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How do microbes spread from a small place to a very large place?

How do microbes spread from a small place to a very large place?


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Bacteria are very small, so they cannot move very far on their own. Viruses cannot move themselves at all. So how does a specific type of bacteria or virus spread from a small place to a very large area (such as the whole Earth)?


Birds migrate for thousands of miles, carrying diseases on a time scale of months or less. With climate shifts, insects and animals shift their ranges on a time scale of hundreds of years or more. Bacterial spores like anthrax can be in a form that is easily blown around the whole Earth, ready to thrive wherever they touch down. Plant diseases travel with their plant hosts, and over time scales of thousands of years the plants - e.g., dandelions and conifers - can spread thousands of miles of latitude and longitude.


The answer by @SMcGrew is essentially correct, but let me add a technical term (at least in the context of infectious diseases): the bacteria and viruses a carried by vectors. Since word vector is a kind of overused, even if we limit ourselves to biology, it is also common to be more specific and call the disease vectors.

Vectors are classified into biological vectors and mechanical vectors, depending on whether they biologically interact with the microbe (i.e., they get infected) or whether they are simply carried from one place to another.


Food poisoning

© A. Dowsett, Health Protection Agency / Science Photo Library The bacterium Campylobacter jejuni is a common cause of food poisoning. Contaminated poultry, meat and milk are sources of infection. It takes about 3 days for the symptoms of diarrhoea, stomach cramps and fever to develop.

The number of cases of food-borne illness remains high with an estimated 1 million people in the UK becoming infected each year. The symptoms, including vomiting, diarrhoea, abdominal pain and fever, are not only unpleasant they also cost an estimated £1.5 billion a year in lost working days and medical care. Most food-borne illness is preventable.

Preventing food poisoning is the responsibility of everyone in the chain from the plough to the plate. This includes farmers and growers, manufacturers, shops, caterers and consumers. The activities of food suppliers are governed by UK and EU food safety law. In the home correct hygiene, cooking and storage must be practised.

Some of the bacteria that can cause food poisoning

Name of bacterium Original source Risky foods Time to develop Symptoms
Bacillus cereus soil cooked rice and pasta meat products vegetables 1&ndash5 hours nausea, sickness and diarrhoea
Campylobacter jejuni raw meat and poultry undercooked meat and poultry raw milk and cross-contaminated food 3&ndash5 days of eating infected food fever, severe pain and diarrhoea
Clostridium botulinum (very rare) soil faulty processed canned meat and vegetables cured meat and raw fish 1&ndash7 days affects vision, causes paralysis and can be fatal
Clostridium perfringens the environment large joints of meat reheated gravies 8&ndash24 hours nausea, pain and diarrhoea
Escherichia coli &ndash
E. coli O157:H7 is a very nasty strain and it can be fatal
the gut of all humans and animals contaminated water, milk, inadequately cooked meat, cross-contaminated foods 3&ndash4 days inflammation, sickness and diarrhoea
Listeria monocytogenes everywhere soft cheeses, paté, pre-packed salad cook-chill products varies fever, headache, septicaemia and meningitis
Salmonella gut of birds and mammals including humans - spread by faeces into water and food poultry, eggs and raw egg products, vegetables 6&ndash48 hours diarrhoea, sickness and headaches
Staphylococcus aureus the skin and noses of animals and humans cured meat milk products unrefrigerated, handled foods 2&ndash6 hours sickness, pain and sometimes diarrhoea

An in-depth look at a bacterium that causes food poisoning

Campylobacter

The bacterium Campylobacter is part of the normal flora living in the intestines of healthy chickens and other animals. At the factory when a chicken is killed and gutted, the contents of its intestines, including the Campylobacter, could come into contact with the bird&rsquos skin. This means the raw chicken meat could become contaminated with Campylobacter.

How do you make sure chicken is safe to eat?

Campylobacter is sensitive to heat so cooking the chicken properly will kill it and make the meat safe to eat. If the chicken is served undercooked, then the Campylobacter could survive and be eaten along with the chicken. After the bacteria have been swallowed they multiply inside the person&rsquos intestine and cause the illness known as food poisoning. It takes about 3 days for the symptoms of diarrhoea, stomach cramps and fever to develop. The illness lasts between 2 days and a week.

Cross-contamination is the transfer of microbes from raw foods to prepared and cooked foods, it can take place by:

  • raw food touching or splashing on cooked food
  • raw food touching equipment or surfaces that are then used for cooked food
  • or people touching raw food with their hands and then handling cooked food.

To prevent cross-contamination it is important to maintain good kitchen hygiene such as storing cooked and raw food separately and good personal hygiene by washing hands correctly and tying hair back.

Spoilers

When microbes grow on food it soon beings to smell nasty, look slimy, change colour, taste awful or even get a furry coating and is inedible. Find out what’s causing this.

Producers

Microbes ferment sugar to make energy for themselves – luckily for us food like bread and yoghurt can be made by microbial fermentations.

Microbes and the human body

Ever wondered why when we are surrounded by microbes we are not ill all the time?

Microbes and the outdoors

The function of microbes as tiny chemical processors is to keep the life cycles of the planet turning.


Classification of Microorganisms

Microorganisms are classified into taxonomic categories to facilitate research and communication.

Learning Objectives

Assess how early life changed the earth

Key Takeaways

Key Points

  • The classification system is constantly changing with the advancement of technology.
  • The most recent classification system includes five kingdoms that are further split into phylum, class, order, family, genus, and species.
  • Microorganisms are assigned a scientific name using binomial nomenclature.

Key Terms

  • DNA fingerprinting: A method of isolating and mapping sequences of a cell’s DNA to identify it.

Life on Earth is famous for its diversity. Throughout the world we can find many millions of different forms of life. Biologic classification helps identify each form according to common properties (similarities) using a set of rules and an estimate as to how closely related it is to a common ancestor (evolutionary relationship) in a way to create an order. By learning to recognize certain patterns and classify them into specific groups, biologists are better able to understand the relationships that exist among a variety of living forms that inhabit the planet.

Classification of E. coli: Domain: Bacteria, Kingdom: Eubacteria, Phylum: Proteobacteria, Class: Gammaproteobacteria, Order: Enterobacteriales, Family: Enterobacteriaceae, Genus: Escherichia, Species: E. coli.

The first, largest, and most inclusive group under which organisms are classified is called a domain and has three subgroups: bacteria, archae, and eukarya. This first group defines whether an organism is a prokaryote or a eukaryote. The domain was proposed by the microbiologist and physicist Carl Woese in 1978 and is based on identifying similarities in ribosomal RNA sequences of microorganisms.

The second largest group is called a kingdom. Five major kingdoms have been described and include prokaryota (e.g. archae and bacteria), protoctista (e.g. protozoa and algae), fungi, plantae, and animalia. A kingdom is further split into phylum or division, class, order, family, genus, and species, which is the smallest group.

The science of classifying organisms is called taxonomy and the groups making up the classification hierarchy are called taxa. Taxonomy consists of classifying new organisms or reclassifying existing ones. Microorganisms are scientifically recognized using a binomial nomenclature using two words that refer to the genus and the species. The names assigned to microorganisms are in Latin. The first letter of the genus name is always capitalized. Classification of microorganisms has been largely aided by studies of fossils and recently by DNA sequencing. Methods of classifications are constantly changing. The most widely employed methods for classifying microbes are morphological characteristics, differential staining, biochemical testing, DNA fingerprinting or DNA base composition, polymerase chain reaction, and DNA chips.


Learning from Earth's Smallest Ecosystems (Kavli Hangout)

Alan Brown, writer and blogger for the Kavli Foundation, contributed this article to Live Science's Expert Voices: Op-Ed & Insights.

From inside our bodies to under the ocean floor, microbiomes — communities of bacteria and other one-celled organisms — thrive everywhere in nature. Emerging at least 3.8 billion years ago, they molded our planet and created its oxygen-rich atmosphere. Without them, life on Earth could not exist.

Yet we know surprisingly little about the inner workings of nature's smallest and most complex ecosystems.

Microbiomes have a great deal to teach us. By learning how members of microbiomes interact with one another, scientists might discover innovative green chemistry and life-saving pharmaceuticals, or learn how to reduce hospital infections, fight autoimmune diseases, and grow crops without fertilizers or pesticides.

