Role of microbes, effect on infectious disease dynamics

In the field, UCSB graduate student Andrea Jani uses a sterile swab to sample mucus on the skin of a frog. Frogs are released unharmed after sampling. Credit: Abby Mayer

The adult human body is made up of about 37 trillion cells. Microbes, mainly bacteria, outnumber body cells by 10 to 1. Increasingly, scientists recognize that this huge community of microbes, called the microbiome, affects the health, development and evolution of all multicellular organisms, including humans.

Studies show symbiotic microbes can help prevent infection by disease-causing pathogens. But sometimes the interaction goes the other way, with a pathogen or disease disrupting the normal community of symbiotic bacteria. In a new study, a team of scientists from UC Santa Barbara demonstrates that a fungal pathogen of amphibians does just that. The findings appear today in the Early Edition of the Proceedings of the National Academy of Science.

Landmark experiments with model organisms such as mice have shown that infectious pathogens can disrupt the "normal" microbiome, but the extent to which this process shapes symbiotic microbial communities during disease outbreaks in nature is largely unknown. This new work, conducted by Andrea Jani, a UCSB graduate student in Cherie Briggs' lab in the Department of Ecology, Evolution and Marine Biology (EEMB), addresses a fundamental gap in disease ecology and microbiome research.

Co-authors Jani and Briggs -- also affiliated with UCSB's Biomolecular Science and Engineering program -- found that the chytrid fungus Batrachochytrium dendrobatidis (Bd) appears to drive dramatic changes in symbiotic bacterial communities during natural disease episodes in four populations of the endangered Sierra Nevada yellow-legged frog (Rana sierrae). Chytridiomycosis, an emerging infectious disease of amphibian skin caused by the Bd pathogen, is a leading cause of amphibian biodiversity loss worldwide.

"In the California Sierra Nevada, this disease has led to the rapid extirpation of frogs from hundreds of high-elevation lakes; however, in other lakes, infected frogs of the same species are surviving and persisting with the fungus," explained Briggs, who is the Duncan and Suzanne Mellichamp Chair in Systems Biology. "Given that amphibian skin is the organ infected by Bd, there has been a lot of interest in how antifungal properties of some skin-associated bacteria may protect frogs against this fungal pathogen. In this study we focused on the flip side of this interaction -- that is, how infection with Bd can disrupt the skin microbial community."

"We used next-generation DNA sequencing to document significant shifts in skin-associated bacterial communities of the Sierra Nevada yellow-legged frog during natural Bd outbreaks," Jani explained. "We paired these field surveys with a laboratory infection experiment, demonstrating a causal relationship in which Bd alters the Rana sierrae microbiome."

The researchers found a remarkable consistency in the response of the microbiome to Bd infection among field populations and between the field and laboratory. Several key taxa -- a group of one or more populations of an organism or organisms -- consistently responded in the same direction to Bd infection, suggesting some predictability in the effect of Bd on the microbiome.

"What we found was that the severity of infection with Bd is strongly correlated with the composition of bacterial communities on the skin of frogs," Jani continued. "What was surprising was that across the different frog populations there was pretty striking consistency in this correlation with Bd. One of the frog populations crashed due to Bd infection; the other three populations seemed to tolerate Bd infections. So there are different disease dynamics going on, yet they have a similar relationship between the microbiome and Bd."

Still, the underlying mechanism for Bd-induced changes in the microbiome is not clear. The researchers hypothesize that the pathogen might compete directly with certain bacteria for space or resources or release compounds that negatively or positively affect certain bacterial species. Alternatively, they say, some pathogens could control immune responses of the host to favor their own growth and disrupt the normal symbiotic bacterial community.

Jani noted that some promise exists for probiotic treatments as a tool to fight the decline of frogs due to Bd, but she was careful to qualify that statement by saying that there is still a lot that scientists do not understand about either the environmental impact that might have or what the interactions are between the natural bacteria that exist on frogs and the pathogen. "We find that some taxa previously identified as having anti-Bd properties are driven to low abundances by Bd infection, which may limit their effectiveness as probiotic agents," she said.

"This study shows the importance of knowing how the many benign microbes living on and in our bodies interact with those that cause disease," said Sam Scheiner, National Science Foundation (NSF) director for the joint NSF/National Institutes of Health/United States Department of Agriculture Ecology and Evolution of Infectious Disease Program, which funded the research. "The results are important for developing responses to a disease causing amphibians to go extinct worldwide and also have implications for future studies of human health.

Source:  University of California - Santa Barbara

New species of beetle discovered in the world's deepest cave

This is a drawing of Duvalius abyssimus. Credit: Sinc - José Antonio Peñas

The unusual habitat of the Krubera cave in the Western Caucasus remains a mystery. Researchers from two Spanish universities have discovered a new species of beetle in the depths of this cave.

Cave beetles are one of the most iconic species found in subterranean habitats. They were historically the first living organisms described by science that are adapted to the conditions of hypogean or subterranean life.

