Phage , the virus that cures

[William Gaatjes]

Bacteria that can transport electrons over "vast" distances.
It seems i am experiencing the vast range of symptoms of the current flu epidemic.
For now, this is all the commenting i can provide for i feel largely depleted of energy.

http://www.nature.com/nature/journal...e11586_F1.html




http://en.wikipedia.org/wiki/Desulfobulbaceae

The discovery of filamentous Desulfobulbaceae in 2012 elucidates the cause of the small electrical currents in the top layer of sediment on large portions of the ocean floor. The currents were first measured in 2010. Thousands of these currently unnamed Desulfobulbus cells are arranged in fibrous microorganisms up to a centimeter in length. They transport electrons from the sediment that is rich in hydrogen sulfide up to the oxygen-rich sediment that is in contact with the water.

http://www.wired.com/wiredscience/20...electric-wires

The world's deep seafloors are dark and airless places, but vast swaths may pulse gently with energy conducted through a type of newly discovered bacteria that forms living electrical cables.
The bacteria were first detected in 2010 by researchers perplexed at chemical fluctuations in sediments from the bottom of Aarhus Bay in Denmark. Almost instantaneously linking changing oxygen levels in water with reactions in mud nearly an inch below, the fluctuations occurred too fast to be explained by chemistry.
Only an electrical signal made sense -- but no known bacteria could transmit electricity across such comparatively vast distances. Were bacteria the size of humans, the signals would be making a journey 12 miles long.
Now the mysterious bacteria have been identified. They belong to a microbial family called Desulfobulbaceae, though they share just 92 percent of their genes with any previously known member of that family. They deserve to be considered a new genus, the study of which could open a new scientific frontier for understanding the interface of biology, geology and chemistry across the undersea world.
The bacteria are described Oct. 24 in Nature by researchers led by microbiologists Christian Pfeffer, Nils Risgaard-Petersen and Lars Peter Nielsen of Aarhus University. On the following pages, Wired takes a look at these marvelous microbes.
Seen through an electron microscope, the Desulfobulbaceae -- the researchers haven't yet given them a genus or species name -- appear in blue. They link end-to-end, forming filaments nearly an inch in length.

http://www.wired.com/wiredscience/20...cean-bacteria/

According to findings that could have been pulled from a deep-sea sequel to Avatar, bacteria appear to conduct electrical currents across the ocean floor, driving linked chemical reactions at relatively vast distances.
Noticed only when reseachers happened to test sediment leftovers from another experiment, the phenomenon may add a new mechanism to Earth’s biogeochemistry.
“The cycling of elements and life at the bottom of the sea, and in soil, and anywhere else you’re short of oxygen — this could help us understand those processes,” said microbiologist Lars Peter Nielsen of Denmark’s Aarhus University, co-author of the study, published Feb. 24 in Nature.
The original focus of Nielsen’s team wasn’t seafloor conductivity, but an especially interesting species of sulfur bacteria found on the floor of Aarhus Bay. To help quantify their chemical activity, the researchers kept a few beakers of seawater and sulfur bacteria-free sediment for comparison.
After those experiments ended, the beakers were almost forgotten. Then, a few weeks later, the researchers noticed strange patterns of activity. Changing oxygen levels in water above the top sediment layer were almost immediately followed by chemical fluctuations several layers down. The distance was so great, and the response time so quick, that usual methods of chemical transport — molecular diffusion, or a slow drift from high to low concentration — couldn’t explain it.
At first, the researchers were stumped. Then they realized the process made sense if bacteria in the top and bottom layers were linked. Anything that affected oxygen-processing bacteria up top would also affect the sulfide-eating microbes below. It would explain the apparent connection; and an electrical linkage would explain the speed. It would also boggle the mind.
“Such hypotheses would at one time have been considered heretical,” wrote Kenneth Nealson, a University of Southern California microbiologist, in an accompanying commentary in Nature. A half-inch gap “doesn’t seem like much of a distance. But to a bacterium it amounts to 10,000 body lengths, equivalent to about 20 kilometers (12 miles) in human terms.”
In recent years, however, scientists have found species of microbes with outer membranes covered by electron-transporting enzymes, or studded with conductive, micrometer-scale filaments. These are used in driving experimental microbial fuel cells, and are known to be found in the Aarhus Bay mud. Those sediments also contain trace amounts of pyrite, an electrically conductive mineral.
The top sediment layer also had a low concentration of hydrogen ions, something that could only be explained through an electrochemical reaction, with electrons conducted from a distance, said Nielsen.
Nealson called the findings “astonishing,” and said they “may be relevant to energy transfer and electron flow through many different environments.” They could eventually applied to bacteria-based schemes for bioremediation, carbon sequestration and energy production.
Asked if he’d seen the blockbuster movie Avatar, with its storyline involving electrochemically linked forests that stored the inhabitants’ souls in a planet-spanning biological computer, Nielsen said, “One of my colleagues saw this, and immediately sent me a message: ‘You’ve discovered the secret of Avatar! Go see it!’ The similarities are quite striking.”
He continued, “I don’t think there is much spirit in the networks we’ve seen here. It might be only about energy. But there are connections.”

