Concrete-dissolving bacteria are destroying our sewers

Sarah Zhang in Gizmodo: Underground in places nobody likes to look, bacteria are doing terrible things to our sewage pipes. The concrete pipes that carry our waste are literally dissolving away, forcing engineers into a messy, expensive battle against tiny microbes.

“The veins of our cities are in serious trouble, and they’re in serious trouble because of corrosion, and this corrosion has been unanticipated and it’s accelerating,” said Mark Hernandez at a symposium on the microbiology of the built environment in Washington DC yesterday. Hernandez is a civil engineer, but he’s meeting with microbiologists because this problem is bacterial. Essentially, it’s an infection of the nation’s sewage system.

....One set of microbes emits hydrogen sulfide, the gas that is also responsible for raw sewage’s unpleasant smell. This gas fills the empty space between the top of the pipe and the water flow. Another set of microbes living in this headspace turns hydrogen sulfide to sulfuric acid, which eats away at concrete, leaving behind gypsum, the powdery stuff you find in drywall.

“Essentially what we’re ending up with is wet drywall,” said Hernandez. This is one reason the American Society of Civil Engineers has gave our wastewater infrastructure a D grade. The current solution is to put plastic liners into the concrete pipes, a process that is almost as expensive as digging them up entirely. But if the problem is microbial, perhaps the solution is, too?

...The solution they settled on was shotcrete — a type of concrete that can be sprayed onto the inside of pipes — embedded with small amounts of charcoal and bacteria-killing metals like chrome. As the acid ate through this concrete, metal would be released. Based on Hernandez’s tests, this concrete did hold up better against sewage microbes — suggesting a promising solution to corrosion....

Concrete sewer pipes, shot by TUBS, Wikimedia Commons, under the Creative Commons Attribution-Share Alike 3.0 Unported, 2.5 Generic, 2.0 Generic and 1.0 Generic license

A new weapon in the war against superbugs

A press release from the American Friends of Tel Aviv University: In the arms race between bacteria and modern medicine, bacteria have gained an edge. In recent decades, bacterial resistance to antibiotics has developed faster than the production of new antibiotics, making bacterial infections increasingly difficult to treat. Scientists worry that a particularly virulent and deadly "superbug" could one day join the ranks of existing untreatable bacteria, causing a public health catastrophe comparable with the Black Death.

Now research led by Dr. Udi Qimron of Tel Aviv University's Department of Clinical Microbiology and Immunology at the Sackler Faculty of Medicine has discovered a protein that kills bacteria. The isolation of this protein, produced by a virus that attacks bacteria, is a major step toward developing a substitute for conventional antibiotics. "To stay ahead of bacterial resistance, we have to keep developing new antibiotics," said Dr. Qimron. "What we found is a small protein that could serve as a powerful antibiotic in the future."

...Bacteriophages, often referred to as "phages," are viruses that infect and replicate in bacteria. Because they coevolved with bacteria, they are optimized to kill them. As proof of their endurance, phages are the most common life form on earth, outnumbering bacteria 10 to one. In places like the former Soviet Union, phages have been used to treat bacterial infections for the past hundred years. Harmless to humans, they inject their DNA into bacteria and rapidly replicate, killing their hosts.

...Dr. Qimron and his colleagues set out to understand how all 56 proteins found in T7, a particularly virulent phage that infects Escherichia coli bacteria, contribute to its functioning. They discovered that one of the proteins, called 0.4, impedes cell division in E. coli, causing the cells of the bacteria to elongate and then die. The protein is common to many bacteria and a similar process occurs in all bacteria, so the finding may have wide application.

...The major challenge for pharmaceutical companies will be figuring out how exactly to deliver the protein as a drug, said Dr. Qimron. In the meantime, he continues to hunt for other proteins that kill bacteria.

