New to Science – March 2015

3913311844_fc901b4096_zEach 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.

I’ve been thinking a lot about soil over the past few weeks. Here in the UK, it looks like the last frost of the year has passed, so I can enjoy a bit of time in the garden planting some vegetable seeds.

As always, soil is a big inspiration for microbiologists, with the ecosystem supporting a vast network of undiscovered microbes. The soils that are investigated seem slightly more exciting than those in my back garden, to be honest. For example, researchers from Thailand and Japan have discovered the new species Actinomadura rayongensis living in the soil of a peat forest in Thailand. In another forest, this time a mangrove forest in Malaysia, researchers have isolated the new soil bacterium Sinomonas humi.

Moving from one extreme to another, Chinese scientists have isolated Arthrobacter liuii from desert soil in the Xinjiang Uygur Autonomous Region, China. Soil from a rice field at the Kanagi Farm of the Faculty of Agriculture and Life Science of Hirosaki University is now known to be home to Clostridium oryzae.

One of the things I will be trying to grow this year is tomatoes. Healthy soil is important for growing these fruit (“Knowledge is knowing a tomato is a fruit; wisdom is not putting tomato in a fruit salad.”). Researchers in South Korea have identified Pedobacter ureilyticus in the rhizosphere surrounding the tomato plant’s roots. Other members of the genus Pedobacter have been isolated from soils used to grow potatoes, ginseng and cabbages.

One species of bacterium I’m not hoping to meet in my garden is Clavibacter michiganensis subsp. michiganensis, which, as I’m sure you’re aware, causes ‘bacterial canker’, a difficult to control tomato disease. This month, researchers working at the University of Hawaii at Manoa have identified two further subspecies of non-pathogenic Clavibacter michiganensis that were isolated from tomato and pepper seeds. These subspecies are important for seed producers as they can elicit a false-positive test, leading to the unnecessary destruction of seeds.

These are just a few of the new species described this month; you can see the full list on the IJSEM website. We’ll be back again next month with a host of new ones  look out for us then!

Benjamin Thompson

Image credit: Luke Addison on Flickr under CC BY-SA 2.0
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Voice of the Future 2015

Kevin MaringerLast week, the Society for General Microbiology sponsored my attendance at the Voice of the Future event, which gave early-career researchers like myself the opportunity to grill MPs from the UK Parliament’s Science and Technology Committee (STC). It was an event of pleasant surprises for me: I was surprised at how approachable the politicians taking part seemed, how collegiate members of different political parties were with each other, and how honestly many of the MPs spoke about their motivations for engaging with science. I was especially surprised to find out that many of the MPs even have a sense of humour!

Voice of the Future followed the format of a Select Committee hearing, which saw attendees put questions to Sir Mark Walport, the Government Chief Scientific Adviser; Greg Clark MP, Minister of State for Universities, Science and Cities; Liam Byrne MP, Shadow Minister for Universities, Science and Skills; and MPs who sit on the STC.

All of the panellists demonstrated an impressive insight into the nature of academic and industry research, science education in this country and knowledge of the specific scientific issues that were brought up throughout the event. I had the opportunity to ask a question to Sir Mark about low levels of vaccine uptake and how the Government could encourage an increase. He admitted that there was no “one-size-fits-all answer” and acknowledged the important role the Government, and in particular he as Chief Scientific Adviser, plays in ensuring the public are well informed on public health issues. He also reminded us that the uptake of some, but not all, vaccines has improved. I thought Sir Mark’s final point, that, with social media giving everyone a louder voice, it is up to all of us as scientists to communicate effectively about scientific issues, was a particularly timely one.

I was surprised to find that many of the STC have a scientific background and it was fascinating to hear them explain the pressures they are under from their constituents and their party, while trying to bring together often-conflicting advice from scientists and other diverse interest groups.