[William Gaatjes]

I created this thread once long ago out of personal interest and to show to others that are interested as well... All the wonders of microscopic life and the impact that microscopic life has on us in every day life.
I never knew about the biologist Lynn Margulis who had already drawn the conclusion that becomes so apparent when reading this entire thread. How much microscopic life has an impact.
Something that is easily ignored. Life on this planet (and i am sure even in our solar system) can exist without dinosaurs or mammals. But life cannot exist without bacteria, viruses, fungi, single celled organisms.
I am waiting for the cover of the Madonna song "We are living in a material world". It will not be long before the cover "We are living in a bacterial world" will appear.


A wiki about the Late Lynn Margulis.
http://en.wikipedia.org/wiki/Lynn_Margulis

The percentage of the human genome that arose at a series of stages in evolution. 37% of human genes originated in bacteria.

Bacteria in an animal’s microbiota, such as those in the gut, in the mouth, and on the skin, communicate among themselves and exchange signals with the animal’s organ systems.
Some of the chemical signals are noted in this illustration. Credit: Margaret McFall-Ngai, et al. ©2013 PNAS

You can read the entire article here at phys.org.
http://phys.org/news/2013-02-bacteri...ht.html#ajTabs

An excerpt :

Credit: Margaret McFall-Ngai, et al. ©2013 PNAS (Phys.org)—Throughout her career, the famous biologist Lynn Margulis (1938-2011) argued that the world of microorganisms has a much larger impact on the entire biosphere—the world of all living things—than scientists typically recognize. Now a team of scientists from universities around the world has collected and compiled the results of hundreds of studies, most from within the past decade, on animal-bacterial interactions, and have shown that Margulis was right. The combined results suggest that the evidence supporting Margulis' view has reached a tipping point, demanding that scientists reexamine some of the fundamental features of life through the lens of the complex, codependent relationships among bacteria and other very different life forms.
The project to review the current research on animal-bacterial interactions began when some scientists recognized the importance of bacteria in their own fields of study. For Michael Hadfield, Professor of Biology at the University of Hawaii at Manoa, the recognition grew over many years while studying the metamorphosis of marine animals. He found that certain bacteria influence marine larvae to settle to particular places on the sea floor, where they transform into juveniles and live out the rest of their lives. "Once we determined that specific biofilm bacteria provide an essential and unique ligand to stimulate the larvae of one globally distributed marine worm, our research naturally progressed to a study of the portion of the bacterial genome responsible for the signaling, and to other species, where we found the same genes involved," Hadfield told Phys.org. "Coming from different perspectives on the study of animal-bacterial interactions, and recognizing many more, Margaret McFall-Ngai [Professor of Medical Microbiology and Immunology at the University of Wisconsin, Madison] and I discussed the current situation extensively and then decided to attempt to draw together a significant number of experts on various approaches to the study of bacterial-animal interactions to draft a paper such as the one you have in hand. We proposed a 'catalysis meeting' on the subject to the National Science Foundation's National Evolutionary Synthesis Center (NESCent), which was funded, and the project took off." Bacteria surround us In many respects, it's easy to see the prominent role that bacteria play in the world. Bacteria were one of the first life forms to appear on Earth, about 3.8 billion years ago, and they will most likely survive long after humans are gone. In the current tree of life, they occupy one of the three main branches (the other two are Archaea and Eucarya, with animals belonging to the latter). Although bacteria are extremely diverse and live nearly everywhere on Earth, from the bottom of the ocean to the inside of our intestines, they have a few things in common. They are similar in size (a few micrometers), they are usually made of either a single cell or a few cells, and their cells don't have nuclei. Although scientists have known for many years that animals serve as a host for bacteria, which live especially in the gut/intestines, in the mouth, and on the skin, recent research has uncovered just how numerous these microbes are. Studies have shown that humans have about 10 times more bacterial cells in our bodies than we have human cells. (However, the total bacteria weigh less than half a pound because bacterial cells are much smaller than human cells.) While some of these bacteria simply live side-by-side with animals, not interacting much, some of them interact a lot. We often associate bacteria with disease-causing "germs" or pathogens, and bacteria are responsible for many diseases, such as tuberculosis, bubonic plague, and MRSA infections. But bacteria do many good things, too, and the recent research underlines the fact that animal life would not be the same without them. "The true number of bacterial species in the world is staggeringly huge, including bacteria now found circling the Earth in the most upper layers of our atmosphere and in the rocks deep below the sea floor," Hadfield said. "Then add all of those from all of the possible environments you can think of, from cesspools to hot springs, and all over on and in virtually every living organism. Therefore, the proportion of all bacterial species that is pathogenic to plants and animals is surely small. I suspect that the proportion that is beneficial/necessary to plants and animals is likewise small relative to the total number of bacteria present in the universe, and surely most bacteria, in this perspective, are 'neutral.' However, I am also convinced that the number of beneficial microbes, even very necessary microbes, is much, much greater than the number of pathogens." Animal origins and coevolution From our humble beginnings, bacteria may have played an important role by assisting in the origins of multicellular organisms (about 1-2 billion years ago) and in the origins of animals (about 700 million years ago). Researchers have recently discovered that one of the closest living relatives of multicellular animals, a single-celled choanoflagellate, responds to signals from one of its prey bacterium. These signals cause dividing choanoflagellate cells to retain connections, leading to the formation of well-coordinated colonies that may have become multicellular organisms. However, such questions of origin have been subjects of intense debate, and scientists have many hypotheses about how these life forms emerged. A bacterial role in these processes does not exclude other perspectives but adds an additional consideration.