Bacteriophages shot by Mostafa Fatehi, Wikimedia Commons, under the Creative Commons Attribution 3.0 Unported license

Bacteria in drinking water are key to keeping it clean

The University of Sheffield News: Bacteria commonly found in drinking water creates conditions which enable other- potentially harmful – bacteria to thrive, says research by engineers from the University of Sheffield.

The research, published in the latest issue of Water Science and Technology: Water Supply, points the way to more sophisticated and targeted methods of ensuring our drinking water remains safe to drink, while still reducing the need for chemical treatments and identifying potential hazards more quickly.

The research team, from the University of Sheffield’s Faculty of Engineering, studied four bacteria found in the city’s drinking water to see which combinations were more likely to produce a ‘biofilm’. Biofilms are layers of bacteria which form on the inner surfaces of water pipes.

“Biofilms can form on all water pipes and as these are usually non-harmful bacteria, they don’t present a problem,” explains lead researcher, Professor Catherine Biggs. “However, biofilms can also be a safe place for harmful bacteria such as Escherichia coli or Legionella to hide. If the bacterial growth is too heavy, it can break off into the water flow, which at best can make water discoloured or taste unpleasant and at worst can release more dangerous bacteria. Our research looks at what conditions enable biofilms to grow, so we can find ways to control the bacteria in our water supply more effectively.”

Funded by the Engineering and Physical Sciences Research Council, the research isolated four bacteria from water taken from a domestic tap: two were widely found in drinking water everywhere, one was less common and one was unique to Sheffield. The researchers mixed the bacteria in different combinations and found that, in isolation, none of them produced a biofilm. However, when any of the bacteria were combined with one of the common forms, called Methylobacterium, they formed a biofilm within 72 hours.

...“This means it should be possible to control or even prevent the creation of biofilms in the water supply by targeting these particular bacteria, potentially reducing the need for high dosage chemical treatments...

From the tap, shot by Alex Anlicker, Wikimedia Commons, under the Creative Commons Attribution-Share Alike 3.0 Unported license

Scientists develop more accurate model of climate change’s effect on soil

University of California-Irvine: Scientists from UC Irvine and the National Center for Atmospheric Research have developed a new computer model to measure global warming’s effect on soil worldwide that accounts for how bacteria and fungi in soil control carbon. They found that soil outcomes based on their microbial model were more reliable than those forecast by traditional models. Study results appear online in Nature Climate Change.

While standard models project modest carbon losses with global warming, the microbial models generate two novel scenarios: One is that soil around the world will accumulate carbon if microbial growth declines with higher temperatures. The second assumes that microbial growth increases with global warming, resulting in large soil carbon losses, meaning much more carbon will be released into the atmosphere.

“The microbial soil model is extremely important to understanding the balance of carbon in the soil versus the atmosphere and how carbon mass in soil is affected by these bacteria and fungi,” said the study’s senior author, Steven Allison, an associate professor of ecology & evolutionary biology and Earth system science at UC Irvine. “Our hope is that this new soil model will be applied to the global Earth system models to better predict overall climate change.”

The researchers also discovered that in cases of increased carbon input to soil (such as carbon dioxide or nutrient fertilization), microbes actually released the added carbon to the atmosphere, while traditional models indicate storage of the additional carbon. This, they said, is further evidence that the Earth system models should incorporate microbial impact on soil to more accurately project climate change ramifications.

“In our microbial model, we directly simulate how the activity of organisms like bacteria and fungi control the storage and losses of soil carbon,” said Will Wieder, a postdoctoral scientist with the National Center for Atmospheric Research in Boulder, Colo. “Now that we can more accurately measure what happens to soil as temperatures increase, we hope to study the potential effects of soil carbon fluctuations within a changing environment.”...

March of the pathogens: Parasite metabolism can foretell disease ranges under climate change

Morgan Kelly in News at Princeton: Knowing the temperatures that viruses, bacteria, worms and all other parasites need to grow and survive could help determine the future range of infectious diseases under climate change, according to new research.