It was then slightly disappointing (though not surprising) that the final two speakers of the day, the Minister and his shadow were more openly party political about their answers. I guess this is unavoidable so close to a general election and it was certainly a stark reminder that the various Ministers and scientific advisers that work together to form science policy are constrained in different ways by their roles in parliament.

The one thing everyone could agree on was that Westminster wants more scientists to engage with policy. Although it was useful to hear about the STC and other formal science policy reviews, it was interesting that many of the MPs noted that one of the most powerful and accessible ways to put science on the political agenda is for constituents to contact their local MP directly. In fact, almost every MP shared anecdotes about how specific scientific issues had been brought to their attention first by their own constituents.

Throughout the event, there were little reminders that we really were at the heart of British politics, like the division bell signalling that a vote was about to take place, or the television screens advertising what was being debated in the House. Somehow this energy was amplified by the upcoming election. The members of the STC reflected nostalgically and frankly about what they considered to be their successes and failures of their current term, with some hoping and looking forward to serving on the committee again in the future. This enthusiasm for science, and the fact that so many important people took the time to take part in Voice of the Future, made the event incredibly enjoyable and informative. It has certainly made policy engagement feel more accessible to me, and I can only commend the organisers for running such a successful event.

Dr Kevin Maringer

Kevin is a Sir Henry Wellcome Postdoctoral Fellow researching Dengue virus. You can read about his work here. Voice of the Future is organised by the Society of Biology; you can read their write up of the event here.

Image Credit: Kevin Maringer
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What gives wine its taste? (We heard it’s on the grapevine…)

ResearchBlogging.orgStacked wine bottlesWine connoisseurs, or oenophiles, possess a seemingly endless vocabulary for describing their tipples of choice. To the uninitiated, it may sound like they are describing an entire gourmet meal, or even a good friend, but this is not just make-believe: those in the know can sometimes pinpoint not just the country or region a wine came from, but the exact vineyard. How can this be possible?

While we cannot hope to distinguish every single chemical in a wine using just our five senses, experienced wine tasters can still perceive hundreds of different compounds that contribute to the drink’s unique flavour and aroma. These compounds are a result of enzymatic and microbial activities during the alcoholic fermentation process, in which yeasts and other microbes convert sugar into ethanol and carbon dioxide.

Getting the mixture right

Winemakers often exert control over the fermentation process by culturing specifically selected yeast strains that they add to their wine in order to achieve certain flavours. However, wild yeasts are also present everywhere in a vineyard, living in the soil and on the processing equipment that turns grapes into ‘must’, the unfiltered, freshly-pressed grape juice that is the precursor of wine. Yeast spores are even found in the air around vines. These wild yeasts all end up in the final product and are called ‘autochthonous’ yeasts, meaning that they are a part of the local environment. Continue reading

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Q&A: Professor Jeff Errington

Jeff ErrringtonNext month, Society member Professor Jeff Errington FRS will be awarded the prestigious Leeuwenhoek Medal by the Royal Society. The award, named after pioneering Dutch microscopist Antonie van Leeuwenhoek, is awarded triennially and recognises excellence in the fields of bacteriology, virology, mycology, parasitology and microscopy.

Professor Errington’s lecture will focus on his work on the fundamentals of bacterial cell division and how the bacterial cell wall – a flexible layer of proteins and sugars found in almost all bacteria – is important in cell shape. We caught up with him to ask about his work and about his forthcoming prize lecture.

How would you describe your research?

My long-term interests are on some of the most basic questions in biology: “What makes a cell a particular shape?”, “How do chromosomes get replicated and then pulled apart?”, “How do cells know where to divide, and how is division achieved?” I’m investigating the molecular basis for each of these processes. Answers to many of these questions – in bacterial cells at least – relate to cell wall synthesis. In order for bacteria to grow and divide correctly they have to be able to accurately manipulate their cell walls.

How does a bacterium achieve its desired shape?

