In our Bacterial World exhibition we offer a selection of ten bacteria that have changed the world, some in profound ways. In this series of short fact-file posts we present one of the ten each week. This week’s bacteria are…
Escherichia coli
– the medicine-manufacturers
Where they live Millions of Escherichia coli live harmlessly in your gut, keeping more dangerous bacteria at bay. A few strains cause food poisoning.
Why they are important E. coli can act as a protein factory, accepting genes from other species and reproducing them. By combining DNA from more than one source, scientists can manipulate E. coli so that it manufactures human insulin.
How they are named Escherichia coli’s name reflects its discoverer, Theodor Escherich, and the fact that he found it in the human colon.
How they work Bacteria often contain plasmids, extra DNA rings that confer particular properties. Researchers can introduce genes into E. coli using plasmids, enabling the bacteria to make all kinds of biotechnology products from foods to medicines.
Top image: Coloured transmission electron micrograph (TEM) of two Escherichia coli bacteria. E. coli are Gram-negative bacilli (rod-shaped) bacteria. Long flagellae (thin thread-like structures) are used by the bacteria to move themselves. The spiky filaments on the sides of the bacteria are pili, thin strands of protein used when two bacteria conjugate (transfer DNA). E. coli is a normal inhabitant of the human intestine. However, under certain conditions its numbers may increase, causing infection. Magnification: x17,200 at 10 centimetres high. Copyright: Science Photo Library
In our Bacterial World exhibition we offer a selection of ten bacteria that have changed the world, some in profound ways. In this series of short fact-file posts we present one of the ten each week. This week’s bacteria are…
Rhizobium leguminosarum
– the Crop-Boosters
Where they live Rhizobia leguminosarum have a special relationship with plants, living inside little nodules on their roots and receiving shelter and food from them.
Why they are important
In return for its comfortable life, the bacteria bring about hugely increased crop yields. They enable the plant to use nitrogen from the air as a fertiliser, a process called nitrogen fixing.
How they are named
The family of bacteria called Rhizobia got its name in 1889 – it means ‘root living’. Leguminosarum indicates that the species lives in leguminous plants such as peas, beans and lentils.
How they work
The two-way relationship between plants and rhizobia is called mutual symbiosis. Scientists boost crop yields even further by selecting the best strains of bacteria to pair up with plants in specific environments.
Top image: Electron micrograph of root nodules with Rhizobium leguminosarum bacteria grown by The Rhizosphere Group (University of Oxford)
Copyright: Kim Findlay (John Innes Centre)
This article is taken from European research magazine Horizon as part of our partnership to share natural environment science stories with readers of More than a Dodo. Our Bacterial World exhibition is open until 28 May.
A study in mice has indicated that the make-up of bacteria in the gut is linked with learning abilities and memory, providing a potential avenue of research into how to maintain cognitive functioning as we age.
It’s part of a field of research looking at the link between gut bacteria and ageing to help people live healthier lives in old age. The proportion of the EU population aged 80 or over is predicted to more than double between 2017 and 2080, with those aged 65-plus rising from 20 to almost 30%.
However, the connection between the make-up of microbiota in the gut, brain functions and ageing has been unclear – with cause and effect difficult to establish. Dr Damien Rei, a postdoctoral researcher into neurodegenerative and psychiatric diseases at the Pasteur Institute in France, decided to examine the different types of microbiome that appear in younger and older mice to understand better what might happen in people too.
Coloured scanning electron micrograph (SEM) of Escherichia coli bacteria (red) taken from the small intestine of a child. E. coli are part of the normal flora of the human gut, though some strains cause illness.
He found that when he transferred gut bacteria in older mice to young adult mice, there was a strong effect on reducing learning and memory. And when the opposite was done, with older mice receiving microbiota from younger mice, their cognitive abilities returned to normal. The older mice were aged about a year and a half – equivalent to about 60-plus human years.
‘Despite being aged animals, their learning abilities were almost indistinguishable from those of young adult mice after the microbiota transfer,’ said Dr Rei – adding that this indicated strong communication between the gut and brain. ‘When I saw the data, I couldn’t believe it. I had to redo the experiment at least a couple of times.’
Furthermore, by seeing what was happening to the neuronal pathways of communication between the gut and brain when the aged microbiota was transferred to the younger mice, they were then able to manipulate these pathways. By doing this, he says they could block or mimic the effects of the aged microbiota.