Princeton University researchers developed a model that can identify the prospects for nearly any disease-causing parasite as the Earth grows warmer, even if little is known about the organism. Their method calculates how the projected temperature change for an area would alter the creature's metabolism and life cycle, the researchers report in the journal Ecology Letters.

Lead author Péter Molnár, a Princeton postdoctoral researcher of ecology and evolutionary biology, explained that the technique is an all-inclusive complement to current methods of predicting how climate change will affect disease, which call for a detailed knowledge of the environmental factors a specific parasite needs to thrive. But for many parasites, that information doesn't exist.

The more general Princeton model is based on the metabolic theory of ecology. Under this premise, all biological organisms need a balance between body size and body temperature to maintain the metabolism that keeps their organs functioning. Like any cold-blooded creature, disease-causing parasites rely on external temperatures for this balance. Scientists with knowledge of a parasite's body size and life cycle could use the Princeton metabolic model to predict how the organism would fare in altered climates.

"Our framework is applicable to pretty much any parasite, and utilizes established metabolic patterns shown to hold across a wide variety of species," Molnár said. "It would be impossible to ever gather enough data to develop a separate climate-change model for each existing and emerging disease in humans, wildlife and livestock," Molnár said. "With our physiological approach, many of the parameters for a specific pathogen can be predicted based on what is known about metabolic processes in all parasites, so that the model remains applicable to new and less-studied species as well."...

A cameo by the Marburg virus, image from the CDC

A war without end - with earth’s carbon cycle held in the balance

Oregon State University: The greatest battle in Earth’s history has been going on for hundreds of millions of years - it isn’t over yet - and until now no one knew it existed, scientists reported today in the journal Nature.

In one corner is SAR11, a bacterium that’s the most abundant organism in the oceans, survives where most other cells would die and plays a major role in the planet’s carbon cycle. It had been theorized that SAR11 was so small and widespread that it must be invulnerable to attack.

In the other corner, and so strange-looking that scientists previously didn’t even recognize what they were, are “Pelagiphages,” viruses now known to infect SAR11 and routinely kill millions of these cells every second. And how this fight turns out is of more than casual interest, because SAR11 has a huge effect on the amount of carbon dioxide that enters the atmosphere, and the overall biology of the oceans.

“There’s a war going on in our oceans, a huge war, and we never even saw it,” said Stephen Giovannoni, a professor of microbiology at Oregon State University. “This is an important piece of the puzzle in how carbon is stored or released in the sea.”

Researchers from OSU, the University of Arizona and other institutions today outlined the discovery of this ongoing conflict, and its implications for the biology and function of ocean processes. The findings disprove the theory that SAR11 cells are immune to viral predation, researchers said.

“In general, every living cell is vulnerable to viral infection,” said Giovannoni, who first discovered SAR11 in 1990. “What has been so puzzling about SAR11 was its sheer abundance; there was simply so much of it that some scientists believed it must not get attacked by viruses.” What the new research shows, Giovannoni said, is that SAR11 is competitive, good at scavenging organic carbon, and effective at changing to avoid infection. Because of that, it thrives and persists in abundance even though it’s constantly being killed by the new viruses that have been discovered....

A SAR-11 bacterium infected with the pelagiphage virus. Photo courtesy of the University of Oregon

Amazon deforestation brings loss of microbial communities

EurekAlert via the University of Massachusetts at Amherst: An international team of microbiologists led by Klaus Nüsslein of the University of Massachusetts Amherst has found that a troubling net loss in diversity among the microbial organisms responsible for a functioning ecosystem is accompanying deforestation in the Amazon rainforest.

Nüsslein, an expert in tropical rain forest microbial soil communities, says, "We found that after rainforest conversion to agricultural pastures, bacterial communities were significantly different from those of forest soils. Not only did the pasture soils show increased species numbers, these species were also less related to one another than in rainforest soil. This is important because the combination of lost forest species and the homogenization of pasture communities together signal that this ecosystem is now a lot less capable of dealing with additional outside stress."

