Five answers to the question ‘why microbes?’

Last month, Amelia gave us five great reasons to love plants. But plants aren’t the only species worked on at the John Innes Centre that lack the respect they deserve.

 

As a microbiologist I thought it was only fair to come up with my own ‘five answers’ – and show that microorganisms aren’t just here to cause us harm. In fact, they are essential for many processes, and have great potential for many more.

 

1. Antibiotics

The world is facing a crisis: antibiotic resistance. The best way to fight this is to treat antibiotics with a bit more respect – stop prescribing them when unnecessary, and follow treatment schedules properly. Until we solve this problem, however, we need to go out and find more to battle the strains that are multi-drug resistant.

 

Antibiotics are produced in nature as a defence against bacteria in the environment – such as streptomycin produced by Streptomyces, found in the soil. We are in a ‘drought’ of antibiotic discovery, with few breakthroughs in the past few decades. Scientists are now searching far and wide for new bacterial strains that can produce novel antibiotics to compete in the ‘arms race’ between humans and their pathogens.

 

We have barely scratched the surface with microbe discovery – and there may be more hiding away that we are unable to culture, or in environments we barely know. Examples of these are in deep sea trenches or the guts of insects. Some people even think there may be bacteria on Mars – and I’m sure if we do find them, people will be looking for antibiotics there too.

 

2. Genetic engineering

Microbes can be easily manipulated, and so have huge potential for genetic engineering. The best example of this is for the production of human insulin for treatment of diabetes.

 

Initially, diabetics were treated with insulin derived from animals – which often came with side-effects. As biology progressed the structure of insulin could be characterized (earning Fred Sanger a Nobel Prize), and entirely synthetic human insulin could be produced. Further developments meant that yeast could be engineered to produce human insulin – and this is how medical insulin is now produced.

 

Another example of a medicine produced by microbes is human growth hormone. Before we engineered microbes to make this, it would come from human cadavers!

 

Other potential uses for bacteria include developing them to clean up pollution (‘bioremediation’), fight tumours or detect arsenic in drinking water.

 

3. Food

If you say the words ‘microbes’ and ‘food’ to most people, they would probably think of food poisoning. However, some of our favourite foods wouldn’t exist without microbes.

 

Many industries rely on ‘fermentation’ – the ability of microorganisms to break down chemicals. Both brewing and baking require yeast fermentation (specifically Saccharomyces cerivisiae) to produce the gas bubbles that we need for beer and bread. Another example of fermentation is in the production of yoghurt, which uses a bacteria that converts lactose sugar in milk to lactic acid, giving yoghurt its sharp taste.

 

Bacteria aren’t the only microbes that are used in the food industry. Quorn, the popular meat alternative is produced from mycoprotein – produced from the fungus Fusarium venenatum.

 

Another use for fungi in food production is in cheese-making. Blue cheeses are treated with moulds which grow within, creating veins full of flavour. Soft cheeses such as brie have a bacteria growing on their outsides, allowing them to age from the outside in and allowing the interior to become runny.

 

4. Fuel

Our fossil fuel reserves are running out, and the race is on to find alternative sources of energy to sustain us.

 

Scientists are looking to bacteria for help. Like all organisms, bacteria are able to convert chemical energy (such as glucose) to other forms of energy (such as movement). In 1911 a scientist was able to produce an (albeit very small) electric current from E. coli. So the concept of microbial fuel cells was born.

 

Humans respire using oxygen, converting fuel (sugars) to energy, producing carbon dioxide and water. Many bacteria are able to respire without oxygen, and so instead of producing water in this reaction, produce protons and electrons. If we can harvest these electrons, then we have bacteria that produce electricity – a microbial fuel cell.

 

It is hoped that these fuel cells can be developed to be more efficient, and to use waste products such as those from industry as their fuel. If this can be achieved, it could have a huge impact on electricity production, as well as waste processing.

 

5. Symbiosis

The soil is a world full of microbes of all shapes and sizes – from bacteria to fungi to oomycetes. Although some aren’t friendly and can cause plant disease, many of them play quite the opposite role. Plants and specialised fungi can live together in harmony, and even help each other out. These beneficial relationships are known as symbioses.

