Sophisticated swarming: Bacteria support each other across generations

When bacteria build communities, they cooperate and share nutrients across generations. Researchers at the University of Basel have been able to demonstrate this for the first time using a newly developed method. This innovative technique enables the tracking of gene expression during the development of bacterial communities over space and time.

In nature, bacteria usually live in communities. They collectively colonize our gut, also known as the gut microbiome, or form biofilms such as dental plaque.

Living in communities provides many advantages to the individual microbes.

They are more resilient against adverse environmental conditions, conquer new territories and benefit from each other.

Analyzing microbial communities in space and time

The development of bacterial communities is a highly complex process where bacteria form intricate three-dimensional structures.

In their latest study published in Nature Microbiology, the team led by Professor Knut Drescher from the Biozentrum of the University of Basel has investigated the development of bacterial swarm communities in detail.

They achieved a methodological breakthrough enabling them to simultaneously measure gene expression and image the behaviour of individual cells in microbial communities in space and time.

Bacteria provide resources for future generations

"We used Bacillus subtilis as a model organism. This ubiquitous bacterium is also found in our intestinal flora. We have revealed that these bacteria, which live in communities, cooperate and interact with each other across generations," explains Prof Knut Drescher, head of the study.

"Earlier generations deposit metabolites for later generations."

They also identified different subpopulations within a bacterial swarm, which produce and consume different metabolites.

Some of the metabolites secreted by one subpopulation become the food for other subpopulations that emerge later during swarm development.

Distribution of tasks within the community

The researchers combined state-of-the-art adaptive microscopy, gene expression analyses, metabolite analyses, and robotic sampling.

Using this innovative approach, the researchers have been able to simultaneously examine gene expression and bacterial behavior at precisely defined locations and specific times as well as to identify the metabolites secreted by the bacteria.

The bacterial swarm could thus be divided into three major regions: the swarm front, the intermediate region and the swarm center.

However, the three regions display gradual transitions.

"Depending on the region, the bacteria differ in appearance, characteristics and behavior. While they are mostly motile at the edges, the bacteria in the center form long non-motile threads, resulting in a 3D biofilm. One reason is the varying availability of space and resources," explains first author Hannah Jeckel.

"The spatial distribution of bacteria with distinct behavior enables the community to expand but also to hide in a protective biofilm." This process appears to be a widespread strategy in bacterial communities and is crucial for their survival.

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Scientists discover secret of virgin birth, and switch on the ability in female flies

Scientists have pinpointed a genetic cause for virgin birth for the first time, and once switched on the ability is passed down through generations of females.

For the first time, scientists have managed to induce virgin birth in an animal that usually reproduces sexually: the fruit fly Drosophila melanogaster.

Once induced in this fruit fly, this ability is passed on through the generations: the offspring can reproduce either sexually if there are males around, or by virgin birth if there aren't.

For most animals, reproduction is sexual -- it involves a female's egg being fertilised by a male's sperm. Virgin birth, or 'parthenogenesis', is the process by which an egg develops into an embryo without fertilisation by sperm -- a male is not needed.

The offspring of a virgin birth are not exact clones of their mother but are genetically very similar, and are always female.

"We're the first to show that you can engineer virgin births to happen in an animal -- it was very exciting to see a virgin fly produce an embryo able to develop to adulthood, and then repeat the process," said Dr Alexis Sperling, a researcher at the University of Cambridge and first author of the paper.

She added: "In our genetically manipulated flies, the females waited to find a male for half their lives -- about 40 days -- but then gave up and proceeded to have a virgin birth."

In the experiments, only 1-2% of the second generation of female flies with the ability for virgin birth produced offspring, and this occurred only when there were no male flies around. When males were available, the females mated and reproduced in the normal way.

Switching to a virgin birth can be a survival strategy: a one-off generation of virgin births can help to keep the species going.

The study is published today in the journal Current Biology.

To achieve their results, researchers first sequenced the genomes of two strains of another species of fruit fly, called Drosophila mercatorum. One strain needs males to reproduce, the other reproduces only through virgin birth. They identified the genes that were switched on, or switched off, when the flies were reproducing without fathers.

With the candidate genes for virgin birth ability identified in Drosophila mercatorum, the researchers altered what they thought were the corresponding genes in the model fruit fly, Drosophila melanogaster. It worked: Drosophila melanogaster suddenly acquired the ability for virgin birth.

The research involved over 220,000 virgin fruit flies and took six years to complete.

Key to the discovery was the fact that this work was done in Drosophila melanogaster -- the researchers say it would have been incredibly difficult in any other animal. This fly has been the 'model organism' for research in genetics for over 100 years and its genes are very well understood.

Sperling, who carried out this work in the Department of Genetics, has recently moved to Cambridge Crop Science Centre to work on crop pests and hopes to eventually investigate why virgin birth in insects may be becoming more common, particularly in pest species.

"If there's continued selection pressure for virgin births in insect pests, which there seems to be, it will eventually lead to them reproducing only in this way. It could become a real problem for agriculture because females produce only females, so their ability to spread doubles," said Sperling.

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The impacts from using genetic testing to track down relatives

Genetic genealogy has become a popular hobby over the past several years, thanks to direct-to-consumer (DTC) genetic testing and relative-finder services offered by some DTC genetic testing companies. In a paper published February 24 in the American Journal of Human Genetics, researchers report results from a survey that asked people who had participated in these services what effect the discovery of previously unknown relatives had on their lives.