After helping get animals started, bacteria also played an important role in helping them along their evolutionary path. While animal development is traditionally thought to be directed primarily by the animal's own genome in response to environmental factors, recent research has shown that animal development may be better thought of as an orchestration among the animal, the environment, and the coevolution of numerous microbial species. One example of this coevolution may have occurred when mammals evolved endothermy, or the ability to maintain a constant temperature of approximately 40 °C (100 °F) by metabolic means. This is also the temperature at which mammals' bacterial partners work at optimum efficiency, providing energy for the mammals and reducing their food requirement. This finding suggests that bacteria's preferred temperature may have placed a selection pressure on the evolution of genes associated with endothermy. Bacterial signaling Evidence for a deep-rooted alliance between animals and bacteria also emerges in both groups' genomes. Researchers estimate that about 37% of the 23,000 human genes have homologs with bacteria and Archaea, i.e., they are related to genes found in bacteria and Archaea that were derived from a common ancestor. Many of these homologous genes enable signaling between animals and bacteria, which suggests that they have been able to communicate and influence each other's development. One example is Hadfield and his group's discovery that bacterial signaling plays an essential role in inducing metamorphosis in some marine invertebrate larvae, where the bacteria produce cues associated with particular environmental factors. Other studies have found that bacterial signaling influences normal brain development in mammals, affects reproductive behavior in both vertebrates and invertebrates, and activates the immune system in tsetse flies. The olfactory chemicals that attract some animals (including humans) to their prospective mates are also produced by the animals' resident bacteria. Bacterial signaling is not only essential for development, it also helps animals maintain homeostasis, keeping us healthy and happy. As research has shown, bacteria in the gut can communicate with the brain through the central nervous system. Studies have found that mice without certain bacteria have defects in brain regions that control anxiety and depression-like behavior. Bacterial signaling also plays an essential role in guarding an animal's immune system. Disturbing these bacterial signaling pathways can lead to diseases such as diabetes, inflammatory bowel disease, and infections. Studies also suggest that many of the pathogens that cause disease in animals have "hijacked" these bacterial communication channels that originally evolved to maintain a balance between the animal and hundreds of beneficial bacterial species. Signaling also appears in the larger arena of ecosystems. For example, bacteria in flower nectar can change the chemical properties of the nectar, influencing the way pollinators interact with plants.