The sheer complexity of microbiomes makes them difficult to study by conventional biochemical means. Nanoscience provides a different and complementary set of tools that promises to open a window into this hidden world. [The Nanotech View of the Microbiome]

Earlier this month, The Kavli Foundation hosted a Google Hangout with two leaders in the emerging applications of nanoscience for studying microbiomes. They discussed the potential of natural biomes, why they are so difficult to understand, and how nanoscience may help us unlock microbiome secrets.

Joining the conversation were:

Eoin Brodie, a staff scientist in the Ecology Department at Lawrence Berkeley National Laboratory. He was part of the team that pioneered a device capable of identifying thousands of the bacterial species found in microbiomes, and is currently developing ways to combine data from many different types of measurement tools into a more coherent picture of those ecosystems.

Jack Gilbert is a principal investigator in the Biosciences Division of Argonne National Laboratory and an associate professor of ecology and evolution at the University of Chicago. He has studied the microbiomes of hospitals and is working on ways to use nanostructures containing bacteria to help infants fight immune diseases.

Below is a modified transcript of their discussion. Edits and changes have been made by the participants to clarify spoken comments recorded during the live webcast. To view and listen to the discussion with unmodified remarks, you can watch the original video.

The Kavli Foundation: So let's start with an obvious question, what exactly is a microbiome?

Eoin Brodie: A microbiome is a connection of organisms within an ecosystem. You can think of the ecosystem of microbes in the same way you think of a terrestrial ecosystem, like a tropical forest, a grassland, or something like that. It is a connection of organisms working together to maintain the function of a system.

Jack Gilbert: Yes. In a microbiome, the bacteria, the archaea (one-celled organisms similar to bacteria), the viruses, the fungi, and other single-celled organisms come together as a community, just like a population of humans in a city. These different organisms and species all play different roles. Together, they create an emergent property, something that the whole community does together to facilitate a reaction or a response in an environment.

TKF: How complex can these microbiomes? Are they like tropical forests? Are they more complex, less complex?

J.G.: The diversity of eukaryotic life — all the living animals and plants that you can see — pales into insignificance beside the diversity of microbial life. These bacteria, these archaea, these viruses — they've been on the earth for 3.8 billion years. They are so pervasive, they have colonized every single niche on the planet.

They shaped this planet. The reason we have oxygen in the atmosphere is because of microbes. Before they started photosynthesizing light into biomass, the atmosphere was mostly carbon dioxide. The reason the plants and animals exist on Earth is because of bacteria. The diversity of all the plants and animals — everything that's alive today that you can see with your eyes — that's a drop in the proverbial ocean of diversity contained in the bacterial and microbial world. [Can Microbes in the Gut Influence the Brain?]

E.B.: We tend to think of the earth as being a human planet and that we're the primary organism, or the alpha species. But we're really passengers, we're just blow-in's on a microbial planet. We're recent, recent additions.

TKF: You both wax so poetic about it. Yet we know so little about microbiomes. Why is it so hard to understand what goes on in these ecosystems?

E.B.: Jack eluded to it. The first problem is that microbiomes are very small. We can't see them, and it's very difficult to understand how things work when you can't see them. So tools are needed to be able to see these organisms.

We also can't grow them. It's very hard to bring them from the natural ecosystem into the lab for study. Probably less than one percent, depending on the ecosystem, can actually be cultivated on growth media in the lab so that we can do experiments and understand what functions they carry out. That leaves 99 percent — the vast majority of the microbes on Earth and most of their ecosystems — unknown to us, apart from their DNA signatures and things like that.

Now, Jack has pioneered DNA analyses. When you look at the DNA signatures from these environments, there are all these new organisms, new proteins, and new functions that we have never really seen before. This has been called earth's microbial dark matter. Just like dark matter and energy in the universe, this has been unknown to us, but it is extremely important if the planet — and humans — are to continue to function.

TKF: So, what makes it so hard to grow these microbes in a Petri dish?

E.B.: They're very fussy. You can think of it that way. They don't like to eat the food that we give them, in many cases. They eat things that we don't know they can eat. They breathe things that we don't know that they can breathe.

We breathe oxygen, they breathe oxygen, but they also breathe nitrates, iron, sulfur, even carbon dioxide. Getting the right concentrations and combinations of what they eat and breathe is very difficult.

In some cases, even if you can work that out, there may be something that they need to get from another member of the ecosystem. That member may supply an essential nutrient or a cofactor for them to grow.

So getting all of those possible permutations and combinations right is extremely challenging. A lot of people are working on it, and there's a lot of expertise being put into this, but it's extremely difficult and complicated.

J.G.:& That's an interesting point. I liken it to having a baker. You know, if you have a baker in a human community, the baker needs somebody who can make the flour, somebody who can provide a bit of yeast, and someone who will buy the bread. They exist as a network of individuals living in a community.

If you take the baker out of the community, he or she cannot make the bread and so they are no longer a baker. Removing a microbe from its community reduces the likelihood that it will be able to perform the roles and tasks that it does in that environment.

So it's almost like you don't want to try and grow these things in isolation. Because, while isolating them makes our job as a microbiologist easier, it's also much more difficult to understand what they actually do in the environments in which they live. We can't figure that out in isolation because they are community players.

TKF: What are some of the tools that we can use today to look at microbiomes? Is there a state of the art?

J.G.: So I'll take on that. I mean this is a very dynamic evolving field. It is not a field where everyone seems to rest on their laurels.

To understand microbes, we have a couple of tools that are available to us. One of those tools is genomics, so we can sequence the genome of bacteria, archaea, viruses and fungi, just as we've done for the human genome.

The second one is the transcriptome, which looks at RNA, a transient molecule that creates the cell by translating what's in the genome into proteins. That's useful, because it tells us which genes are being turned on and off when we put those microbes under different conditions.

Then we have the proteome, the proteins that actually make up the cell. They are the enzymes that enable the organism to interact with its environment, to consume its food, to respire carbon dioxide, oxygen or iron, and so on.

Then you have the metabolome, the metabolic molecules living organisms consume as food and produce as waste products.

The genome, transcriptome, proteome, and metabolome are four of the tools in our toolbox that we can actually use to examine the microbial world. But they are by no means the limit of our tools or our goals. We have ambitions far beyond just examining those components. Eoin is developing some of these, and maybe Eoin, you want to jump in now?

E.B.: Yes, I'd add to that. The challenge of understanding the microbiome, and even individual microbes, is that they're just so small. They're complicated and small, so understanding their activity — their transcriptomes or proteins or metabolites — at the scale at which they exist, is extremely challenging.

All the technologies that Jack mentioned are being developed with larger organisms in mind. Scaling them down to deal with the size of microbes, but then increasing their throughput to deal with the complexity of microbes, is a huge, huge challenge.

I'll give you an example. When you look at the activity of an ecosystem, say a tropical forest, you look at the distribution of trees and animals, and look for the association between the vegetation and animals.

So if you want to understand insects, you have a space in mind. You think, "This lives near this. It interacts in this area." So there's an interaction, a fundamental association between those members of the ecosystem.

The way we typically looked at microbiomes — though this is changing now — was to mash up the entire forest in a blender. Then we would sequence all of the DNA, and look at the RNA and proteins, and the metabolites.

Then we try to go back and say, "This tree is interacting with this insect." Whereas, in reality, that tree is hundreds or thousands of kilometers away from that insect, and they never see each other.

That's the problem we have in the microbiome. When we mash up those organisms to look at their DNA, RNA, proteins and metabolites, we get rid of that spatial structure and its associations. And we lose the importance of space in terms of facilitating interactions. [The Nanotech View of the Microbiome (Kavli Roundtable)]

So, really, I think the next wave in microbiome research has to target this microbial activity and interactions at the scale of the microbe. Do they see each other? Do they interact, and how do they interact? What chemicals do they exchange, and under what conditions? I think that's the real challenge. That's why we're talking to the Kavli Foundation, because that's where nanoscience comes in.

TKF: This is an excellent transition to my next question: How do we use nanoscience to learn about microbiomes? For example, could we use some of the same nanoscale probes we are developing to study the brain to, say, investigate microbiomes in the ocean or soil?

E.B.: I think there are some interesting parallels. I mean, you can think of the brain as this extremely complicated network of neurons. The BRAIN Initiative is attempting to map those neurons and to follow their activity.

Similarly, the microbiome is a network of interacting organisms that turn on and turn off. The connections and the structure of that network are extremely important to the functioning of the system, just as it is for the functioning of the brain.