Among the most important findings were that identifying a genetic relative appeared to be somewhat common. Additionally, those discoveries were generally experienced as neutral or positive and didn't appear to have a big impact on participants' lives. However, some participants learned things that could be considered significant and destabilizing -- such as that their biological parent wasn't who they thought. These participants were especially vulnerable to negative outcomes.

"Everyone on our team is involved in studying the ethical, legal, and social implications of DTC genetic testing, and we've been paying attention to stories in the media about individuals who've made surprising family discoveries from these tests and relative-matching services," says lead author Christi Guerrini of the Center for Medical Ethics and Health Policy at Baylor College of Medicine. "We wanted to understand if these and other kinds of discoveries are common, how they're experienced by those making the discoveries, and what people are doing as a result."

The investigators sent the survey to about one million DTC genetic testing customers and genetic genealogy database participants; more than 26,000 responded. The final sample for analysis consisted of 23,196 completed or substantially completed surveys. Among the reasons that respondents said they chose to participate in this type of testing were to learn more about their family or build their family trees; to search for a biological parent, child, or other relative; or to investigate a suspicion that they might not be genetically related to family members.

"It seems that many -- perhaps most -- are just curious about their families and interested in building out their family trees, but it's clear that quite a lot of participants are looking for someone or hoping to confirm something in particular," Guerrini says. "It might be that they're adopted and looking for a biological parent, or that they've always felt out of place in their family and want to see if there's something to that feeling. Or they might be looking for information about a branch of their family tree that's unknown to them, or to confirm a family story that's been passed down over the years."

Most respondents (82%) reported that they learned the identity of at least one genetic relative. Among this subpopulation, 10% identified a biological grandparent, 10% identified a full or half- sibling, and 7% identified a biological father. The survey asked whether the participant had chosen to contact any of their newly identified relatives and, if so, the reasons for doing so. It also asked whether their discoveries resulted in any life changes, including changes in health-related behaviors.

Guerrini says that the high number of people overall who identified an unknown genetic relative was not unexpected, because many of those relatives could be very distant ones. But she acknowledges that the high number of participants who found close relatives could be skewed by the type of people who choose to undergo relative matching in the first place. "Unfortunately, we can't answer that question with our data, but I'm very interested in trying to do so in future research," she says.

She adds that although these experiences appear to be interesting and enjoyable to a large number of people, it's clear that some who are participating in these services have experienced negative outcomes. "In future research, we'd like to better understand those outcomes and what resources could be helpful in managing them," she says.

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Stress on mothers can influence biology of future generations

A mother's response to stress can even influence her grandchildren.

Biologists at the University of Iowa found that roundworm mothers subjected to heat stress passed, under certain conditions and through modifications to their genes, the legacy of that stress exposure not only to their offspring but even to their offspring's children.

The researchers, led by Veena Prahlad, associate professor in the Department of Biology and the Aging Mind and Brain Initiative, looked at how a mother roundworm reacts when she senses danger, such as a change in temperature, which can be harmful or even fatal to the animal. In a study published last year, the biologists discovered the mother roundworm releases serotonin when she senses danger. The serotonin travels from her central nervous system to warn her unfertilized eggs, where the warning is stored, so to speak, and then passed to offspring after conception.

Examples of such genetic cascades abound, even in humans. Studies have shown that pregnant women affected by famine in the Netherlands from 1944 to 1945, known as the Dutch Hunger Winter, gave birth to children who were influenced by that episode as adults -- with higher rates than average of obesity, diabetes, and schizophrenia.

In this study, the biologists wanted to find out how the memory of stress exposure was stored in the egg cell.

"Genes have 'memories' of past environmental conditions that, in turn, affect their expression even after these conditions have changed," Prahlad explains. "How this 'memory' is established and how it persists past fertilization, embryogenesis, and after the embryo develops into adults is not clear. "This is because during embryogenesis, most organisms typically reset any changes that have been made to genes because of the genes' past activity."

Prahlad and her teams turned to the roundworm, a creature regularly studied by scientists, for clues. They exposed mother roundworms to unexpected stresses and found the stress memory was ingrained in the mother's eggs through the actions of a protein called the heat shock transcription factor, or HSF1. The HSF1 protein is present in all plants and animals and is activated by changes in temperature, salinity, and other stressors.

The team found that HSF1 recruits another protein, an enzyme called a histone 3 lysine 9 (H3K9) methyltransferase. The latter normally acts during embryogenesis to silence genes and erase the memory of their prior activity.

However, Prahald's team observed something else entirely.

"We found that HSF1 collaborates with the mechanisms that normally act to 'reset' the memory of gene expression during embryogenesis to, instead, establish this stress memory," Prahlad says.

One of these newly silenced genes encodes the insulin receptor, which is central to metabolic changes with diabetes in humans, and which, when silenced, alters an animal's physiology, metabolism, and stress resilience. Because these silencing marks persisted in offspring, their stress-response strategy was switched from one that depended on the ability to be highly responsive to stress, to relying instead on mechanisms that decreased stress responsiveness but provided long-term protection from stressful environments.

"What we found all the more remarkable was that if the mother was exposed to stress for a short period of time, only progeny that developed from her germ cells that were subjected to this stress in utero had this memory," Prahlad says. "The progeny of these progeny (the mother's grandchildren) had lost this memory. However, if the mother was subjected to a longer period of stress, the grandchildren generation retained this memory. Somehow the 'dose' of maternal stress exposure is recorded in the population."

The researchers plan to investigate these changes further. HSF1 is not only required for stress resistance but also increased levels of both HSF1 and the silencing mark are associated with cancer and metastasis. Because HSF1 exists in many organisms, its newly discovered interaction with H3K9 methyltransferase to drive gene silencing is likely to have larger repercussions.

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