 

There are two cases of soil symbioses that are particularly well-studied. The first of these (and the field in which my PhD falls) is the rhizobia-legume symbiosis – where bacteria convert nitrogen from the air into a form that plants can use in return for plant sugars.

 

The second is the case of mycorrhizal fungi, which associate with plant roots to get direct access to sugars. In return, the fungi scavenge through the soil for important nutrients and minerals such as phosphates.

 

There are many other cases of symbiosis that shape the world we live in – see this post from last year if you want to read more about rhizobia and some of our other favourite mutualistic relationships.

 

Interactions with plants aren’t the only case of bacteria living in harmony with other species. Our guts are full of bacteria with a wide range of benefits. They help us digest our food, stimulate cell growth, protect us from harmful microbes and help train our immune system to protect itself.

So, next time you think of microbes, don’t tarnish them all with the same brush. There is huge diversity across the microbe world – and huge potential for their use in many different areas of science.

To see Amelia’s answers to the question ‘why plants?’, click here

Izzy is a John Innes Centre PhD student. She’s on Twitter as @isabelwebb.

The curse of the four-year PhD

Here in the UK, most research council-funded PhD students will have a thesis deadline four years after their start date. As someone who moved straight from undergraduate to postgraduate study with no breaks, this means I will be a doctor by age 25.

While this is quite nice to know, I’m now at the point of starting to consider my future and career. And I’m coming to realise that only four years of doctoral work may end up being more of a hindrance than I thought.

When applying for postdoctoral positions, your publication record plays a huge role in how successful your applications will be. But getting those first-author publications takes time. Getting results is just the first step. Next, you need to actually write the thing, and get feedback from a supervisor (and anyone else involved, such as others in the lab or collaborators).

Then you begin the process of actually trying to get published: submission, acceptance, peer review, corrections, and finally publication (and even this might take a while if there is a backlog). Although some journals, such as eLife, pride themselves in a quick turnover (90 days submission to acceptance), some can take a lot longer.

Rejections will increase the time – and this can often happen as people try and publish in journals with as high an impact factor as they can. Other factors can affect publication time – such as over-worked supervisors or lack of funds to publish (Nature Communications, for example, costs £3150 to publish).

All things considered, a British PhD student could easily end their PhD with several first-author publications in the pipeline, but none published.

Compare the length of a UK PhD to PhDs in other countries, and you start to see where my concerns lie. Some countries, such as Germany have four-year PhDs like us. But many have postgraduate courses lasting much longer.

In the US there is no set deadline for a PhD thesis. Stanford University suggests that most finish their PhD programme within five and a half years – already gaining a year and a half on us. And a US PhD can easily last much longer than this – students can often expect to be finishing their theses after seven or eight years.

One does not simply finish a PhD

PhDs in the US can be notoriously long.

The decision of when a PhD candidate at an American university can defend their thesis is made by their supervisor. The time taken to complete a PhD in the US is one of the most common topics mocked by spoof academic and comic sites such as PhD Comics or #WhatShouldWeCallGradsSchool.

The same thing happens in Sweden, where a student can expect to be studying for longer than five years. These longer PhDs often involve other activities – teaching, for example – but are also important for producing publications. The number of publications may have an effect on when a student will be allowed to defend their thesis.

The longer PhD programmes in other countries allow more time for broadening horizons. Time spent teaching or researching other projects can give PhD students an additional edge when applying for jobs.

The British system has tried to help provide its students with some of this experience. The BBSRC and several other tesearch councils now fund a large proportion of students as part of Doctoral Training Programmes or similar schemes. These programmes have a mandatory three-month internship as part of the four years of study (I recently completed my placement).

Several universities have also opted to put students through training – such as the University of Oxford, where first year PhD students spend their first term having lectures. They may also have ‘rotation projects’, spending their first year trying two or three projects and choosing the one that suits them best.

Although these schemes leave students more ‘well-rounded’, they also take away from the already limited time-frame – leaving many with just three years in which to carry out their research and write-up.

So, looking at the facts, PhD students in the UK are going to be left competing for the best postdoctoral positions against people with far more research experience than us.

I was talking to a careers advisor about this last week, who told me  “you can get that first postdoc position without any publications”. The next day I had the same conversation with a lecturer (and I’ve had this conversation with my supervisor more times than I can count) who had a different view: unless you have a particularly high-profile supervisor who can vouch for you, those jobs are going to go to someone else.