For the BRAIN Initiative, people got together and said, "Well what do we need to do to look at electrical charge and electrical flow through neurons, noninvasively, and in real time?" And they came up with some technologies, that can potentially, do remote sensing on a very small scale, and watch how the system changes noninvasively.

So, one approach to understanding the brain is to use external imaging, and another approach is to embed sensors.

In the BRAIN Initiative some sensors are being developed here at Berkeley lab and elsewhere that use RFID — radio frequency identity — technology. They are similar to tags used to track shipping containers, goods in department stores, and things like that. They both transmit information and harvest energy from radio frequencies, so they're autonomous devices. I think that the challenge now is coupling that technology to sensors that can monitor something in the environment and send that information autonomously — no batteries required — to receivers. Then, if these sensors are distributed in an intelligent way, just like with GPS, you can triangulate where that information is coming from.

How could you use this to understand a microbiome? Well, the sensors that are being developed are still relatively large scale, about one square millimeter in size. That's pretty small for us, but very large for a microbe.

So you can think about this in soil. Let's say we want to understand what happens when a root grows through soil. The root stimulates microbes, and there are ten times more microbes near the root than there are away from the root in soil. They all have different chemistries and different functions that are very important for the nutrition and health of the plant.

If you could distribute very small sensors in the soil and have them sense things like carbon from roots or oxygen consumed by microbes, then you can build a three dimensional picture of how the soil microbiome is changed and altered as a root moves through the soil. That's one example of how advances in other fields, driven by nanotechnology, could be applied to microbiome.

TKF: These RFID sensors would be based on semiconductor chips, right? So you could take a wafer, make a lot of them cheaply, distribute them in the soil, and get a picture you couldn't get any other way?

E.B.: Yes. There's an emerging field called predictive agriculture. It's like personalized agriculture, where fertilizer addition, for example, in a field would not be uniform. Instead, you would deliver the fertilizer where it's needed. You would irrigate the field exactly where it's needed. So you have this massive network of distributed autonomous sensors, and that would allow us to more efficiently use fertilizer. Then it wouldn't be leached or lost from the system, and cause water pollution and things like that. These examples are not on a microbial scale, but microbial processes control the availability and uptake of these fertilizers.

TKF: Thank you. Hold that thought and we'll come back to it in a few moments. In the meantime, Jack has been studying microbiomes in a new hospital to see how they evolve and affect the spread of disease. Could you tell us what you are doing, and how nanotechnology might help?

J.G.: Yes. The microbes that exist in a hospital have been a focus of clinicians and medical researchers for a couple of hundred years. Ever since we uncovered that bacteria might actually be causing disease, we've been trying to eradicate as much microbial life as possible.

That paradigm is shifting to one where we're more interested in trying to understand how bacterial communities in a hospital may facilitate the spread of disease and antibiotic resistance, and maybe promote health as well.

We've been going into hospitals and, with a very, very high temporal resolution, exploring how their bacterial communities change over time. So, looking at a scale of hours to days, we're trying to understand how — when a patient moves into a new room to have an operation or to undergo a procedure — the microbes that are already in that room affect the outcome of the patient's stay in the hospital. We want to know if it makes them either healthier or sicker.

So, we've been cataloging the microbes at these very fine scales. And what we see is an exchange between the bacteria in the room and inside the patient's body.

But we've also discovered that the vast majority of bacteria that we would normally associate with so-called healthcare-associated infections — pathogens that we thought people acquire during hospital stays — appear to be bacteria that patients brought into the hospital themselves. They're bacteria that we have inside us.

Remember, we have one hundred trillion bacteria living inside us. They weigh about two pounds, about the same as the brain. So if you think that the BRAIN Initiative is important, well maybe a microbiome initiative would also be important, because it weighs about the same as the brain.

The human microbiome has a lot of players. Most of them are friendly to us, but they can turn on us too. I liken this to a riot spreading in the city. You know, if you take things away from people, they will generally rise up and try to overthrow the very thing which was supporting them in the first place.

Microbes are the same way. We give a hospital patient antibiotics and radiation therapy to kill bacteria. Then we cut open his or her intestine and expose the bacteria to oxygen, which they don't like, and stitch the gut back up. When we look at the bacteria, we see that previously friendly bacteria have started to riot. They've been insulted so many times by the patient's treatment that they've decided that they've had enough. Then they go and attack the host to regain the resources which are being taken away from them.

This is very important. Understanding a patient's hospital stay from the microbes' perspective is helping us to design better ways to treat patients and reduce the likelihood that those microbes inside us will rebel, attack us, and make us sick.

Nanotechnology is helping us to achieve a finer scale of visual resolution, so we can see exactly when, during a surgical procedure, bacteria go rogue and start to attack the host, and the molecular mechanisms that underpin that behavior.

We have a great example that we found by placing nanoscale molecular biosensors in the gut. It measures phosphate levels. Phosphate is a very important molecule that is used to create the DNA and proteins in our body, and in the cells of those bacteria.

When the phosphate level drops below a certain threshold, the microbes turn on a mechanism to acquire phosphate from their environment. And where's the best source of phosphate? It's in the gut lining of their host. So they migrate to the gut and start to break down the human cells. We experience that as a several pathogenic infection, which often kills us.

Because we understand that process, we are developing mechanisms to release phosphate at exactly the right time during surgery to prevent those bacteria from ever experiencing that phosphate reduction. To do those micro phosphate releases, we're developing nanotech scaffolds to hold phosphate, and placing them into the gut during surgery. This will reduce the likelihood that microbes will become pathogenic.

TKF: Not only is that interesting, but it leads one of our viewers to ask whether we can adjust microbiomes so that they can target diseases and other human conditions. Can they go beyond just adjusting acidity or phosphate levels and do something more aggressive?

J.G.: Yes. The case where we've had the best success is in treating chronic infections caused by Clostridium difficile bacteria. C. diff infections are chronic gastrointestinal infections. Our treatments use a shotgun approach. We take the bacteria from a healthy person and transplant them into somebody with a chronic C. diff infection. That's overridden the C. diff infection, and established a healthy microbiome in the patient's gut so that he or she is no longer sick.

The Chinese did this about 2,000 to 3,000 years ago. They called it yellow soup, and they fed the stool from a healthy person to a sick person, and that made the sick person healthy. We just rediscovered this process, and we are now applying it in a more clinical setting.

So far, it's a very untargeted approach. What we're trying to do with our research arm, American Guts, and programs associated with autism, Alzheimer's, and Parkinson's, is to identify specific bacterial community members that are either absent or overgrown in those patients. Then we want to explore how to adjust them — maybe we implant one that is missing or knock one back that is over-grown, to make that person healthier.

E.B.: I'd like to add something to that. There's an interesting analogy, I think, in what we're doing for C. diff — fecal transplants — and restoration ecology. That's where you weed out an invasive plant species and plant another species to out-compete that invasive plant species. It's the exact same process, so the same ecological principles and ecological theory that's used in restoration ecology can be used in medicine. In some cases, it may not be as simple as removing one organism or adding one or two other organisms. It might be a community function, where we may actually need that complexity to be able to out-compete the organism that's causing the disease.

J.G.: That's a really interesting point. Both Eoin and I are microbial ecologist at our core. I started out in marine microbial ecology, and now I work in soils, plants, humans, and disease. Eoin does the same. And both of us can apply the ecological principles of microbes to any environment because microbes are everywhere.

TKF: Good. So, Eoin, we have two questions for you from our audience. The first involves agriculture. A viewer want to know whether nanoscience help us alter microbiomes in ways that change how we grow, fertilize, and protect plants from pests?

E.B.: That's a great question, and I think a really timely one as well. The world population is seven billion, heading to nine, and then 11 billion. We're going to run out of fertilizer, we're going to run out of space to grow food, and we're running out of water — we're in a severe drought in California. These are our challenges, feeding a global population and providing fuel for a global population.

The things microbes and nanotechnology can do mainly revolve around improving the resistance of plants to stresses, such as drought. Microbes can help plants acquire water. For example, mycorrhiza fungi can increase the root system, improve its drought tolerance, and improve nutrition.

We can also identify bacteria that can produce fertilizer in or near the plant. So bacteria that can take nitrogen from the atmosphere and fix nitrogen can potentially offset the use of nitrogen fertilizer, which takes a lot of energy and causes a lot of pollution to manufacture.

Bacteria can also mine critical minerals from the soil. We can have bacteria growing with the plants that acquire phosphorous, like Jack was saying. We can choose bacteria so that they mine more phosphorous than they need and supply that to the plant.