He and colleagues studied a large farm site over the past four years at the frontier where farmers drive agriculture into pristine rainforest in Rondonia, Brazil, to convert rainforest to agricultural use. Findings in part validated previous research showing that bacteria in the soil became more diverse after conversion to pasture. However, in its fourth year, their study overcame limitations of earlier investigations to show that changes in microbial diversity occurred over larger geographic scales. Results appear in the current issue of Proceedings of the National Academy of Sciences.

In addition to Nüsslein at UMass Amherst, the research group includes first author Jorge Rodrigues at the University of Texas at Arlington with Brendan Bohannan at the University of Oregon, James Tiedje at Michigan State University, and others at the University of Sao Paulo. Lead investigators Nüsslein and Rodrigues emphasize that the study is an equal collaboration among the four research groups.

Findings do not support earlier study conclusions, instead they show that the loss of restricted ranges for different bacteria communities results in a biotic homogenization and net loss of diversity overall. Scientists worry that the loss of genetic variation in bacteria across a converted forest could reduce ecosystem resilience. The researchers hope their work will provide valuable data to those making decisions about the future of the Amazon rainforest....

From NASA: The 38-kilometer-long Lago do Erepecu (Lake Erepecu) in Brazil runs parallel to the lower Rio Trombetas (Trombetas River), which snakes along the upper half of this astronaut photograph. Water-bodies in the Amazon Rainforest are often so dark they can be difficult to distinguish. In this image, however, the lake and river stand out from the uniform green of the forest in great detail as a result of sun-glint on the water surface. Sun-glint is the mirror-like reflection of sunlight off of a surface directly back towards the viewer, in this case an astronaut on-board the International Space Station. Forest soil is red, as shown by airfield clearings near Porto Trombetas (image far upper left), a river port on the south side of the Trombetas River.

Fertile soil doesn't fall from the sky: The contribution of bacterial remnants to soil fertility has been underestimated until now

Helmholtz Centre for Environmental Research: Remains of dead bacteria have far greater meaning for soils than previously assumed. Around 40 per cent of the microbial biomass is converted to organic soil components, write researchers from the Helmholtz Centre for Environmental Research (UFZ), the Technische Universität Dresden (Technical University of Dresden) , the University of Stockholm, the Max-Planck-Institut für Entwicklungsbiologie (Max Planck Institute for Developmental Biology) and the Leibniz-Universität Hannover (Leibniz University Hannover) in the professional journal Biogeochemistry.

Until now It was assumed that the organic components of the soil were comprised mostly of decomposed plant material which is directly converted to humic substances. In a laboratory experiment and in field testing the researchers have now refuted this thesis. Evidently the easily biologically degradable plant material is initially converted to microbial biomass which then provides the source material to soil organic matter.

Soil organic matter represent the largest fraction of terrestrially bound carbon in the biosphere. The compounds therefore play an important role not only for soil fertility and agricultural yields. They are also one of the key factors controlling the concentration of carbon dioxide in the atmosphere. Climatic change can therefore be slowed down or accelerated, according to the management of the soil resource.

In laboratory incubation experiment, the researchers initially labelled model bacteria with the stable isotope 13C and introduced the bacteria to soil deriving from the long-term cultivation experiment "Ewiger Roggenbau" in Halle/Saale. Following the incubation time of 224 days the fate of the carbon of bacterial origin was determined. "As a result we found fragments of bacterial cell walls in sizes of up to 500 x 500 nanometres throughout our soil samples. Such fragments have also been observed in other studies, but have never been identified or quantified", declares Professor Matthias Kästner of the UFZ.

...."This new approach explains many properties of organic soil components which were previously viewed as contradictory", says Matthias Kästner....