Dr Rei’s study, which was carried out as part of a project called Microbiota and Aging, has not yet been published, but he hopes this could happen by the end of the summer. He is also looking into human gut microbiota in older people and those with Alzheimer’s disease, but said it is too early to reveal further details about this research.
Translating
However, Dr Rei pointed out that there is a big challenge in translating results in mice to people, not only because of the significant ethical barriers, but also the differences in physiology. ‘The immune system of a mouse is very different to one of a human. The gut microbiota is also very different because mice eat very different things to what we do,’ he said.
Research is still a long way off from making real inroads into using this type of research to combat neurodegenerative diseases such as Alzheimer’s, says Dr Rei. Indeed, he says, there is no convincing evidence yet that looking at the gut microbiota is the way to go. But he believes the mouse study opens doors to further investigation into mechanisms behind age-related changes.
‘The data on the mice was really the first stepping stone, and it was a way for us to understand the potential of manipulating the gut microbiota,’ said Dr Rei.
Pinning down the link between gut bacteria and ageing is not straightforward, according to Dr Thorsten Brach, a postdoctoral researcher at the University of Copenhagen in Denmark. ‘It’s known that ageing is a multifactorial process and it’s hard, especially when it comes to the microbiome, to separate the effects of ageing specifically from all other aspects,’ he said.
He worked on a project called Gut-InflammAge, which looked at the link between gut microbes, inflammation and ageing, led by associate professor Manimozhiyan Arumugam.
As part of their work, the team investigated the effects of mild periodic calorie restriction in mice to explore the potential impact of healthy-ageing diets involving fasting. Unexpectedly, calorie-restricted mice accumulated more body fat – which the researchers speculate may have been down to overeating between these periods – but also saw a mild ‘rejuvenation’ of their blood profile so it more closely resembled that of younger mice.
Despite being aged animals, their learning abilities were almost indistinguishable from those of young adult mice after the microbiota transfer.
Damien Rei, Pasteur Institute, France
The researchers did observe a difference between the microbiota composition in the different groups, but overall in the study the differences found were not big enough to suggest more than healthy variability between individuals. The study therefore supported the view that diet and lifestyle are more critical than age and gender in shaping the microbiota, said the researchers – though Prof. Arumugam said it would be more revealing to follow changes in individual people’s microbiomes over time.
The studies carried out so far indicate there is still a long way to go in painting an accurate picture of the link between microbiota and the ageing process. Prof. Arumugam also pointed out that microbiome analysis is lagging behind technologically compared with genetics research, with disease cause and effect harder to establish than with genes.
But research is gradually improving our understanding. Prof. Arumugam said that though his team’s study did not achieve a ‘breakthrough’, it helped give more insight into this area and raised questions over previous assumptions.
And research in this area could ultimately change how we view ageing, says Dr Rei, seeing it as more fluid than just ‘a totally one-way road with no turning back, except in the movies like Benjamin Button.’
The research in this article was funded by the EU.
To mark International Women’s Day Professor Judith Armitage, lead scientist on the Bacterial World exhibition, reflects on the ground-breaking – and controversial – work of evolutionary biologist Lynn Margulis
Iconoclastic, vivacious, intuitive, gregarious, insatiably and omnivorously curious, partisan, bighearted, fiercely protective of friends and family, mischievous, and a passionate advocate of the small and overlooked.
Lynn Margulis at the III Congress about Scientific Vulgarization in La Coruña, Spain, on November 9, 2005. Image: Jpedreira, CC BY-SA 2.5
These are all words used to describe evolutionary biologist and public intellectual Lynn Margulis. Intellectually precocious, Margulis got her first degree from the University of Chicago aged 19, but it was her exposure to an idea about the evolution of a certain type of cell that ignited a lifelong focus of her work.
This idea claimed that eukaryotic cells – cells with a nucleus, found in all plants and animals, but not bacteria – were first formed billions of years ago when one single-celled organism – a prokaryote – engulfed another to create a new type of cell. This theory, known as endosymbiosis, was laid down in a paper by Margulis in 1967. It brought her into conflict with others, including the so-called neo-Darwinists who believed in slow step-wise evolution driven by competition between organisms, not cooperation.