We’ve found genes that if mutated interfere with a bacterial cell’s shape. The most famous of these genes is mreB, which is a homologue of actin, an important cytoskeletal or “scaffolding” protein found in eukaryotic cells. Before our work, people assumed that bacteria didn’t have cytoskeletons, but we now know they have many proteins that are used in a similar way to the cytoskeletal proteins found in eukaryotic cells, in the sense that they direct the shape of the cell, the division machinery, things like that. If you have a Staphylococcus it’s always a sphere and if you have a Bacillus it’s always elongated. The MreB protein, and the proteins it controls, are pivotal in determining the shape of a cell. Continue reading

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Pathways of resistance: from mercury to methicillin

ResearchBlogging.orgMercury BeadIn a climate of rising fear over the diminishing efficacy of antibiotics, microbiologists from the Universities of Nottingham and East Anglia have looked back at the bacteria-killing substances of the pre-antibiotic era: metals. Dr Jon Hobman and Dr Lisa Crossman’s review, published in the Journal of Medical Microbiology, concludes that the ancient pathways of resistance which bacteria have evolved against these metals may be intimately linked to the antibiotic resistance genes that are circulating in bacterial populations today.

Metals and metallic compounds have been used for medical and biological purposes for millennia: as antiseptics, diuretics, and dental fillings; cosmetics, tonics and chemical weapons. Most are indiscriminately toxic, and you wonder whether some of these historical cures were actually worse than the ailments they were intended to treat – mercury-laced teething powder, anyone?

Metals and their ions can damage cells in multiple ways: binding to enzymes, DNA and membranes, disrupting their function; taking part in reactions that generate harmful free radicals; or binding to the cell’s pool of antioxidants that usually protects against free radicals. It is the lethal damage that these mechanisms can inflict on bacterial cells that underlies the utility of metal compounds in controlling infections in plants, animals and humans. Continue reading

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New to Science: February 2015

Each 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.

It is the Society for General Microbiology’s 70th birthday this month – it was formally inaugurated on 16 February 1945 and Sir Alexander Fleming became its first President. Such anniversaries are always a time for reflection on the past and its lessons and challenges.

Microbiologists from South Africa and Italy undertook a similar journey into the past, providing New to Science with the most unusual microbe discovery location we have seen so far. The researchers were studying the damage caused by microbial communities in the catacombs of St Callixtus in Rome, which were founded in the very earliest years of Christianity and once housed the tombs of many popes from the first millennium AD. Here, the researchers isolated Kribbella italica from a biofilm growing on the walls of one of the tombs. Continue reading

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Antibiotic resistance transfer: where’s the culprit?

ResearchBlogging.orgColorized low-temperature electron micrograph of a cluster of E. coli bacteriaEscherichia coli is a species of bacteria that forms an essential part of the gut microbiome of many warm-blooded animals, including humans. Most strains are completely harmless to us, but some cause diseases including food poisoning and urinary tract infections. A group of antibiotics known as cephalosporins are often used to treat harmful E. coli infections, but some strains of the bacterium produce substances called extended-spectrum beta-lactamases (ESBL) that confer immunity to these antibiotics.

ESBL-producing E. coli used to be most commonly found in hospital environments, but they are now increasingly causing infections outside of hospitals, as well. The presence of such bacteria in the meat we consume is thought to contribute to the rising prevalence of community-acquired infections. After all, antibiotics are used heavily in the farming industry, so the development of resistant bacterial strains is to be expected.

Previous studies concluded that the ESBL-producing E. coli strains found in farm animals, retail meat and humans were extremely similar, suggesting that consumption of contaminated meat had allowed the bacteria to spread to humans. However, as Mark de Been, a bioinformatician at the Utrecht Medical Centre, explains, this research was based on studies of only a small part of the bacterial genomes. de Been is the lead author of a new study recently published in the journal PLOS Genetics, which shows that the bacteria found in animals and humans are actually significantly different. Continue reading

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