A canyon formed in the soft loess soil by a small stream that flows from the west into the Daxia He River, in the northeastern part of Linxia County (probably, Xihe Township), in western China. Shot by Vmenkov, Wikimedia Commons,  under the Creative Commons Attribution-Share Alike 3.0 Unported license

Researchers find MRSA superbug in reused wastewater

Alan McStravick in RedOrbit:  Most people are already exposed to the common bacterium Staphylococcus aureus as it is typically found on human skin and respiratory tracts. ... A mutated form of this germ, a so-called ‘superbug’ known as methicillin-resistant Staphylococcus aureus (MRSA), is immune to first-line antibiotics and can cause a dangerous form of staph infection. People most at risk include athletes who share towels and razors, children in daycare settings, members of the military who live in close quarters and individuals who have recently received tattoos. Additionally, people who have had surgery within the past year are subject to a particularly high risk of contracting an infection due to MSRA.

...A research team led by scientists at the University of Maryland School of Public Health has recently discovered that this superbug has been found in significant amounts in several U.S. wastewater treatment plants. MSRA is known to cause difficult-to-treat and potentially fatal bacterial infections. Typically, these infections are found in hospital patients. However, since the 1990’s, it has also been infecting members of the general community that were otherwise considered healthy.

“MRSA infections acquired outside of hospital settings – known as community-acquired MRSA or CA-MRSA – are on the rise and can be just as severe as hospital-acquired MRSA. However, we still do not fully understand the potential environmental sources of MRSA or how people in the community come in contact with this microorganism,” says Amy R. Sapkota, assistant professor in the Maryland Institute for Applied Environmental Health and leader of the study....

This 2005 scanning electron micrograph (SEM) depicted numerous clumps of methicillin-resistant Staphylococcus aureus bacteria, commonly referred to by the acronym, MRSA; Magnified 9560x. Recently recognized outbreaks, or clusters of MRSA in community settings have been associated with strains that have some unique microbiologic and genetic properties, compared with the traditional hospital-based MRSA strains, which suggests some biologic properties, e.g., virulence factors like toxins, may allow the community strains to spread more easily, or cause more skin disease. A common strain named USA300-0114 has caused many such outbreaks in the United States. Shot from the Centers for Disease Control

Bacterial communication could affect earth's climate

Woods Hole Oceanographic Institution (WHOI): ...[Woods Hole] scientists have discovered that bacterial communication could have a significant impact on the planet’s climate.

In the ocean, bacteria coalesce on tiny particles of carbon-rich detritus sinking through the depths. WHOI marine biogeochemists Laura Hmelo, Benjamin Van Mooy, and Tracy Mincer found that these bacteria send out chemical signals to discern if other bacteria are in the neighborhood. If enough of their cohorts are nearby, then bacteria en masse commence secreting enzymes that break up the carbon-containing molecules within the particles into more digestible bits. It has been suggested that coordinated expression of enzymes is very advantageous for bacteria on sinking particles, and Hmelo and her colleagues have uncovered the first proof of this in the ocean.

“We don’t often think about bacteria making group decisions, but that is exactly what our data suggest is happening,” said Hmelo, now at the University of Washington. The paper is published in the current online, “early view,” issue of Environmental Microbiology Reports.

The source of carbon in the particles is atmospheric carbon dioxide, a heat-trapping greenhouse gas. Bacterial communication could lead to the release of carbon from the particles at shallower depths, rather than sinking to the ocean’s depths. According to the WHOI scientists, this means that bacterial communication results in less carbon dioxide being drawn out of the air and transferred to the bottom of the ocean from where it cannot easily return to the atmosphere. This represents the first evidence that bacterial communication plays a crucial role in Earth’s carbon cycle.

“So microscopic bacteria buffer the amount of carbon dioxide in the atmosphere through their ‘conversations,’ ” Van Mooy said. “I think it’s amazing that there are a near- infinite number of these conversations going on in the ocean right now, and they are affecting Earth’s carbon cycle.”

Summer phytoplankton bloom off the coast of New Zealand, shot by NASA

Nitrogen-fixing bacterial symbiont promises trove of natural products

Science Daily: Soil-dwelling bacteria of the genus Frankia have the potential to produce a multitude of natural products, including antibiotics, herbicides, pigments, anticancer agents, and other useful products, according to Bradley S. Moore of the Scripps Oceanographic Institute, La Jolla, and his collaborators in an article in the June 2011 issue of the journal Applied and Environmental Microbiology.