All of these things would reduce our reliance on mining phosphorous from strip mines or using five percent of our world's energy to product nitrogen fertilizer. I think it's a big, big challenge.

Nanotechnology, as I mentioned earlier, can be used to characterize these organisms and understand how they work. We can also build sensor systems to identify when nutrients are limiting growth. So instead of spreading nutrients and fertilizer in a very inefficient way, we can use it in a very targeted, specific, and much more sustainable way.

TKF: Can we take a step beyond that, and perhaps use microbiomes to control pests?

E.B.: Actually, that's been done for a long time. As you know, there are GMO crops out there that have taken genes from microbes that are used to kill insects. This could be carried out in a more natural way, as well, for example, by growing these bacteria with the plants and potentially inhibiting insects from grazing and feeding on the plants. We can learn a lot from nature. Nature has already developed these strategies for pest control, and we can learn from that to design our protections in a more, controllable and intelligent way.

TKF: Another question from a viewer: Is it possible to make an artificial microbiome community do a particular task?

J.G.: Yes. We've actually been working in that area, trying to create what we call a simple minimal community. This is a community of organisms that performs a task, such as creating acetate or generating hydrogen or butanol as potential biofuel source. So we're looking at microbes that grow on the surface of cathodes, and take raw electrons from those cathodes and integrate them with a carbon dioxide source, such as blue gas from a factory. We want to create a community that drives it's metabolism towards a set goal.

That will take a mathematical modeling approach. So metabolic modeling, trying to synthesize in a computer how these microbes interact to release a certain product. So, in that sense, you need nanotechnology to sense the metabolic relationships that exist between those organisms, so that you can engineer that community towards producing a particular product. That's going to be very important to achieve biotechnology results.

E.B.: Actually, I've got to turn that question on its head. I would like to take a natural microbial community and stop it doing something, in certain cases.

Let's say, for example, you've got cattle livestock. They are a significant source of global methane that contributes to global warming. Part of that is because of their diets, which provide an excess energy. That results in increased hydrogen, which results in a lot of methane, and cows release a lot of methane.

So, could we go in and use targeted synthetic biology or chemical interference approaches to stop the production of methane? To alter the balance of the cow's rumen, the cow's gut microbial ecosystem? We could not only inhibit methane production, but improve nutrition to the animal, because it's microbes that control the flow of energy to the animal from the food that it eats.

It's a complicated ecosystem, but specifically tweaking it for the benefit of the animal and the benefit of the planet, is an interesting challenge and there are people working on that.

J.G.: I'd like to take that exact system and apply it to coal, in order to make more methane that we can then capture and pump into people's homes as biofuel.

TKF: Interesting thought. I have another question from a viewer, and Jack, I think you are the one to answer this. She has of experimental treatments that involve implanting health gut bacteria into people with autism. Why might this work? And will this be something that we see soon?

J.G.: The bacteria in our gut have an impact upon neurological behavior — the way we behave — through our immune system. They elicit a certain immune response in our gut, which feeds back on our nervous system to create a certain characteristic behavior in our brain.

We've known this in animal models for a number of years now. We're just starting to understand the extent to which neurological diseases, such as autism, Parkinson's, and conditions such as Alzheimer's, are attributable to a disruption in the bacterial community in somebody's intestine.

There have been several experiments with very low numbers of children. In several cases in South America and a number in Australia, the children have had a fecal microbiome transplant, a healthy microbial community implanted into their own gut.

The results are variable, and not exactly something that you would want to try at home. But they do hint, in some instances, of a favorable outcome where the child's neurological disorder is lessened, or significantly reduced.

There are groups at Cal Tech are generating probiotics, particular bacteria species, that they hope to add to a child's diet or put into a capsule that can be swallowed. They seem to have a benefit in reducing the neurological abnormalities associated with autism, though they are still in their early days.

TKF: That leads to another question I wanted to ask you. Jack, you're also working on encapsulating microbiomes in some sort of nanostructure and applying them to homes or offices. Your hope is that these biomes will expose people to microbiomes that will help their immune system develop resistance to these neurological problems. Could you tell us about that?

J.G.: Yes, we're working on animal models at the moment. Imagine recreating structures that these animals can interact with. Imagine I build you a building that was biologically alive, where the walls were deliberately teeming with a healthy microbial community.

Now, we have only a very limited idea what healthy means, but essentially what we're doing is creating structures, 3D printable structures, impregnated with certain nutrients. We're working with Ramille Shah at Northwestern University to create a 3D structure which allows that bacterial community to thrive.

We can then introduce these structures into a mouse's cage. The bacteria associated with the 3D surface will colonize that mouse, and reduce certain abnormalities that we see in that mouse, such as an allergy response. So we've been growing bacteria which can produce a chemical that, once released into the gut of the mouse, will form a colony and reduce the likelihood of that mouse having a food allergy.

I'm also working with Cathy Nagler at the University of Chicago. We're hoping to prove that we don't have to pump kids full of probiotics. Instead, we can just redesign homes, schools, and maybe daycare centers, so that children will get an appropriate microbial exposure that would mirror how they would have grown up if they were in a natural ecosystem. Hopefully, that will be the future of architecture.

E.B.: And, you know, as a possible alternative, we can send our kids outside to play more.

J.G.: You got it.

E.B.: Not bad.

Follow all of the Expert Voices issues and debates — and become part of the discussion — on Facebook, Twitter and Google+. The views expressed are those of the author and do not necessarily reflect the views of the publisher. This version of the article was originally published on Live Science.


Water Microbiology

Water microbiology is concerned with the microorganisms that live in water, or can be transported from one habitat to another by water.

Water can support the growth of many types of microorganisms. This can be advantageous. For example, the chemical activities of certain strains of yeasts provide us with beer and bread. As well, the growth of some bacteria in contaminated water can help digest the poisons from the water.

However, the presence of other disease causing microbes in water is unhealthy and even life threatening. For example, bacteria that live in the intestinal tracts of humans and other warm blooded animals, such as Escherichia coli, Salmonella, Shigella, and Vibrio, can contaminate water if feces enters the water. Contamination of drinking water with a type of Escherichia coli known as O157:H7 can be fatal. The contamination of the municipal water supply of Walkerton, Ontario, Canada in the summer of 2000 by strain O157:H7 sickened 2,000 people and killed seven people.

The intestinal tract of warm-blooded animals also contains viruses that can contaminate water and cause disease. Examples include rotavirus, enteroviruses, and coxsackievirus.

Another group of microbes of concern in water microbiology are protozoa. The two protozoa of the most concern are Giardia and Cryptosporidium. They live normally in the intestinal tract of animals such as beaver and deer. Giardia and Cryptosporidium form dormant and hardy forms called cysts during their life cycles. The cyst forms are resistant to chlorine, which is the most popular form of drinking water disinfection, and can pass through the filters used in many water treatment plants. If ingested in drinking water they can cause debilitating and prolonged diarrhea in humans, and can be life threatening to those people with impaired immune systems. Cryptosporidium contamination of the drinking water of Milwaukee, Wisconsin with in 1993 sickened more than 400,000 people and killed 47 people.

Many microorganisms are found naturally in fresh and saltwater. These include bacteria, cyanobacteria, protozoa, algae, and tiny animals such as rotifers. These can be important in the food chain that forms the basis of life in the water. For example, the microbes called cyanobacteria can convert the energy of the sun into the energy it needs to live. The plentiful numbers of these organisms in turn are used as food for other life. The algae that thrive in water is also an important food source for other forms of life.

A variety of microorganisms live in fresh water. The region of a water body near the shoreline (the littoral zone) is well lighted, shallow, and warmer than other regions of the water. Photosynthetic algae and bacteria that use light as energy thrive in this zone. Further away from the shore is the limnitic zone. Photosynthetic microbes also live here. As the water deepens, temperatures become colder and the oxygen concentration and light in the water decrease. Now, microbes that require oxygen do not thrive. Instead, purple and green sulfur bacteria, which can grow without oxygen, dominate. Finally, at the bottom of fresh waters (the benthic zone), few microbes survive. Bacteria that can survive in the absence of oxygen and sunlight, such as methane producing bacteria, thrive.

Saltwater presents a different environment to microorganisms. The higher salt concentration, higher pH, and lower nutrients, relative to freshwater, are lethal to many microorganisms. But, salt loving (halophilic) bacteria abound near the surface, and some bacteria that also live in freshwater are plentiful (i.e., Pseudomonas and Vibrio). Also, in 2001, researchers demonstrated that the ancient form of microbial life known as archaebacteria is one of the dominant forms of life in the ocean. The role of archaebacteria in the ocean food chain is not yet known, but must be of vital importance.