Human infants who are born vaginally have different gut bacteria than those delivered by Caesarean section, which may have long-lasting effects. And bacteria feeding on dead animals can repel animal scavengers—organisms 10,000 times their size—by producing noxious odors that signal the scavengers to stay away. In the gut In the earliest animals, gut bacteria played an important role in nutrition by helping animals digest their food, and may have influenced the development of other nearby organ systems, such as the respiratory and urogenital systems. Likewise, animal evolution likely drove the evolution of the bacteria, sometimes into highly specialized niches. For example, 90% of the bacterial species in termite guts are not found anywhere else. Such specialization also means that the extinction of every animal species results in the extinction of an unknown number of bacterial lineages that have evolved along with it. Scientists have also discovered that bacteria in the human gut adapts to changing diets. For example, most Americans have a gut microbiome that is optimized for digesting a high-fat, high-protein diet, while people in rural Amazonas, Venezuela, have gut microbes better suited for breaking down complex carbohydrates. Some people in Japan even have a gut bacterium that can digest seaweed. Researchers think the gut microbiome adapts in two ways: by adding or removing certain bacteria species, and by transferring the desired genes from one bacterium to another through horizontal gene transfer. Both host and bacteria benefit from this kind of symbiotic relationship, which researchers think is much more widespread than previously thought. The big picture Altogether, the recent studies have shown that animals and bacteria have histories that are deeply intertwined, and depend on each other for their own health and well-being as well as that of their environments. Although the researchers focused exclusively on animal-bacteria interactions, they expect that similar trends of codependency and symbiosis are universal among and between other groups, such as Archaea, fungi, plants, and animals. Once considered an exception, such intermingling is now becoming recognized as the rule—just as Margulis predicted many decades ago. Due to these symbiotic relationships, the scientists here propose that the very definitions of an organism, an environment, a population, and a genome have become blurred and should be reviewed. It may be, for instance, that animals are better viewed as host-microbe ecosystems than as individuals.

insect (1 mm) living in a forest canopy (10 m) illustrates the effects animal-bacterial interactions across multiple scales. Bacteria (1 micrometer) residing in the animal’s gut (0.1 mm) are essential to the insect’s nutrition, and insects often make up a majority of the animal biomass in forest canopies. Credit: Margaret McFall-Ngai, et al. ©2013 PNAS


In addition, the scientists predict that the recent findings on animal-bacteria interactions will likely require biologists to significantly alter their view of the fundamental nature of the entire biosphere. Along these lines, large-scale research projects such as the Human Microbiome Project and the Earth Microbiome Project are already underway to investigate the wide range of bacteria in the individual and global systems, and to see what happens when the bacteria are disturbed. In the end, the scientists hope that the results will promote more cross-disciplinary collaboration among scientists and engineers from different fields to explore the new microbial frontier. They argue that these discoveries should revolutionize the way that biology is taught from the high school level on up, by focusing more on the relationships between bacteria, their animal partners, and all other life forms. "It is hard to summarize a single 'most important conclusion,' other than the admonition to biologists studying animals, from behavior to physiology and ecology to molecular biology, that no matter what process you think you are studying, you must look for and consider a major role for bacteria," Hadfield said. "In many cases, this may require partnerships across traditional boundaries of research, meaning that zoologists must collaborate with microbiologists to advance their research, that molecular biologists must collaborate with whole-organism biologists, etc. We want badly for the message in 'Animals in a bacterial world,' to be a call for the necessary disappearance of the old boundaries between life science departments (e.g., Depts of Zoology, Botany, Microbiology, etc.) in universities, and societies (e.g., the American Society for Microbiology, etc.). We also want the message disseminated in college and university classes from introductory biology to advanced courses in the various topic areas of our paper." The results will profoundly change the way that the scientists of this collaboration continue with their own areas of research, Hadfield said. "Each of the authors of our paper conducts basic research in one or more areas of animal-bacterial interactions discussed in the paper, and each will continue to focus on her/his own speciality, I'm sure," he said. "However, I'm also certain that the interactions developed during the composition and writing of the paper (starting with our NESCent meeting in October 2011, when most of us met for the first time) will impact our own research and cause us to establish new collaborations with other laboratories. That has already occurred for me; I have a new collaboration with Dianne Newman's group at CalTech, an outstanding group of bacteriologists who are helping us do a much more in-depth investigation of the bacterial gene-products responsible for larval development."

