Nitrososphaera viennensis: a new species, genus, family, order and class of soil-dwelling archaea

Archaea-Post-ImageWhen a new species of microbe is discovered, it often fits into a known genus, forming a new outermost branch in the tree of life. Sometimes, though, organisms are discovered with DNA sufficiently different from all known species that they are placed into a new genus. Additions of new branches to the tree of life become rarer as we move closer to the ‘trunk’, towards ever broader classifications of organisms. Now, a team of Viennese researchers isolated a new species of archaea, named Nitrososphaera viennensis, which is the first known member of not just a new genus, family, or even order – it belongs to a whole new class of archaea. N. viennensis has been officially described in the International Journal of Systematic and Evolutionary Microbiology.

Archaea are considered ancient organisms but are still poorly understood life forms. They have characteristics in common with the two domains of life – bacteria and eukaryotes, the group that includes all other life forms. Like bacteria, archaea have no nucleus – but archaeal proteins are often much more similar to those of eukaryotes. After much debate throughout the 20th century as to whether archaea should be classified with bacteria or eukaryotes, they now form their very own domain in the tree of life.

Until recently, it was also thought that most archaea were extremophiles, thriving in environments with extremes of temperature, acidity, heavy metals, salinity, nuclear radiation, or availability of water or nutrients. It was only nine years ago that the first non-extremophilic, aerobic archaeon was cultivated from a marine sample. Similarly, N. viennensis was discovered in soil from the gardens of the Faculty of Ecology at the University of Vienna: a decidedly moderate environment.

N. viennensis and its relatives are interesting in another respect: they perform a chemical reaction called ammonia oxidation, transforming ammonia (NH3) and producing nitrite (NO2-). This is a vital step in the global nitrogen cycle, which ensures that nitrogen is transformed into compounds more easily accessible to plants. Until 2005, when the marine archaeon Nitrosopumilus maritimus was isolated and found to oxidise ammonia, the consensus was that only bacteria could oxidise ammonia. N. viennensis has become the first ammonia-oxidising archaeon ever isolated from soil in pure culture.

The isolation and production of a pure culture of N. viennensis was groundbreaking as ammonia-oxidising organisms are notoriously difficult to cultivate. Although the genetic material of microbes can be detected and analysed in their natural environment, it is much more difficult to understand their functioning in this manner, let alone characterise a new species. As such, the work of one of Dr Stieglmeier’s former postdocs at the faculty, proved invaluable: Dr Maria Tourna used soil samples from a variety of environments and started cultures under various environmental conditions to look for ammonia-oxidising archaea. N. viennensis was the crowning result.

In the marine environment, neutrophilic ammonia-oxidising archaea such as N. maritimus contribute very significantly to the global nitrogen cycle simply because there are so many of them: in some parts of the ocean, ammonia-oxidising archaea make up nearly 40% of picoplankton (the smallest non-virus ocean organisms). Dr Stieglmeier also estimates that ammonia-oxidising archaea such as N. viennensis may make up as much as 1% of the total microbiota in soil. By isolating the first such species, she has made an important step forward towards finding out more about their metabolism, and their potential contribution of greenhouse gases such as nitrous oxide to the atmosphere.

It is not certain whether N. viennensis will prove to play a major role in ammonia oxidation in soil – other, as yet uncultivated archaeal species may be more numerous and make bigger contributions. Nevertheless, the isolation and classification of this archaeon has made an enormous contribution to archaeal taxonomy and to our understanding of what organisms contribute to the global nitrogen cycle.

Jon Fuhrmann

Stieglmeier, M., Klingl, A., Alves, R. J., Simon, K. M. R., Melcher, M., Leisch, N., & Schleper, C. (2014). Nitrososphaera viennensis sp. nov., an aerobic and mesophilic ammonia-oxidizing archaeon from soil and member of the archaeal phylum Thaumarchaeota. International Journal of Systematic and Evolutionary Microbiology, 64(8), 2738-2752. doi:10.1099/ijs.0.063172-0

Image credit: Stieglmeier, M.
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New to Science – August Edition

200329304-001Each month, the Society for General Microbiology publishes the International Journal of Systematic and Evolutionary Microbiology, which details newly discovered species of bacteria, fungi and protists. Here are a few of the new species that have been discovered, and the places they’ve been found. The full papers are available to journal subscribers, but the abstracts are free to read.

The glorious weather here in the capital has seen London Zoo become a visitor magnet as city dwellers and tourists alike. In particular, the newborn black-capped squirrel monkey baby has been drawing squeals of delight from an adoring crowd.

Close cousins of this tiny new world monkey, a group of marmosets, has been found to be home to a new species of bacterium – Bifidobacterium aesculapii – which was discovered by Italian scientists in the faeces of a baby marmoset. Similarly, lion-tailed macaques in Fota Wildlife Park, Cork, Ireland, yielded Campylobacter corcagiensis upon investigation by researchers from Cork and Belgium.