The researchers found genetic structures in this bacterium that resemble those of various valuable natural product categories through bioinformatics and genome mining. "This tremendous biosynthetic capacity is reminiscent of many industrially important bacteria such as those belonging to the genus, Streptomyces that produce the majority of the natural antibiotics used as drugs," says Moore.

"To see this capacity in a well-known microbe not previously exploited for its chemical richness was very rewarding from both an applied and basic science point of view," says Moore. Frankia are nitrogen-fixing bacteria that live in symbiosis with actinorhizal plants (whose ranks include beech and cherry trees, and various gourd-producing plants). "Since the vast majority of the deduced [biosynthetic] pathways are unique to Frankia, it suggests that they employ a very complex and specialized communication with their plant host to establish and maintain their symbiosis. So lots to discover there."

Frankia have not previously been exploited partly because these bacteria are difficult to grow in the lab. But new genetic methods make it easier to transplant genes for promising natural products from Frankia into "more user-friendly host bacteria for production," says Moore.

Moreover, genome mining, a recent technique that involves searching for genetic sequences, was critical to the results, and "complementary to the far more laborious traditional natural product drug discovery that has gone unchanged for decades," says Moore. A greater understanding of how complex organic molecules are synthesized in nature laid additional groundwork for this, and for "a new revolution in the discovery of natural chemicals that will fuel new research into what functions these chemicals play in nature, and how they can be used to benefit society," says Moore….

Frankia alni, for all your actinorhizal needs, shot by Lebrac, Wikimedia Commons, under the Creative Commons Attribution-Share Alike 3.0 Unported

Evidence of 'rain-making' bacteria discovered in atmosphere and snow

Science Daily: Brent Christner, LSU professor of biological sciences, in partnership with colleagues in Montana and France, recently found evidence that rain-making bacteria are widely distributed in the atmosphere. These biological particles could factor heavily into the precipitation cycle, affecting climate, agricultural productivity and even global warming. Christner and his colleagues published their results on Feb 29 in the journal Science.

Christner's team examined precipitation from global locations and demonstrated that the most active ice nuclei -- a substrate that enhances the formation of ice -- are biological in origin. This is important because the formation of ice in clouds is required for snow and most rainfall. Dust and soot particles can serve as ice nuclei, but biological ice nuclei are capable of catalyzing freezing at much warmer temperatures. If present in clouds, biological ice nuclei may affect the processes that trigger precipitation.

Biological precipitation, or the "bio-precipitation" cycle, as David Sands, Montana State University professor of plant sciences and plant pathology calls it, basically is this: bacteria form little groups on the surface of plants. Wind then sweeps the bacteria into the atmosphere, and ice crystals form around them. Water clumps on to the crystals, making them bigger and bigger. The ice crystals turn into rain and fall to the ground. When precipitation occurs, then, the bacteria have the opportunity to make it back down to the ground. If even one bacterium lands on a plant, it can multiply and form groups, thus causing the cycle to repeat itself.

"We think if (the bacteria) couldn't cause ice to form, they couldn't get back down to the ground," Sands said. "As long as it rains, the bacteria grow."

The team's work is far-reaching. Sands and his colleagues have found the bacteria all over the world, including Montana, California, the eastern U.S., Australia, South Africa, Morocco, France and Russia.

These research findings could potentially supply knowledge that could help reduce drought from Montana to Africa, Sands said. The concept of rain-making bacteria isn't far-fetched. Cloud seeding with silver iodide or dry ice has been done for more than 60 years. Many ski resorts use a commercially available freeze-dried preparation of ice-nucleating bacteria to make snow when the temperature is just a few degrees below freezing…

Rain near the village Lunde, the north of Funen, Denmark, by Malene Thyssen, Wikimedia Commons