So what happened in the earliest evolution of these crucial cells? Initially, one bacterium ate a different, oxygen-using bacterium but didn’t digest it. Over time the two became interdependent and the bacterium took over almost all of the energy-generating processes of the host cell, becoming what we now call a mitochondrion. This allowed the cell to evolve into bigger cells and eventually form communities and develop into multicellular organisms.
Animal cells evolved when one single cell, possibly an archaeon, engulfed an aerobic bacterium – one that used oxygen to release energy. The bacterium evolved into the mitochondrion, the powerhouse of the cells of humans and other animals. A similar process created the chloroplasts found in plant cells.
These early mitochondria-containing organisms continued to eat other bacteria, and on more than one occasion they ate a photosynthesising cyanobacterium which evolved into a chloroplast, a structure now found inside plant cells.
The revolution in DNA sequencing that started in the 1970s, and continues today, eventually vindicated Margulis’ position on this ancient sequence of events. It revealed that chloroplasts and mitochondria both contain DNA with the same ancestry as cyanobacteria and proteobacteria respectively. In other words, both chloroplasts and mitochondria have evolved from ancient bacteria.
Margulis’ enthusiastic support for these ideas led her to think about the role of biology in the geology of Earth and some of its major changes, in particular the oxygenation of the atmosphere by cyanobacteria around 2.5 billion years ago. Mitochondria use oxygen, and so must have evolved from bacterial ancestors that arose after the cyanobacteria started to produce oxygen through photosynthesis.
Margulis met Gaia theorist James Lovelock soon after her seminal publication on endosymbiosis. At the time, Lovelock was looking at the composition of the atmosphere and factors causing change, including oxygen levels. He was starting to think of the Earth as a system – Gaia as it became known – where the planetary environment is regulated and kept stable by biological activity.
This meeting brought together two scientific outliers. Together they produced highly controversial articles on the “atmosphere as a biological contrivance”. Lovelock believed in concentrating on examining the systems as they are now, while Margulis brought deep time and evolutionary depth into the picture.
Margulis’ ideas were not always right, and she was enormously controversial in her time, but she made people think again. And in doing so she moved our understanding of things as apparently academically distant as the evolution of tiny cells billions of years ago to the stability of Earth’s environment today.
Top image: Euglena, a single cell eukaryotic. By Deuterostome [CC BY-SA 3.0]
In our Bacterial World exhibition we offer a selection of ten bacteria that have changed the world, some in profound ways. In this series of short fact-file posts we present one of the ten each week. This week’s bacteria are…
Prochlorococcus
– the Oxygen-Makers
Where they live Prochlorococcus bacteria grow anywhere damp, in salt water or fresh. They are similar to the blue cyanobacteria which thrived in the far-distant past on Earth.
Why they are important
2.3-2.4 billion years ago, cyanobacteria in the oceans began producing oxygen for the first time, changing the Earth’s environment completely.
How they are named
The Greek word for blue is cyan, giving the blue cyanobacteria their name. Until recently, they were known as blue-green algae, but cyanobacteria are actually an earlier and simpler form of life than algae.
How they work
Like all cyanobacteria, Prochlorococcus bacteria harvest energy from the Sun, absorb carbon dioxide and give out oxygen – the process called photosynthesis.
Top image: Transmission Electron Micrograph (TEM) image of Prochlorococcus coloured green
Copyright: Luke Thompson, Chisholm Lab; Nikki Watson, Whitehead (MIT), 2007
This article is taken from European research magazine Horizon as part of our partnership to share natural environment science stories with readers of More than a Dodo.
Researchers have found that many internal defence mechanisms that are quiet in rural birds are much more active in those in cities. These biological pathways are pumping out extra antioxidants, immune system cells and detoxifiers – a sign that urban life is challenging their health.
Globally, bird numbers are dropping. According to figures published by conservation organisation BirdLife International last year, 40% of bird species have declining populations while 7% are increasing in number. BirdLife cites urbanisation as a force destructive to many bird species, but a few do well in cities, such as the adaptable great tit, whose population is on the rise.
City wildlife have a different experience of predators, food availability and diseases than those in the country. This may be helpful to them – for example, humans leave food out for birds in their gardens. But they also have to cope with a fragmented habitat and with noise, air and light pollution. Scientists want to understand these forces in order to get a better grasp of the dramatic drop in some bird populations.