Another microorganism found in saltwater are a type of algae known as dinoflagellelates. The rapid growth and multiplication of dinoflagellates can turn the water red. This "red tide" depletes the water of nutrients and oxygen, which can cause many fish to die. As well, humans can become ill by eating contaminated fish.

Water can also be an ideal means of transporting microorganisms from one place to another. For example, the water that is carried in the hulls of ships to stabilize the vessels during their ocean voyages is now known to be a means of transporting microorganisms around the globe. One of these organisms, a bacterium called Vibrio cholerae, causes life threatening diarrhea in humans.

Drinking water is usually treated to minimize the risk of microbial contamination. The importance of drinking water treatment has been known for centuries. For example, in pre-Christian times the storage of drinking water in jugs made of metal was practiced. Now, the anti-bacterial effect of some metals is known. Similarly, the boiling of drinking water, as a means of protection of water has long been known.

Chemicals such as chlorine or chlorine derivatives has been a popular means of killing bacteria such as Escherichia coli in water since the early decades of the twentieth century. Other bacteria-killing treatments that are increasingly becoming popular include the use of a gas called ozone and the disabling of the microbe's genetic material by the use of ultraviolet light. Microbes can also be physically excluded form the water by passing the water through a filter. Modern filters have holes in them that are so tiny that even particles as miniscule as viruses can be trapped.

An important aspect of water microbiology, particularly for drinking water, is the testing of the water to ensure that it is safe to drink. Water quality testing can de done in several ways. One popular test measures the turbidity of the water. Turbidity gives an indication of the amount of suspended material in the water. Typically, if material such as soil is present in the water then microorganisms will also be present. The presence of particles even as small as bacteria and viruses can decrease the clarity of the water. Turbidity is a quick way of indicating if water quality is deteriorating, and so if action should be taken to correct the water problem.


Words to know:

Acidity - the concentration of acid in a substance
Algae - an organism belonging to a group that lives mainly in water and includes the seaweeds. Algae differ from plants in not having true leaves, roots, or stems
Antibiotics - a naturally produced substance that kills bacteria, but has no effect against viruses, used as a medication
Bacteria – single-celled microorganism
Colonies - groups of organisms of the same kind that are living together and dependent on each other
Diseases - medical conditions in humans, plants, or animals that is not the direct result of physical injury
Environment - all the factors influencing the life and activities of people, plants, and animals
Fungi - plural of fungus. A single-celled or many-celled organism that reproduces by spores and lives by absorbing nutrients from organic matter.
Generate - to bring something into existence or effect
Infections - the transmission of infectious microorganisms from one person to another or an infecting microorganism
Infectious - a disease that is capable of being passed from one person to another
Inorganic - composed of minerals rather than living material
Micro-organisms - a tiny organism such as a virus, protozoan, or bacterium that can only be seen under a microscope
Minerals - a substance that occurs naturally in rocks and in the ground and has its own characteristic appearance and chemical composition
Parasites - a plant or animal that lives on or in another, usually larger, host organism in a way that harms or is of no advantage to the host
Particle - a very small piece of something
Protozoa - a single-celled organism that can move
Spherical - shaped like a sphere
Spores - a small, usually one-celled structure produced by seedless plants, algae, fungi, and some protozoans that is capable of developing into a new individual
Sustaining - to make something continue to exist
Viruses - a very simple microbe which requires a host to reproduce


Obtaining Pure Culture of Microorganisms: 6 Methods

The following points highlight the top six methods used for obtaining pure culture of microorganisms. The methods are: 1. Streak Plate Method 2. Pour Plate Method 3. Spread Plate Method 4. Serial Dilution Method 5. Single Cell Isolation Methods 6. Enrichment Culture Method.

1. Streak Plate Method:

This method is used most commonly to isolate pure cultures of bacteria. A small amount of mixed culture is placed on the tip of an inoculation loop/needle and is streaked across the surface of the agar medium (Fig. 16.13). The successive streaks “thin out” the inoculum sufficiently and the micro-organisms are separated from each other.

It is usually advisable to streak out a second plate by the same loop/needle without reinoculation. These plates are incubated to allow the growth of colonies. The key principle of this method is that, by streaking, a dilution gradient is established across the face of the Petri plate as bacterial cells are deposited on the agar surface.

Because of this dilution gradient, confluent growth does not take place on that part of the medium where few bacterial cells are deposited. Presumably, each colony is the progeny of a single microbial cell thus representing a clone of pure culture. Such isolated colonies are picked up separately using sterile inoculating loop/needle and re-streaked onto fresh media to ensure purity.

2. Pour Plate Method:

This method involves plating of diluted samples mixed with melted agar medium (Fig. 16.14). The main principle is to dilute the inoculum in successive tubes containing liquefied agar medium so as to permit a thorough distribution of bacterial cells within the medium.

Here, the mixed culture of bacteria is diluted directly in tubes containing melted agar medium maintained in the liquid state at a temperature of 42-45°C (agar solidifies below 42°C). The bacteria and the melted medium are mixed well.

The contents of each tube are poured into separate Petri plates, allowed to solidify, and then incubated. When bacterial colonies develop, one finds that isolated colonies develop both within the agar medium (subsurface colonies) and on the medium (surface colonies). These isolated colonies are then picked up by inoculation loop and streaked onto another Petri plate to insure purity.

Pour plate method has certain disadvantages as follows:

(i) The picking up of subsurface colonies needs digging them out of the agar medium thus interfering with other colonies, and

(ii) The microbes being isolated must be able to withstand temporary exposure to the 42-45° temperature of the liquid agar medium therefore this technique proves unsuitable for the isolation of psychrophilic microorganisms.

However, the pour plate method, in addition to its use in isolating pure cultures, is also used for determining the number of viable bacterial cells present in a culture.

3. Spread Plate Method:

In this method (Fig. 16.15), the mixed culture or microorganisms is not diluted in the melted agar medium (unlike the pour plate method) it is rather diluted in a series of tubes containing sterile liquid, usually, water or physiological saline.

A drop of so diluted liquid from each tube is placed on the center of an agar plate and spread evenly over the surface by means of a sterilized bent-glass-rod. The medium is now incubated.

When the colonies develop on the agar medium plates, it is found that there are some plates in which well-isolated colonies grow. This happens as a result of separation of individual microorganisms by spreading over the drop of diluted liquid on the medium of the plate.

The isolated colonies are picked up and transferred onto fresh medium to ensure purity. In contrast to pour plate method, only surface colonies develop in this method and the microorganisms are not required to withstand the temperature of the melted agar medium.

4. Serial Dilution Method:

As stated earlier, this method is commonly used to obtain pure cultures of those microorganisms that have not yet been successfully cultivated on solid media and grow only in liquid media.

A microorganism that predominates in a mixed culture can be isolated in pure form by a series of dilutions. The inoculum is subjected to serial dilution in a sterile liquid medium, and a large number of tubes of sterile liquid medium are inoculated with aliquots of each successive dilution.

The aim of this dilution is to inoculate a series of tubes with a microbial suspension so dilute that there are some tubes showing growth of only one individual microbe. For convenience, suppose we have a culture containing 10 ml of liquid medium, containing 1,000 microorganisms (Fig. 16.16.), i.e., 100 microorganisms/ml of the liquid medium.

If we take out 1 ml of this medium and mix it with 9 ml of fresh sterile liquid medium, we would then have 100 microorganisms in 10 ml or 10 microorganisms/ml. If we add 1 ml of this suspension to another 9 ml. of fresh sterile liquid medium, each ml would now contain a single microorganism.

If this tube shows any microbial growth, there is a very high probability that this growth has resulted from the introduction of a single microorganism in the medium and represents the pure culture of that microorganism.

5. Single Cell Isolation Methods:

An individual cell of the required kind is picked out by this method from the mixed culture and is permitted to grow.

The following two methods are in use:

i. Capillary pipette method:

Several small drops of a suitably diluted culture medium are put on a sterile glass-coverslip by a sterile pipette drawn to a capillary. One then examines each drop under the microscope until one finds such a drop, which contains only one microorganism. This drop is removed with a sterile capillars pipette to fresh medium. The individual microorganism present in the drop starts multiplying to yield a pure culture (Fig. 16.17).

ii. Micromanipulator method:

Micromanipulators have been built, which permit one to pick out a single cell from a mixed culture. This instrument is used in conjunction with a microscope to pick a single cell (particularly bacterial cell) from a hanging drop preparation. The micro-manipulator has micrometer adjustments by means of which its micropipette can be moved right and left, forward, and backward, and up and down.

