accumulated all that they need for growth, they proceed into cell division. The exponential or log phase of growth is marked by predictable doublings of the population, where 1 cell become 2 cells, becomes 4, becomes 8 etc. Conditions that are optimal for the cells will result in very rapid growth (and a steeper slope on the growth curve), while less than ideal conditions will result in slower growth. Cells in the exponential phase of growth are the healthiest and most uniform, which explains why most experiments utilize cells from this phase.

Due to the predictability of growth in this phase, this phase can be used to mathematically calculate the time it takes for the bacterial population to double in number, known as the generation time (g). This information is used by microbiologists in basic research, as well as in industry. In order to determine generation time, the natural logarithm of cell number can be plotted against time (where the units can vary, depending upon speed of growth for the particular population), using a semilogarithmic graph to generate a line with a predictable slope.

The slope of the line is equal to 0.301/g. Alternatively one can rely on the fixed relationship between the initial number of cells at the start of the exponential phase and the number of cells after some period of time, which can be expressed by:

where (N) is the final cell concentration, (N_0) is the initial cell concentration, and (n) is the number of generations that occurred between the specified period of time.

Generation time (g) can be represented by t/n, with t being the specified period of time in minutes, hours, days, or months. Thus, if one knows the cell concentration at the start of the exponential phase of growth and the cell concentration after some period of time of exponential growth, the number of generations can be calculated. Then, using the amount of time that growth was allowed to proceed (t), one can calculate g.

Stationary Phase

All good things must come to an end (otherwise bacteria would equal the mass of the Earth in 7 days!). At some point the bacterial population runs out of an essential nutrient/chemical or its growth is inhibited by its own waste products (it is a closed container, remember?) or lack of physical space, causing the cells to enter into the stationary phase. At this point the number of new cells being produced is equal to the number of cells dying off or growth has entirely ceased, resulting in a flattening out of growth on the growth curve.

Physiologically the cells become quite different at this stage, as they try to adapt to their new starvation conditions. The few new cells that are produced are smaller in size, with bacilli becoming almost spherical in shape. Their plasma membrane becomes less fluid and permeable, with more hydrophobic molecules on the surface that promote cell adhesion and aggregation. The nucleoid condenses and the DNA becomes bound with DNA-binding proteins from starved cells (DPS), to protect the DNA from damage. The changes are designed to allow the cell to survive for a longer period of time in adverse conditions, while waiting for more optimal conditions (such as an infusion of nutrients) to occur. These same strategies are used by cells in oligotrophic or low-nutrient environments. It has been hypothesized that cells in the natural world (i.e. outside of the laboratory) typically exist for long periods of time in oligotrophic environments, with only sporadic infusions of nutrients that return them to exponential growth for very brief periods of time.

During the stationary phase cells are also prone to producing secondary metabolites, or metabolites produced after active growth, such as antibiotics. Cells that are capable of making an endospore will activate the necessary genes during this stage, in order to initiate the sporulation process.

Death or Decline phase

In the last phase of the growth curve, the death or decline phase, the number of viable cells decreases in a predictable (or exponential) fashion. The steepness of the slope corresponds to how fast cells are losing viability. It is thought that the culture conditions have deteriorated to a point where the cells are irreparably harmed, since cells collected from this phase fail to show growth when transferred to fresh medium. It is important to note that if the turbidity of a culture is being measured as a way to determine cell density, measurements might not decrease during this phase, since cells could still be intact.

It has been suggested that the cells thought to be dead might be revived under specific conditions, a condition described as viable but nonculturable (VBNC). This state might be of importance for pathogens, where they enter a state of very low metabolism and lack of cellular division, only to resume growth at a later time, when conditions improve.

It has also been shown that 100% cell death is unlikely, for any cell population, as the cells mutate to adapt to their environmental conditions, however harsh. Often there is a tailing effect observed, where a small population of the cells cannot be killed off. In addition, these cells might benefit from their death of their fellow cells, which provide nutrients to the environment as they lyse and release their cellular contents.

Key Words

binary fission, multiple fission, budding, spores, cell cycle, closed system, batch culture, growth curve, lag phase, exponential or log phase, generation time (g), N, N0, n, t, stationary phase, DNA-binding proteins from starved cells (DPS), oligotrophic, secondary metabolites, death or decline phase, viable but nonculturable (VBNC).


Watch the video: Whats behind the slowdown in productivity growth? (May 2022).