More information: Margaret McFall-Ngai, et al. "Animals in a bacterial world, a new imperative for the life sciences." PNAS Early Edition. DOI: 10.1073/pnas.1218525110
Journal reference: Proceedings of the National Academy of Sciences

[William Gaatjes]

Bacteria produce their own set of tools to process a soluble form of uranium.
In reality, bacteria produce tiny nano-particles and use these nano particles to convert uranium from one form to another. Using this as part of their food cycle using redox reactions where electrons are "stripped" from one atom and passed on to another atom of a molecule.

I assume here, that when bacteria feed, they actually breakdown molecules by breaking apart the atoms that form covalent bonding by stripping electrons, weakening the atomic crystal.

Well, you can read the full story here :

http://phys.org/news/2013-03-unexpec...oundwater.html

(Phys.org) —Since 2009, SLAC scientist John Bargar has led a team using synchrotron-based X-ray techniques to study bacteria that help clean uranium from groundwater in a process called bioremediation. Their initial goal was to discover how the bacteria do it and determine the best way to help, but during the course of their research the team made an even more important discovery: Nature thinks bigger than that. The researchers discovered that bacteria don't necessarily go straight for the uranium, as was often thought to be the case. The bacteria make their own, even tinier allies – nanoparticles of a common mineral called iron sulfide. Then, working together, the bacteria and the iron sulfide grab molecules of a highly soluble form of uranium known as U(VI), or hexavalent uranium, and transform them into U(IV), a less-soluble form that's much less likely to spread through the water table. According to Barger, this newly discovered partnership may be the basis of a global geochemical process that forms deposits of uranium ore. And it's all done using one of the most basic types of chemical reactions known: oxidation and reduction, commonly known as "redox." Redox reactions can be thought of as the transfer of electrons from donor atoms to atoms that are hungry for electrons, and they are a primary source of chemical energy for both living and non-living processes. Photosynthesis involves redox reactions, as does cell respiration. Iron oxidizes to form rust; batteries depend on redox reactions to store and release energy. "Redox transitions are a very fundamental process," Bargar said. "It's the stuff of life. It's how you breathe." The study, published Monday in the Proceedings of the National Academy of Sciences, was conducted at the Old Rifle site on the Colorado River, a former uranium ore processing site in the town of Rifle, Colo. The aquifer at the site is contaminated with uranium and is the focus of bioremediation field studies conducted by a larger team of scientists at Lawrence Berkeley National Laboratory and funded by the Department of Energy's Office of Biological and Environmental Research. As part of their study, the LBNL team added acetate – essentially vinegar – to the aquifer in a series of injection wells to "feed the bugs," as Bargar put it, allowing acetate to flow throughout the aquifer around the wells. The SLAC team wanted to know what happened to the uranium during bioremediation. "We didn't want to study uranium only in the lab," Bargar said. "We wanted to understand uranium redox behavior in a living, breathing aquifer." They saw a bigger picture, including a molecular- to micron-scale view of what happened to other elements in the aquifer, such as sulfur and iron. During a series of redox reactions, the microbes dine on the acetate, and then pass extra electrons from their vinegar meal to – among other substances – naturally occurring sulfates. This liberates sulfur from the sulfates. A closer look at the soil, provided by X-ray microscopy images taken at the Stanford Synchrotron Radiation Lightsource and electron microscopy images recorded by collaborators at the Swiss Federal Institutes of Technology in Lausanne, Switzerland, revealed that the sulfur combined with iron in the soil to form iron sulfide nanoparticles, which did the actual work of transforming the uranium. At the same time, organic polymers produced by bacteria grabbed the transformed uranium and immobilized it. Discovering that bacteria work together with minerals to transform uranium was a surprise, said Bargar. Bargar said the discovery that a variety of processes immobilize the uranium sheds light on previous, seemingly conflicting observations, and also explains how the process can continue even when the uranium-munching bugs are in short supply. Better understanding Nature's methods for concentrating uranium could also lead to more efficient, environmentally friendly methods for uranium mining. But as a scientist, he appreciates the glimpse he's been given into Nature's abilities to multitask. "Originally we wanted to see what happened to uranium and how it could help bioremediation technology to be successful," he said. "But scientifically the results are much deeper than that." And since their original hypothesis focused on bacteria alone, it's a little humbling, too. "As is usual with science," said Bargar, "you learn your original ideas were a little naive, but finding out what's really going on is very exciting." Journal reference: Proceedings of the National Academy of Sciences Provided by SLAC National Accelerator Laboratory

http://en.wikipedia.org/wiki/Covalent_bond