Quasi-sexual gene transfer and recombination drives genetic diversity of hot spring bacteria
New work from a team including Carnegie's Devaki Bhaya and Michelle Davison used massive DNA sequencing of bacterial populations that grow in the hot springs in Yellowstone National Park to determine their genetic diversity and explore the underlying evolutionary dynamics.
They found an unexpectedly high degree of sharing and exchange of genetic material between the tiny, green, photosynthetic cyanobacteria Synechococcus, which are abundant in these scalding, inhospitable environments.
The team discovered that the pattern of differences in genome organization between various individuals of the same species indicates that the bacteria transfer DNA, including whole genes, back and forth. This swapping or "recombination" allows gene variations to spread rapidly through a population. Their findings are published by Science.
There is a great deal of small-scale genetic diversity in naturally occurring bacterial populations--as opposed to the carefully managed bacterial clones used in laboratory research and clinical work. Bacterial populations in the natural environment represent a dynamic genetic resource that changes over time, but the quantification of this diversity, and the exact mechanisms creating its dynamics, has remained elusive.
"Biologists have long been interested in determining the evolutionary and ecological forces that drive the population genetics of bacterial communities," Bhaya explained.
The research team, which also included lead author Michael Rosen as well as Daniel Fisher, both of the Applied Physics Department at Stanford University, set out to investigate this question by combining the power of so-called "deep sequencing" ( highly detailed and extensive DNA sequence determination) with powerful statistical analysis.
Several possible scenarios were considered. For instance, one theory predicts that bacterial populations are genetically diverse because they adapt to their surrounding conditions on a very small-scale, local level, leading to the establishment of distinct subpopulations, called ecotypes.
Another possibility was that all of the diversity in the bacterial genes is 'neutral'--no particular version of a gene makes an organism more or less fit for its environment. Bacteria reproduce by asexual division, which means that each new generation is stuck with a nearly exact replica of its sole parent's genetic material. Genetic changes can occur through mutation or the transfer of segments of DNA between individual organisms.
Using sophisticated statistical analysis of the massive "DNA deep sequencing" data enabled the team to trace the evolutionary forces that shaped these natural Synechococcus populations. They found that neither models of neutral drift, nor the concept of micro-niches of different ecotypes fit the data.
Rather, the population occupies a broad niche that includes a range of environmental conditions. Diversity is created by frequent swapping of genetic material between organisms. This apparently happens often enough that the population can be viewed as "quasi-sexual" in comparison to organisms like humans, where the process of sexual reproduction, specifically fertilization, combines genes from two parents.
In sexual reproduction, new combinations of genes are the rule. Although this is not generally true for bacterial populations, for these particular hot spring bacteria, new combinations are also the rule, rather than the exception. Since DNA moves between individuals, a new generation will not be stuck with just a copy of its parental genes. Because of this level of variation, natural selection acts on the level of individual genes, not the whole genome. Transfers of DNA happen so much that bacteria can have all sorts of different combinations of genes and gene variants.
"Without deep sequencing and careful analysis, we never would have been able to detect and identify the forces at work and it will be exciting to discover if these insights extend to other microbial communities," Bhaya noted. "Microbial diversity is found everywhere from deep sea vents to the human gut or in association with plant roots. Using methods such as single cell sequencing, proteomics, and microscopy will allow exploration of this invisible and important world with great accuracy and depth."
This work was supported by the National Science Foundation, the Carnegie Institution for Science, a Stanford Graduate Fellowship, and an IBM fellowship
The Carnegie Institution for Science (carnegiescience.edu) is a private, nonprofit organization headquartered in Washington, D.C., with six research departments throughout the U.S. Since its founding in 1902, the Carnegie Institution has been a pioneering force in basic scientific research. Carnegie scientists are leaders in plant biology, developmental biology, astronomy, materials science, global ecology, and Earth and planetary science.
Devaki Bhaya | EurekAlert!
Nonstop Tranport of Cargo in Nanomachines
20.11.2018 | Max-Planck-Institut für molekulare Zellbiologie und Genetik
Researchers find social cultures in chimpanzees
20.11.2018 | Universität Leipzig
Max Planck researchers revel the nano-structure of molecular trains and the reason for smooth transport in cellular antennas.
Moving around, sensing the extracellular environment, and signaling to other cells are important for a cell to function properly. Responsible for those tasks...
Researchers at the University of New Hampshire have captured a difficult-to-view singular event involving "magnetic reconnection"--the process by which sparse particles and energy around Earth collide producing a quick but mighty explosion--in the Earth's magnetotail, the magnetic environment that trails behind the planet.
Magnetic reconnection has remained a bit of a mystery to scientists. They know it exists and have documented the effects that the energy explosions can...
Biochips have been developed at TU Wien (Vienna), on which tissue can be produced and examined. This allows supplying the tissue with different substances in a very controlled way.
Cultivating human cells in the Petri dish is not a big challenge today. Producing artificial tissue, however, permeated by fine blood vessels, is a much more...
Faster and secure data communication: This is the goal of a new joint project involving physicists from the University of Würzburg. The German Federal Ministry of Education and Research funds the project with 14.8 million euro.
In our digital world data security and secure communication are becoming more and more important. Quantum communication is a promising approach to achieve...
On Saturday, 10 November 2018, the research icebreaker Polarstern will leave its homeport of Bremerhaven, bound for Cape Town, South Africa.
19.11.2018 | Event News
09.11.2018 | Event News
06.11.2018 | Event News
20.11.2018 | Life Sciences
20.11.2018 | Life Sciences
20.11.2018 | Physics and Astronomy