A series of hanging drops of a diluted culture are placed on a special sterile coverslip by a micropipette. Now a hanging drop is searched, which contains only a single microorganism cell.

This cell is drawn into the micropipette by gentle suction and then transferred to a large drop of sterile medium on another sterile coverslip. When the number of cells increases in that drop as a result of multiplication, the drop is transferred to a culture tube having suitable medium. This yields a pure culture of the required microorganism.

The advantages of this method are that one can be reasonably sure that the cultures come from a single cell and one can obtain strains with in the species. The disadvantages are that the equipment is expensive, its manipulation is very tedious, and it requires a skilled operator. This is the reason why this method is reserved for use in highly specialised studies.

6. Enrichment Culture Method:

Generally, it is used to isolate those microorganisms, which are present in relatively small numbers or that have slow growth rates compared to the other species present in the mixed culture.

The enrichment culture strategy provides a specially designed cultural environment by incorporating a specific nutrient in the medium and by modifying the physical conditions of the incubation. The medium of known composition and, specific condition of incubation favours the growth of desired microorganisms but, is unsuitable for the growth of other types of microorganisms.


First There Were Microbes. Then Life on Earth Got Big.

How did life go from tiny organisms to large, complex creatures? Scientists see clues in fossils from as far back as 570 million years ago.

Left: FROM 508 MILLION YEARS AGO TO TODAY

On the southeast coast of Newfoundland, near North America’s farthest eastward reach, lies a promontory of rocky cliffs called Mistaken Point. The place got its name from the shipwrecks it helped cause in foggy weather, when sea captains mistook it for somewhere else. Today it represents something quite different: a set of extraordinary clues, recently reinterpreted, to one of the deepest and most puzzling mysteries of life on Earth. After burbling along for more than three billion years as tiny, mostly single-celled things, why did life suddenly erupt into a profusion of complex creatures—multicellular, big, and astonishing? Although these new life-forms spread worldwide, beginning at least 570 million years ago, the earliest evidence of them has been found in one place: Mistaken Point. Paleontologists have been going there for decades. But what the experts think they see now, in small nuances with large implications, is radical and new.

On a cool autumn day I made the journey to Mistaken Point myself, driving south from St. John’s, Newfoundland’s capital, in a rented Jeep, along a black ribbon of highway through forests of spruce and fir. With me were Marc Laflamme of the University of Toronto Mississauga and his longtime colleague Simon Darroch, an Englishman based at Vanderbilt University in Nashville.

We reached Mistaken Point beneath a blue sky and a blazing sun—rare weather, Laflamme told me, but the strong angled light, especially in late afternoon, helped highlight the subtle fossils we had come to see.

At the Mistaken Point Ecological Reserve, established by the provincial government to protect the fossil beds, we took a gravel road to a broken sea bank and climbed down. Laflamme pointed to a single slab of smooth, purplish gray rock, tilted at about 30 degrees. An image in the stone, like an intricate shadow, suggested the skeleton of a snake, a repeating pattern of ribs and spine, about three feet long. But there was no skeleton here, indeed no bone at all—only the imprint of a soft-bodied creature, dead and buried on the sea bottom a very, very long time ago. It didn’t swim it didn’t crawl. It couldn’t have lived like any organism alive today. It belonged to a more obscure period, inhabited by cryptic, otherworldly creatures that most people don’t realize ever existed. “This is the first time that life got big,” Laflamme told me as we knelt on the rock.

From so simple a beginning

The mystery of these life-forms, known as Ediacarans (Ee-dee-AK-arans), begins in the remote Flinders Ranges of South Australia, where a young geologist named Reginald Sprigg, on an assignment to reassess the derelict Ediacara Mines in 1946, noticed some peculiar impressions in exposed sandstone beds. They seemed to him “suggestive of jellyfish.” They weren’t jellyfish. There were other shapes too, some of them bearing no clear resemblance to any known creature, living or extinct. One figure looked like a fingerprint pressed into the sand.

Sprigg didn’t realize (nor did those who had found similar figures in stone before, unsure what to make of them) that the fossils were about 550 million years old—dating to at least 10 million years before a better known evolutionary drama, the famous Cambrian explosion. Scientists until then had believed that the Cambrian explosion was the point when life on Earth opened out, kaboom, like a starburst of wondrous beasts—elaborate and sizable beings (we call them animals), many of whose descendants are still around. Sprigg’s discovery proved important as a first signal that the period now called Ediacaran, not the Cambrian just following it, was where the saga of bigness and complexity began.

Then in 1967 a graduate student named S. B. Misra noticed a fossil-rich slab of mudstone at Newfoundland’s Mistaken Point. Some of its ancient forms seemed to match the “jellyfish” things from South Australia, others looked like fronds, but several resembled nothing known to science. Other beds nearby, sitting one upon another like layers of Precambrian cake, also proved to contain abundant and various fossils, preserved together as whole communities. Many were still covered with thin crusts of fallen volcanic ash, like icing between each layer of cake. The ash, with its traces of radioactive uranium and the lead into which that decays, allowed for precise radiometric dating of the beds. The Mistaken Point fossils, going back 570 million years, are the earliest evidence on Earth of large, biologically complex beings.

There are now more than 50 different Ediacaran forms known, from nearly 40 localities, on every continent except Antarctica. So what was it, after billions of years of only microbes populating the globe, that allowed the Ediacarans to get big and cover the Earth? And what does their bigness suggest about their internal anatomies, their means of feeding, their ways of living?

Before Ediacaran forms flourished on the planet, evolution worked on a mostly microscopic scale, kept in check by a shortage of oxygen, the element that fuels animal metabolism. Thanks to marine bacteria that generated oxygen as a product of photosynthesis, levels of the gas rose about two billion years ago but stayed relatively low for another billion years. Then, between 717 million and 635 million years ago, a series of glaciations took place, so widespread and severe that they may have frozen over the entire planet, a situation some scientists call a “snowball Earth.” During that time oxygen levels bumped up again, for reasons that are still poorly understood.

The great freeze ended as volcanic eruptions spewed carbon dioxide into the atmosphere, creating an early greenhouse effect that warmed the planet and thawed the oceans. Another brief glaciation around 580 million years ago, known as the Gaskiers, may not have been global, but it put Newfoundland, among other places, in a deep freeze. These changes all preceded the earliest appearance of Ediacarans in the fossil record. Were they the causes of what happened next? Did the end of the glaciers, an increase in available oxygen, and the evolution of more complex cells allow the Ediacarans to blossom, like the first crocuses of springtime? Maybe.

Equally enigmatic is their relationship to life today. One eminent German paleontologist, Adolf Seilacher, assigned them to a kingdom all their own, distinct from the animal kingdom, because of what he called their “unique, quilted type of biological construction,” so different from most multicellular animals. The “quilted” effect seemed to offer structural stability that might have compensated for the absence of a skeleton. Maybe the quilting, and the frondy shapes, also helped maximize surface area, so they could better absorb nutrients through their skin.

Nutrition would have been problematic for the Ediacarans because, so far as fossil evidence reveals, almost none of them had a mouth. They had no gut, no anus. No head, no eyes, no tail. In some cases there was a sort of anchoring knob or disk at one end, now known as a holdfast, which gripped the sea bottom and allowed the frond to waft upward in the water. Many sea-bottom areas at that time were coated with thick microbial mats, which helped stabilize the sediments like a layer of crusty soil. But the frond wasn’t a plant—photosynthesis couldn’t have nourished it—because many Ediacarans lived in the depths, thousands of feet underwater, where light didn’t penetrate.

If they couldn’t eat and they couldn’t photosynthesize, how did they nourish themselves? One form, a sluglike thing called Kimberella, may have scratched up and swallowed (this one did have a mouth, major advantage!) sustenance from the microbial mats beneath it. But the leading hypothesis for most Ediacarans is osmotrophy, a fancy word for a very basic process: the uptake of dissolved nutrients by osmosis, or absorption through their outer membrane. It was good enough, maybe, in a simpler world at a simpler time, but it would have been meager sustenance. Some scientists have focused on another fascinating aspect of many Ediacarans: their finer architecture. At a glance they look quilted, but close inspection reveals that their structure is fractal. That is, similar patterns repeat themselves at progressively smaller scales. A big frond was composed of smaller fronds, and those smaller fronds composed of still smaller fronds, all similar except for size. The basic shape echoes itself at three or four scales. Possibly that fractal structuring helps explain how they were able to grow large. It provided some rigidity, it maximized surface area, and perhaps it reflected a genetic shortcut. A simple formula in the genome might have specified: Build a small frondy unit, then repeat that operation over and over, adding one upon another, to make me big.