A research group in Sweden has been studying great tits living in 500 nestboxes in the city of Malmö, and a similar number in the forest. Great tits were chosen partly because they are well-studied and also because their use of nestboxes makes it easy for researchers to locate and examine them. The researchers check the boxes weekly during spring, weighing chicks with tiny balances, measuring them with adapted rulers, and tapping them for blood, according to Dr Hannah Watson, an ecologist at Lund University in Sweden.
An early study revealed that the urban birds had higher levels of antioxidants circulating in their blood than rural birds – a defence mechanism against attack from free radicals – toxic versions of oxygen atoms.
‘Exposure to air pollution would generate more free radicals (in the body) which can then increase what’s called oxidative stress – a kind of cellular level stress,’ said Dr Watson. ‘The free radicals cause damage to DNA, lipids, proteins – all the macromolecules in the cell.’
Switched on To explore the consequences in more detail, she compared RNA (a counterpart to DNA) samples between the two populations, in a project called URBAN EPIGENETICS.
While genes code for the structure and maintenance of a living thing, they only function if they are switched on – or expressed. This happens via a bit of chemistry, methylation, which can be triggered by environmental factors.
Dr Watson found that genes responsible for the city birds’ immune responses had been upregulated, implying that they were fighting off more infections than rural birds. Similarly, other genes, such as those for neutralising poisons, for inflammation and for antioxidant production to combat free radicals, were also switched on.
‘It’s only the birds of really good quality that are able to actually survive the nestling period in the city.’
Dr Hannah Watson, Lund University, Sweden
‘We showed big differences in terms of the genes that are expressed and the levels they are expressed at,’ she said. ‘We interpret this as being consistent with our prediction that birds living in the city are exposed to more of these environmental stressors.’
But this doesn’t necessarily mean that urban birds are suffering, says Dr Watson. ‘It could just indicate that they’re able to respond and cope.’
To understand whether the birds were taking urban stress in their stride, Dr Watson joined a study led by one of her colleagues in which they measured the caps – telomeres – at the ends of the birds’ chromosomes.
Over the last decade, scientists have shown that telomeres gradually shorten each time a cell divides, and also in response to other stressors, eventually reaching a stage of senescence, or deterioration, which corresponds to an organism’s old age and death. In fact, the length of a creature’s telomeres, it turns out, seems to foretell its lifespan. The team conjectured that, if the urban stresses were actually affecting the great tits’ ability to survive, this would be revealed in the lengths of their telomeres.
They found that city chicks that were ready to fledge had on average shorter telomeres than those of fledgling forest chicks.
Great tits living in urban areas fight off more infections than their rural cousins. Image Credit – CC BY-SA 4.0
Weeded out Those with the shortest telomeres were less able to cope with urban stresses and died before reaching adulthood. Paradoxically, that meant that adult great tits in the city were likely to be stronger than the average forest adult because the weaker ones had been weeded out.
‘It’s only the birds of really good quality that are able to actually survive the nestling period in the city,’ said Dr Watson.’ In fact, the researchers think that while multiple stressors in the city are wiping out younger, weaker birds, they may not be of much consequence during adult life for those tough enough to make it that far.
Urban living may also mean that the social structures that served a species well in the natural habitat have become no longer necessary or even harmful.
House sparrows in the wild, for example, compete with each other for food according to a dominance hierarchy that is determined largely by size. But in cities, there are two key differences – food is more abundant and house sparrows are smaller, possibly because they don’t need to store body fat since winters are milder. Either factor could undermine the way they normally compete for food.
Likewise, house sparrows are known for the way they cooperate to mob potential predators. But when the danger shifts from a bird of prey to a cat or dog, this behaviour could become redundant.
With their numbers in decline, but still strong at as many as 1.3 billion globally, their toughness, aggression and ability to survive around humans suggests they seem to do well in urban areas.
Dr Lyanne Brouwer, an animal ecologist at Radboud University Nijmegen in the Netherlands, is studying house sparrows in a variety of urban habitats as they engage in their cooperative and competitive behaviours in a project called UrbanBird, which runs until 2020. She is using observations gathered by ordinary people, as well as her own field work to understand the causes and longterm effects of any behavioural change in the way house sparrows interact with each other. Ultimately this could help predict how urbanisation could affect other species and biodiversity.
‘It’s really interesting to see that all the factors that could affect social behaviour, like for example food availability or the predators that are around, are all very different in cities – so how would that affect these social behaviours? It turns out there is basically nothing known about how such behaviours change in cities,’ she said.
The research in this article was funded by the EU.
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