Now, a Portuguese scientist and a Spaniard have discovered a new species of beetle in the deepest cave known to man; a cave 2,140 metres deep. It is the Krubera cave, situated in the Arabika massif in the Western Caucasus.

Ana Sofía Reboleira, researcher from the Universities of Aveiro and La Laguna, and Vicente M. Ortuño, from the University of Alcalá, have published their discovery in the scientific journal 'Zootaxa'.

"The new species of cave beetle is called Duvalius abyssimus. We only have two specimens, a male and a female. Although they were captured in the world's deepest cave, they were not found at the deepest point," Ortuño, who has dedicated the last 10 years to studying subterranean fauna, said.

The Duvalius genus is a successful colonizer of Earth's depths. The majority of species have a hypogean lifestyle and live in caves or the superficial underground compartment.

"The new species' characteristics indicate that it is moderately adapted to life underground. Proof of this is that they still have eyes, which are absent in the highly specialised cave species," added the expert.

The Arabika massif region in Abkhazia, where this cave is found, is biogeographically a very interesting area. Altitudes fluctuate between 1,900 and 2,500 metres and the cave is composed of lower and upper Jurassic-Cretaceous limestone.

Its large area has provided endless subterranean refuges for fauna. In fact, various genera of endemic cave beetles live in the Western Caucasus. "Its location is strategic, since there are fauna of European, Asian and also endemic origin in the zone," the scientist underlined.

The entrance to the cave is 2,240 metres above sea level and 15 kilometres from the Black Sea. Below numerous vertically-cutting sections, it reaches a depth of 1,400 metres. From this level, it splits into branches and in order to reach the greatest known depth, it is necessary to pass various flooded underground chambers using diving techniques.

"The discovery of the new beetle provides important data on species that co-exist in these almost unknown ecosystems, even more so when they are found in a geographical area that is very difficult to access, such is the case with this cave," Ortuño concluded.

Source:  FECYT - Spanish Foundation for Science and Technology

Ancient, hydrogen-rich waters deep underground around the world: Waters could support isolated life

Energy-rich waters discharge kilometers below the surface in a South African mine.
Credit: G. Borgonie, 2014

A team of scientists, led by the University of Toronto's Barbara Sherwood Lollar, has mapped the location of hydrogen-rich waters found trapped kilometres beneath Earth's surface in rock fractures in Canada, South Africa and Scandinavia.

Common in Precambrian Shield rocks -- the oldest rocks on Earth -- the ancient waters have a chemistry similar to that found near deep sea vents, suggesting these waters can support microbes living in isolation from the surface.

The study, to be published in Nature on December 18, includes data from 19 different mine sites that were explored by Sherwood Lollar, a geoscientist at U of T's Department of Earth Sciences, U of T senior research associate Georges Lacrampe-Couloume, and colleagues at Oxford and Princeton universities.

The scientists also explain how two chemical reactions combine to produce substantial quantities of hydrogen, doubling estimates of global production from these processes which had previously been based only on hydrogen coming out of the ocean floor.

"This represents a quantum change in our understanding of the total volume of Earth's crust that may be habitable," said Sherwood Lollar.

"Until now, none of the estimates of global hydrogen production sustaining deep microbial populations had included a contribution from the ancient continents. Since Precambrian rocks make up more than 70 per cent of the surface of Earth's crust, Sherwood Lollar likens these terrains to a "sleeping giant," a huge area that has now been discovered to be a source of possible energy for life," she said.

One process, known as radiolytic decomposition of water, involves water undergoing a breakdown into hydrogen when exposed to radiation. The other is a chemical reaction called serpentization, a mineral alteration reaction that is common in such ancient rocks.
This study has important implications for the search for deep microbial life. Quantifying the global hydrogen budget is key to understanding the amount of Earth's biomass that is in the subsurface, as many deep ecosystems contain chemolithotrophic -- so-called "rock-eating" -- organisms that consume hydrogen. In the deep gold mines of South Africa, and under the sea, at hydrothermal vents where breaks in the fissure of Earth's surface that release geothermally heated waters -- hydrogen-rich fluids host complex microbial communities that are nurtured by the chemicals dissolved in the fluids. This study identifies a global network of sites with hydrogen-rich waters that will be targeted for exploration for deep life over the coming years.

Further, because Mars -- like the Precambrian crust -- consists of billions-of-year-old rocks with hydrogen-producing potential, this finding has ramifications for astrobiology. "If the ancient rocks of Earth are producing this much hydrogen, it may be that similar processes are taking place on Mars," said Sherwood Lollar.

Other key members of the research team are Chris Ballentine of Oxford University, Tulis Onstott at Princeton University and Georges Lacrampe-Couloume of the University of Toronto. The research was funded by the Canada Research Chairs program, the Natural Sciences & Engineering Research Council, the Sloan Foundation Deep Carbon Observatory, the Canadian Space Agency and the National Science Foundation.

Source: University of Toronto