This sort of fractal structure showed in the snakelike creature Marc Laflamme and I saw in the purplish gray rock at Mistaken Point. It shows too in a number of other Ediacarans, collectively called rangeomorphs, named for a Namibian exemplar of the form, known as Rangea. During our day on the Newfoundland rocks, Laflamme steered my eyes onto many more rangeomorphs, inconspicuous from 10 feet away but spooky when viewed closely. Here was Beothukis mistakensis, a paddle-shaped frond, named for its locale of discovery. Over there was Fractofusus, a spindle-shaped form, tapered at both ends. It lived flat on the sea bottom. When death came to a community of Ediacarans, as when a blizzard of volcanic ash settled through the seawater to smother them or an avalanche of sediment came off a steep slope to bury them, the vertical frondy things sometimes got smashed over (as the fossil evidence shows), but the Fractofusus spindles seem to have died gently where they lay.

Although these rangeomorphs dominated the deep-sea ecosystem at Mistaken Point for millions of years and flourished elsewhere in somewhat shallower water, they all disappeared, leaving no known descendants. By the start of the Cambrian period 541 million years ago, or soon after, they had almost entirely vanished from the fossil record as we know it. That’s why some scientists have suggested that the Ediacarans represent “failed experiments” in the early evolution of multicellular life.

Why did the Ediacarans suddenly disappear? Was the extinction absolute, or were there descendants in different forms? And if the end wasn’t so abrupt and complete, what finished the Ediacarans as Ediacarans, dying off species by species in obscurity?

Laflamme’s colleague Simon Darroch has offered one possible answer. On the afternoon of our visit to Mistaken Point, Darroch reached into his day pack and produced a surprise: small pieces of flat brown stone from the late Ediacaran beds he studies in Namibia. He had brought them from his lab at Vanderbilt to show me some trace fossils. A trace fossil, as distinct from a body fossil, records traces of animal activity—moving, chewing, defecating—as preserved in rock. It’s a record of behavior, not of bodily shape. Any such traces are notable in the Ediacaran period, because most Ediacarans couldn’t do those things: move, chew, or defecate.

“This is a very static, sessile ecosystem,” Darroch said, referring to a famously rich early Ediacaran fossil bed on which we stood.

The later Ediacaran, as revealed in Namibian rocks, was much different. One big difference, he said, was that “for the first time we have complex burrowing.” Experts disagree about just when the intricate patterns of burrowing creatures first appeared, but by any judgment those traces signaled a big change from the Ediacaran to the Cambrian. Wormy creatures had long been wriggling along on the sea bottom now they were tunneling down into it as well. Darroch showed me a little slab marked with dotted-line traces. “They’re on the surface, and they disappear, then they come to the surface again.” That was evidence of an organism with complicated musculature, allowing it to move about in three dimensions. If it moved that way, it had a front and a rear end. On its front end, probably a mouth. In the mouth, maybe teeth. These were extraordinary new tools and capacities at the time. The worms crawled in, the worms crawled out, disrupting the microbial mats, possibly munching directly on Ediacarans. In a recent paper, Darroch and his co-authors (led by James Schiffbauer, and including Laflamme) have called this early Cambrian time the “Wormworld.” It was no place for Ediacarans.

Worminess wasn’t the only factor that brought oblivion to the Ediacarans and triggered the Cambrian explosion—there also were changes in ocean chemistry that allowed animals to acquire hard parts (calcium-rich skeletons, teeth, and shells), a generalized increase in modes of mobility (not just burrowing), and the rise of predatory habits, among other things. But the worminess of that transitional time, in the late Ediacaran period, may have played a crucial role. A few weeks after our Mistaken Point outing, I talked with James Gehling, a leading Ediacaran researcher. Go up to the Flinders Ranges in South Australia, near the Ediacara Hills, he told me by phone from his office in Adelaide, and look at the first formation of Cambrian sedimentary layers. “It’s just Swiss cheese.” Burrowed all through by wormy creatures that had churned the sand and “recycled” the soft-bodied Ediacarans. “That’s where the Cambrian begins,” Gehling said. “The advent of the musculature to burrow.”

Guy Narbonne, at Queen’s University in Ontario, largely agrees with the importance of burrowing. But together with his graduate student Calla Carbone, he has taken Wormworld a step further. Based on careful analysis of trace fossils from the late Ediacaran and the early Cambrian, Narbonne and Carbone noticed a significant difference in how those wormy creatures turned. By the early Cambrian, burrowing animals became more systematic in their searches for food, as well as more muscled. They ranged more efficiently, tracking the resources better and crossing their own tracks less. “It reflects the evolution of braininess,” Narbonne told me. “Our interpretation,” he added, “is that the Cambrian explosion is when behavior became coded on the genome.” They titled that paper, “When Life Got Smart.”

Most experts would agree that smartness, even on a level expressed by a primitive worm, wasn’t a wrench in the Ediacaran tool kit. Those creatures’ genomes may have been coded for fractal repetition—at least in the rangeomorphs, where it yielded a simple sort of complexity—but not for responsiveness to circumstances, or efficiency. Still, it’s a mistaken point to dismiss the Ediacarans as doomed. People made that error with the dodo, when they branded it an emblem of ill-fated stupidity. But the real dodo, Raphus cucullatus, a large, flightless, fruit-eating bird endemic to the island of Mauritius, had thrived in its peaceable home for many thousands of years—until Homo sapiens and other predators arrived. Likewise the Ediacarans, with their own new threats. You can call them “failed experiments” in evolution if you want, but they succeeded and flourished, within their preferred but challenging environments, for more than 30 million years. We humans should be so steadfast and lucky.


Aerobic Decomposition

When organic materials decompose in the presence of oxygen, the process is called “aerobic.” The aerobic process is most common in nature. For example, it takes place on ground surfaces such as the forest floor, where droppings from trees and animals are converted into a relatively stable humus. There is no accompanying bad smell when there is adequate oxygen present.

In aerobic decomposition, living organisms, which use oxygen, feed upon the organic matter. They use the nitrogen, phosphorus, some of the carbon, and other required nutrients. Much of the carbon serves as a source of energy for the organisms and is burned up and respired as carbon dioxide (C02). Since carbon serves both as a source of energy and as an element in the cell protoplasm, much more carbon than nitrogen is needed. Generally about two-thirds of carbon is respired as C02, while the other third is combined with nitrogen in the living cells. However, if the excess of carbon over nitrogen (C:N ratio) in organic materials being decomposed is too great, biological activity diminishes. Several cycles of organisms are then required to burn most of the carbon.

When some of the organisms die, their stored nitrogen and carbon becomes available to other organisms. As other organisms use the nitrogen from the dead cells to form new cell material, once more excess carbon is converted to C02. Thus, the amount of carbon is reduced and the limited amount of nitrogen is recycled. Finally, when the ratio of available carbon to available nitrogen is in sufficient balance, nitrogen is released as ammonia. Under favorable conditions, some ammonia may oxidize to nitrate. Phosphorus, potash, and various micro-nutrients are also essential for biological growth. These are normally present in more than adequate amounts in compostable materials and present no problem.

During composting a great deal of energy is released in the form of heat in the oxidation of the carbon to C02. For example, if a gram-molecule of glucose is dissimilated under aerobic conditions, 484 to 674 kilogram calories (kcal) of heat may be released. If the organic material is in a pile or is otherwise arranged to provide some insulation, the temperature of the material during decomposition will rise to over 170°F. If the temperature exceeds 162°F to 172°F, however, the bacterial activity is decreased and stabilization is slowed down.

Initially, mesophilic organisms, which live in temperatures of 50°F to 115°F, colonize in the materials. When the temperature exceeds about 120°F, thermophilic organisms, which grow and thrive in the temperature range 115°F to 160°F., develop and replace the mesophilic bacteria in the decomposition material. Only a few groups of thermophiles carry on any activity above 160°F.