In Prague, Czech scientists have painstakingly reared bumblebee queens in a laboratory. In their digestive tract, they discovered the new Lactobacillus bombi, a new member of a genus of bacteria that convert sugar to lactic acid. Working in the field, a team of Korean researchers isolated Flavobacterium faecale from the stool of penguins near King Sejong Base, King George Island, Antarctica, while another group isolated Litoreibacter ascidiaceicola from a golden sea squirt in the Sea of Japan.

Further north in the Sea of Japan, in Russia’s Peter the Great Bay, a Japanese team studied sediments on the seashore. In this remote spot in the southeast corner of Russia, they isolated two new species of bacteria, Simiduia litorea and Tamlana sedimentorum.

In the rather more urban environment of Tsukuba Science City, just north of Tokyo, a team of local researchers isolated the acidophilic bacterium Granulicella cerasi from the bark of one of the area’s ubiquitous cherry trees. At the other end of Tokyo, Povalibacter uvarum was isolated from grapes grown in the region.

More culinarily inclined scientists, meanwhile, investigated Nukadoko, the rice bran mash used around Japan to ferment vegetables for a dish called Nukazuke. They discovered Lactobacillus furfuricola. Unless colonies of Lactobacillus are transferred into Nukazuke from a previous batch of rice mash, they have to grow fresh from fermenting vegetables or even following contact from human hands preparing the mixture.

Rice husks were also the subject of a Korean team’s research, which yielded the discovery of Bacillus oryzaecorticis. Chinese scientists, meanwhile, isolated Enterobacter xiangfangensis from traditional sourdough bread in Heilongjiang province in northeastern China. They also suggested the reclassification of Enterobacter sacchari to a different genus, renaming it Kosakonia sacchari.

Closer to home, Spanish researchers isolated Enterococcus olivae from vats of fermenting brine at an olive manufacturing company in Seville province, Spain. In Vienna, Austria, a team of researchers studied a soil sample from one of the Faculty of Ecology’s gardens and isolated a novel archaeon named Nitrososphaera viennensis. This new species is thought to play a major role in the terrestrial nitrogen cycle and has been assigned new phylogenetic class, a very high-level taxonomic rank.

In the spirit of discovery and continued exploration of the tree of life, the Society would like to wish all faithful readers of its blog a very pleasant summer.

Jon Fuhrmann

Image Credit: Thinkstock
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Learning more about the Chikungunya virus

ResearchBlogging.org8013880499_c7ec99ee21_zChikungunya, an emerging viral infection carried by mosquitoes, has been making headlines across the US over the past few weeks. But what is Chikungunya? How does it spread? Jon Fuhrmann investigates.

The American Centre for Disease Control (CDC) first reported the existence of Chikungunya in the Caribbean as recently as December 2013. Since then, the number of infections in Americans returning from the Caribbean have steadily risen and have been confirmed in 35 states – a remarkable feat for a virus that, until less than a year ago, was undetected in the Western hemisphere. To make matters worse, two infected patients in Florida had not travelled at all: mosquitoes within the United States had transmitted the virus for the first time.

Chikungunya is transmitted by the tiger mosquito (Aedes albopictus) and the yellow fever mosquito (Aedes aegypti). Discovered in Tanzania in 1952, the virus’s name means “that which bends up” in the language of the Makonde people of Tanzania and Malawi. This is in reference to the extreme joint and muscle pain caused by the virus, which sees many patients writhing in agony. While Chikungunya infections are rarely fatal, chronic arthritis and long-term pain can persist for years after infection in older patients. Continue reading

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The Longitude Prize 2014 needs YOU

481459339The Longitude Prize 2014 was announced a few weeks ago to much media fanfare. After a vote, the British public decided that the prize should focus on the rise of antibiotic resistance. Joshua Ryan-Saha, Assistant Manager of the Longitude Prize, blogs here, asking members of the Society for General Microbiology to have their say on the design of the prize.

The growth of anti-microbial resistance will impact all of us. The World Health Organization estimates that antibiotic treatments add an average of 20 years to our lives. However, our overuse of antibiotics has allowed bacteria to evolve resistance, leading to the emergence of untreatable superbugs that threaten one of the cornerstones of modern medicine. How we respond to the growing global antimicrobial resistance is one of the most important science policy questions of our age.

The Longitude Prize 2014 will encourage the development of new point-of-care diagnostics that will help clinicians make better informed decisions when prescribing antibiotics, restricting their use only to those cases when they are beneficial. We know that diagnostics alone can’t solve the problem of anti-microbial resistance, but they are a central part of addressing the problem of antibiotic overuse. While the £10m prize fund is comparatively small when compared with the total global research spend in this area, a prize of this scale could make a tremendous difference in stimulating new and innovative diagnostic methods.

Over the last year, Nesta and our partners Science Practice have been working with a range of experts in this field to design a challenge prize that will encourage individuals and teams from across the world to try and solve it. In our paper for open review, we have outlined what we have come up with so far. We have tried to design this prize in a way that makes it potentially achievable within the five-year timescales, while ensuring it is challenging enough to encourage breakthrough innovations. We also hope that this challenge is accessible to a wide pool of potential competitors.