This is clear when you start looking at the statistics. According to an article in the Times Higher Education, up to 200 people may be chasing the same post at top Universities.

And if you can’t get those top posts, perhaps you will end up struggling to get high-impact publications from your first postdoc – leaving you struggling to get the next position, and so the cycle continues.

Only 0.45 percent of UK science PhD graduates end up as professors – so every step of that career ladder matters if that’s your ambition. The realisation of this competition has almost certainly driven some people off the ladder – and the “confidence gap” of women faced with such tough competition may partly explain the leaky pipeline of women from academia.

Of course, this doesn’t mean you should lose hope. Most likely, a student will manage to get their name on a few other publications during their PhD, and though their names may be lower down the list, at least it’s something.

I’m also starting to see that there is still a huge ‘who-you-know’ aspect to finding jobs in academia. So get out and network with people whose work interests you. Presenting at international conferences can also help with this – and as PhD students begin to get results, they often have abstracts for oral presentations accepted and get the chance to give talks.

Networking with the other group leaders in your university or institute may also give you the edge you need. Even social media can help – I’ve met at least one group leader in my research area who recognised my name from Twitter.

It isn’t just the PhD to postdoc gap that publishing affects. Publication records count throughout your career. Newly-appointed group leaders face huge pressures to publish – and this continues even after tenure is awarded. As they say, “publish or perish”.

Even a career break such as parenthood or taking time out for caring responsibilities can mean a gap in your publication record which could affect your career. The government is trying to make changes in the career structure for postdocs to recognise career breaks – but it’s happening slowly.

I have my fingers crossed that those who want to pursue a career in academia will be able to fight off the competition and find the jobs that they want. And as for the rest – perhaps those internships will help them get the jobs that they want too.

Izzy is a John Innes Centre PhD student. She’s on Twitter as @isabelwebb.

Featured image: Kat (swimparallel)/Flickr.

Rose by Olivier Blitzblum

A plant scientist’s Valentine’s Day

On 14 February, people across the world will be presenting those they care about with gifts. In some countries these gifts are given to a partner or spouse, while in others they are used to share love with friends and family.

Here in the UK, these gifts are typified by roses, chocolates and champagne – or, as we plant scientists might call them, Rosa, Theobroma cacao, and Vitis vinifera.

Since plants and Valentine’s Day share this link, I thought I’d do a bit of searching and find out more about the species behind our favourite gifts – and for each, I’ve given my own alternative suggestion to our traditions. Continue reading

Peas in pods

150 years of Mendelian genetics

Last Sunday, the world celebrated its musicians and film stars in flashy ceremonies. But another celebration was due at the same time.

8 February 2015 marked 150 years since the first of Mendel’s lectures where he presented his results on pea breeding for the first time. These lectures, based on his paper Versuche über Pflanzen-Hybriden (Experiments on Plant Hybridisation), presented the world with a vision of genetics never seen before – and led to him gaining the title ‘The Father of Modern Genetics’.

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Abandoned lab - Paul/Flickr

6 things that happen when you take a four-month break from your PhD

From mid-September until mid-December last year I was on an internship in science policy. Once you count the conference at the start of December and the Christmas holidays, I was left to return to the lab this January after a four-month break.

The aim of my internship was to experience the world outside academic research, and so my project was sent to the back of my mind while I thought about more political topics. Most of my friends did their internships around Norwich, so they had the chance to get into the lab at weekends or in the evenings. But I moved to Cambridge for mine, so I didn’t have the opportunity to nip into the department and get some experiments going. Now, I’m back doing my research, and it’s amazing what’s happened while I was away.

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Eight great technologies

The UK is an important player in academic research worldwide. This includes being one of the world leaders in many emerging scientific fields. The UK government has recognised eight fields as Eight Great Technologies – technologies that, with support, can lead to UK strengths and business capabilities.

In the 2012 autumn statement, £600m was put into these fields, and this week’s Science and Technology Strategy announced continuing support for them, including funding for new research centres.

But what are these eight technologies? Despite working at an institute with clear links to several of the technologies, I admit to only having heard about them recently – and not in my role as a researcher, but through my interest in science policy. So I’ve summarised the eight in this post.

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