Oxidation at thermophilic temperatures takesplace more rapidly than at mesophilic temperatures and, hence, a shorter time is required for decomposition (stabilization). The high temperatures will destroy pathogenic bacteria, protozoa (microscopic one-celled animals), and weed seeds, which are detrimental to health or agriculture when the final compost is used.

Aerobic oxidation of organic matter produces no objectionable odor. If odors are noticeable, either the process is not entirely aerobic or there are some special conditions or materials present which are creating an odor. Aerobic decomposition or composting can be accomplished in pits, bins, stacks, or piles, if adequate oxygen is provided. Turning the material at intervals or other techniques for adding oxygen is useful in maintaining aerobic conditions.

Compost piles under aerobic conditions attain a temperature of 140°F to 160°F in one to five days depending upon the material and the condition of the composting operation. This temperature can also be maintained for several days before further aeration. The heat necessary to produce and maintain this temperature must come from aerobic decomposition which requires oxygen. After a period of time, the material will become anaerobic unless it is aerated.

In this manual the term “aerobic composting” will be used in its commonly accepted meaning of that process. It requires a considerable amount of oxygen and produces none of the characteristic features of anaerobic putrefaction. In its modern sense, aerobic composting can be defined as a process in which, under suitable environmental conditions, aerobic organisms, principally thermophilic, utilize considerable amounts of oxygen in decomposing organic matter to a fairly stable humus.


How do microbes spread from a small place to a very large place? - Biology

An experiment to incorporate Lux Operon containing plasmids into E. coli bacterium through encouraged transformation.

Genetic transformation is “ a process by which the genetic material carried by an individual cell is altered by the incorporation of foreign (exogenous) DNA into its genome” (MedicineNet, 1999). There are many ways that bacterial DNA can be altered including transduction and conjugation but we will use the process of transformation to alter the E. coli genome. A plasmid is a “small circular piece of DNA in bacteria that resembles the bacterial circular chromosome, but is dispensable. Some bacterial strains contain many plasmids and some contain none. Plasmids are often used in genetic engineering as cloning vectors” (Bowden, 2008). An operon is the combination of a promoter, operator, and genes. The operator sits in between the promoter and the genes as a form of negative regulation. Allosteric inhibitors can bind to the operator thereby blocking transcription of that gene. Operons of this sort are only found in bacteria. The Lux operon, that we will be using and that exists of the plasmid being introduced called pVIB, has on it a gene that codes for Luciferase that has the property on enabling bioluminescence. “ The lux operon encodes genes for self-regulation and for the production of luminescent proteins” (Lux, 2008).

The concept behind the experiment is that we can make independent plasmids pass through the membranes of the E. coli bacteria in order to be incorporated as part of the its genome, but still as a plasmid. The plasmids are given to us as independent entities outside of any cell. Through an array of processes, we will attempt to incorporate the plasmids into the E. coli bacteria. The plasmids we will be using contain the Lux operon and a resistance to the antibiotic Ampicillin. The gene that codes for the Ampicillin resistance is called “ amp r ”. During the experiment we will place the two types of bacteria, with and without the plasmid, in solutions of just LB Agar and of LB Agar and Ampicillin. We hypothesized that the bacteria with the plasmid (+plasmid) would survive in both the LB Agar and the LB Agar/Ampicillin solutions, also that the bacteria without the plasmid (-plasmid) would only survive in the just LB Agar dish.

1. Please describe, at the cellular/molecular level, the precise steps involved in heat shock. That is, how can we force a bacterial cell to take up a plasmid?

The cell membrane is a phospholipid bilayer that has negatively charged phosphate groups at the heads. Even though the zones for admittance of foreign DNA are large enough, the negatively charged phosphate groups naturally repel the negatively charged phosphate backbones of the DNA plasmid, stopping its induction. We add calcium chloride molecules to the mix so that positive calcium ions can neutralize the negative charges thereby allowing the induction of the plasmids into the cell. In order to better neutralize the charges we cooled the cells hence stabilizing the membrane further. The temperature within the cell becomes cool. Then we heat shock the solution, creating an imbalance of temperature across the membrane and consequently a current into the cell, bringing the plasmid into the cell.

2. If any of the predictions regarding bacterial growth made in the pre-lab considerations differed from your observed results, please describe them and explain why you believe you obtained these results

The predictions I made in the pre-lab considerations are, on paper, correct but some do not match what I observed. This means that something might have gone wrong during the experiment. I predicted that a -plasmid bacterium put in a plate containing just LB Agar would survive but clearly not be luminescent because of the absence of the pVIB and consequently the Lux operon. I observed that no bacteria of any kind grew in that plate. The bacteria had probably died before being able to cultivate properly. I also had a problem with the +plasmid bacteria growing in the LB Agar/Ampicillin plate. We had a single colony grow so it did work, but they generally failed to grow. The one colony that did was in fact luminescent. Nothing went wrong with the procedure because it did work. There may have been environmental factors like contamination affecting the cultivation of the bacteria in the two plagued plates.

3. What are you selecting for in this experiment? (i.e., what allows you to identify which bacteria have taken up the plasmid?)

We were able to identify which bacteria have taken up the plasmid because the ones that have not will have neither the ampicillin resistance nor be bioluminescent because the Lux operon is a part of the pVIB plasmid. The -plasmid will survive only in the absence of ampicillin. The +plasmid will survive around ampicillin and in the absence of it. So the bacteria that are bioluminescent and are not killed by the Ampicillin are the ones that have incorporated the plasmid we introduced.

4. Transformation efficiency is expressed as the number of antibiotic-resistant colonies per μg of plasmid DNA. The object is to determine the mass of plasmid that was spread on the experimental plate and that was, therefore, responsible for the transformants) the number of colonies) observed. Because transformation is limited to only those cells that are competent, increasing the amount of plasmid does not necessarily increase the probability that a cell will be transformed. A sample of competent cells is usually saturated with the addition of a small amount of plasmid, and excess DNA may actually interfere with the transformation process.

a. Determine the total mass (in μg) of plasmid used. Remember that you used 10 μL of plasmid at a concentration of 0.005 μg/ μL.

10 μL plasmid X 0.005 μg/ μL = 0.05 μg plasmid

b. Calculate the total volume of cell suspension prepared.

250 μL CaCl2 + 250 μL LB + 10 μL plasmid DNA + about 5 μL E. coli = about 515 μL cell suspension

c. Now calculate the fraction of the total cell suspension that was spread on the plate.

100 μL spread/515 μL total = .1942

d. Determine the mass of plasmid in the cell suspension spread.

0.05 μg plasmid X .1942 = .00971 μg plasmid

e. Determine the # of colonies per μg of plasmid DNA. Express your answer in scientific notation. This is your transformation efficiency.

1 colony / .00971 μg plasmid = about 103 colonies/μg plasmid

Transformation Efficiency: 1.0 X 10 2 colonies per μg plasmid

5. What factors might influence transformation efficiency? Explain the effect of each factor that you mention.

If any amount of any given element from the experiment is altered for example if the concentration of the plasmid is more or less, the results and the transmission efficiency. The amount contact between plasmid and bacteria has an affect on the transmission efficiency. If there is not a lot of bacteria but there is a lot of plasmid and more plasmid is added, the transmission efficiency will go down because excessive amounts of plasmid with limited small amounts of bacteria does not increase transformations by number of possible transformations. There is also a delicate balance in regards to heat shock. The bacteria will die if the temperature is too high but the idea of heat shock therapy, in which the gradient in heat causes the current, will not function if the temperature is too low. Also, the exposure time to the heat shock is also a factor because excessive exposure could adversely affect the bacteria and plasmid.

The original hypothesis that I had was that the -plasmid bacteria would only survive in the absence of ampicillin because of the lack of the resistance that lies on the pVIB plasmid. Also, I hypothesized that the +plasmid bacteria would survive in all situations and be bioluminescent, even in the presence of the antibiotic ampicillin. My results showed that the -plasmid E. coli did not grow in the presence or absence of ampicillin. It should have grown in the absence of ampicillin. My results also showed that the +plasmid E. coli grew in both the presence and absence of ampicillin. The +plasmid E. coli did not grow very much in the presence. Only one luminescent colony survived. I am not going to revise my original hypothesis because the hypothesis follows what should by nature have happened if the experiment had been done correctly. I suspect that the plates may have been exposed to the environment for too long during the experiment and subject to contamination.


Watch the video: How do germs spread and why do they make us sick? - Yannay Khaikin and Nicole Mideo (November 2022).