Microbiology is clearly a central aspect of antimicrobial resistance, and microbiologists will likely compete for the Longitude Prize 2014. As such, your input on the open review would be particularly valuable, both for Nesta and for members of the Society for General Microbiology. With the help of your thoughts and comments on the paper for open review we can formulate a truly effective prize.

What happens next?

Working with the Longitude Committee, we will use the responses to the open review to amend and adjust our challenge criteria. Subsequently, in October this year we will announce the full judging criteria and terms and conditions which will explain exactly what you need to do to win the prize.

At this point we will ‘fire the starter’s pistol’ for innovators and inventors from across the world to begin developing new point-of-care diagnostics that will help us preserve the efficacy of antibiotics for future generations by addressing the problem of antibiotic overuse and inappropriate use.

We believe that the Longitude Prize will be more robust and accountable after this process is complete, so please read our report and provide your feedback. The open review closes on 10 August.

Joshua Ryan-Saha

This blog was originally published by Nesta. You can read the original blog post here.

Image credit: Thinkstock
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Subduing the Hive Mind: An enemy’s enemy could become an unlikely friend

ResearchBlogging.org119614761Leafcutter ants form some of the biggest, most remarkable animal societies on Earth, living in sprawling colonies of up to 8 million individuals. These ants harvest more greenery in South American rainforests than any other animal, consuming almost 20% of the annual vegetation growth. Their voracious appetite also makes them a significant agricultural pest.

At the University of Costa Rica, Dr Adrián Pinto-Tomás and his colleagues are looking for ways to minimise the impact of leafcutter ants on agriculture in a sustainable manner, while ensuring that the region’s unique ecosystems remain balanced.

Leafcutter ants cultivate a fungus, Leucoagaricus gongylophorus, in “gardens” within their colonies; the ants feed the leaves they cut to the fungus, which is the colony’s sole food source. Leafcutter ants thus form sophisticated farming societies in symbiosis with the fungal cultivar. Each individual ant is adapted in terms of size and physiology to its specific role in contributing to the success of the fungal garden. Soldiers, for example, are the largest ants, with pincers powerful enough to bite through leather boots. Smaller ants may forage for leaves outside the colony, work as gardeners around the fungal cultivar or feed and clean the queen, the only ant in the entire colony capable of laying eggs and producing offspring. Continue reading

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World Hepatitis Day 2014

5279776905_4f0477d2fc_zToday is World Hepatitis Day, which is marked by the World Health Organization (WHO) to raise awareness of a disease that continues to claim millions of lives around the world every year. Predominantly a viral disease, hepatitis is primarily characterised by an inflammation of the liver, followed in many cases by liver cirrhosis, liver failure or liver cancer.

There are five different hepatitis viruses, known as A, B, C, D and E, which all cause a different variant of the disease. All five hepatitis viruses can cause short-term (“acute”) infection; hepatitis B, C and D infections can also be long-term, or chronic, and may cause liver cancer and liver failure. An estimated 1.5 million people die of hepatitis infections every year, with Hepatitis B and C causing the large majority of these deaths.

Besides the viruses themselves, a number of other factors can also cause hepatitis or increase predisposition to it. Long-term excessive alcohol consumption and some medications and antibiotics increase the likelihood of liver cirrhosis and liver failure. Those with impaired immune systems may experience autoimmune hepatitis, where the body attacks its own liver cells. Finally, some 40% of all babies born to mothers who suffer from hepatitis B also have the disease. A vaccination is required within the first few hours after birth to prevent a continued infection in the child.

In England, hepatitis C is the most common type of viral hepatitis, affecting some 215,000 people. It is mostly spread through sharing needles for intravenous drug use, and many people are unaware that they have the virus, as the disease rarely exhibits symptoms early in the infection. In 75% of cases, the virus stays in the body and causes chronic hepatitis C, which can lead to liver cirrhosis and liver failure. There is no vaccine against hepatitis C, and while antiviral medication does exist, it can have very unpleasant side effects.

Hepatitis B, which is mainly transmitted through blood and other bodily fluids, is one of the most widespread infectious diseases worldwide. The WHO estimates that 240 million people suffer from chronic hepatitis B and 780,000 die every year, making it a major global health problem. Continue reading

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Microbe Talk: July 2014

493374987Dr Bryn Dentinger, a researcher at the Royal Botanic Gardens, Kew, bought a packet of dried porcini mushrooms in a local shop. Being an expert in fungi, Bryn wanted to know what species of porcini he had purchased, so he sequenced the dried mushrooms’ DNA (obviously) and was rather surprised at the result. Ben went to Kew to talk to Bryn about fungi and about his discovery…

Also on the podcast this month, we interviewed Artemis Louyakis, who studies Thrombolites: tough, rock-like structures, which are actually macrocolonies of bacteria. Artemis tells us about her research and the practical uses that these structures might have in space travel.

Show Notes:

  • Bryn’s paper ‘What’s for dinner?: Undescribed species of porcini in a commercial packet’ via PeerJ.
  • Bryn’s homepage.
  • Information on Thrombolites in Australia.

If you’re accessing this page on your iPhone and can’t see the podcast player, you can subscribe to Microbe Talk on iTunes.

Benjamin Thompson

Image Credit: Thinkstock
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