Category: bacteria

What lies below: how soil bacteria fight off sticky roots

Posted on by andy.winfield

By Nicola Temple

The first horror film I ever watched was Invasion of the Body Snatchers. The film was already dated by about 30 years when I saw it and so aspects seemed silly rather than scary. Yet, those alien plants still managed to evoke nightmares in my pre-teen imagination. Antagonistic plants have cropped up in numerous films over the years – from the musical menace in Little Shop of Horrors to the Devil’s Snare that entangles Harry Potter and his friends. Yet, the cinematic nightmare of being entwined and strangled by the (not so) local flora is based in some truth…if you’re a microbe.

Soil is alive with microbes – on the order of 100 million cells per gram of soil. Some of these are friendly microbes and some are less so. So, as plant roots seek out water and nutrients within the soil they must also be wary of what they encounter. The root tips are sheathed in specialised cells known as root border cells and these are the front line of defence. These cells launch themselves from the root tips and through the release of various chemicals, help to manipulate the environment around the extending root tips. They can attract and stimulate growth of helpful microbes and repel or inhibit the growth of others. 

Earlier this year, researchers at the University of Wisconsin, USA looked closely at how the root border cells of peas and tomatoes interact with the bacteria Ralstonia solanacearum.
R. solanacearum is a pathogen that affects a number of economically important plants, including potatoes, tomatoes, peppers, bananas and tobacco. It follows the chemical signals sent out by plant roots and finds natural openings or wounds within the root in order to invade the plant. Once inside, the bacteria replicate rapidly and take up residency in the xylem of the plant. Eventually, they block this important transport system of the plant and cause it to wilt and die.

A false coloured electron micrograph showing bacteria (blue)
tangled in the DNA-based trap (yellow).
Photo credit: Tran et al.
The Wisconsin researchers found that when the root border cells of both the peas and tomatoes encountered R. solanacearum, they released DNA. Surrounded by stands of sticky DNA, the bacteria become entangled. Unable to move, the bacteria die. It truly is the stuff of horror films.
Other friendlier species of bacteria didn’t induce this projectile DNA trap from the root border cells, which suggests that they are able to recognise the threat of R. solanacearum.

However, as is almost always the case with nature, there is always a counter attack. The researchers discovered that only 25% of the bacteria were dying in the plant’s sticky trap, so how were the rest managing to escape?

The Wisconsin group found that when R. solanacearum encountered the DNA, it triggered a release of an enzyme that cuts DNA. In other words, they were using molecular scissors to cut their way out of the trap.

And so the evolutionary arms race continues. It is those individual bacteria that produce more of the defensive enzyme that will escape the traps and replicate. Perhaps over evolutionary time, those that have limited capacity to produce the enzyme will be weaned out of the population, forcing the root border cells to improve their offensive game.

For scientists, this detailed understanding of how hosts interact with different pathogens could help them to develop disease-resistant plant varieties of these economically important crops.

For me, this insight into the quiet battles being fought below the ground give me an even greater appreciation for the fruits and vegetables I harvest from my small little garden – they have been hard-won!

The paper referred to is:
Tran TM, MacIntyre A, Hawes M, Allen C (2016) Escaping Underground Nets: Extracellular DNases Degrade Plant Extracellular Traps and Contribute to Virulence of the Plant Pathogenic Bacterium Ralstonia solanacearum. PLoS Pathog 12(6): e1005686. doi:10.1371/journal.ppat.1005686

Nicola Temple is a science writer and co-author or the book ‘Sorting the Beef from the Bull: The Science of Food Fraud Forensics’ . She dabbles in her small veg patch and regularly contributes to the University of Bristol Botanic Garden blog.

Mud, glorious mud

Posted on by andy.winfield

By Jacqueline Campbell

Connections are often established in the most unexpected manner. How many times do you come away from a situation thinking “it’s a small world”, where just the opportune mention of a single word or phrase strikes a chord and is enough to foster new links and an avenue by which to share new ideas.
As unlikely as it seems, the words “pond mud” brought the Red Maids’ Schooltogether with the University of Bristol Botanic Garden recently. And from this link, students at the school have gone on to create their own miniature sustainable ecosystems using mud gathered from the garden’s mature and established ponds.

Marvellous muddy mesocosms

Mrs Turner, Head of Biology at Red Maids’ School, studying
the mesocosms.
Sixth Form students following the International Baccalaureate biology curriculum are required to complete a number of practical experiments. One of these is the creation of a mesocosm known as a Winogradsky column; essentially a self-contained, sustainable ecosystem grown in a sealed plastic bottle under controlled conditions.
A critical element of this experiment is pond mud. As they are situated no more than a couple of miles apart, the Red Maids’ School approached staff at the Botanic Garden for their advice and assistance in setting up such an ecosystem.  A number of phone calls and a few visits later, two groups of students have used pond mud sourced from the Botanic Garden and are watching to see the bacteria in their stratified ecosystems develop. 
The mesocosms in this image are just a few hours old.
Images are taken every two days to track and record the changes
over time.
The mesocoms now live on a sunny window sill in the Biology Department at Red Maids’, and are a constant source of curiosity to all. Despite a little reluctance mainly associated with the smell of pond mud, the students involved are thrilled to have created their own ecosystems and are often now found enthusing about the colour of their bacteria and amount of respiration they can see.
Images taken every two days are providing a good record of how the ecosystems are developing over time. From an initial cloudy but uniform situation, clearly defined layers are forming coupled with a notable increase in the pressure within the bottles showing the incredible amount of respiration that is occurring within the system.

Bacteria of many colours

Students have seen the pressure within their ecosystems
increase over time thanks to the highly visible levels of
respiration occurring within the sealed environment. A range
of different coloured bacteria are also now present.
The ingredients required to create the Winogradsky column are: pond mud, shredded newspaper, crushed egg shells and raw egg yolk. Pond mud provides a suitable base while the newspaper, egg shell and egg yolk provide sources of carbon, carbon dioxide and sulphur respectively. As a first step, these components are mixed together and poured into the bottom of a plastic fizzy drinks bottle.
On top of this layer comes another of compost, followed finally by some pond water. The idea is that many different coloured layers of bacteria develop, and each of these transforms molecules for the others to use. And as long as there is light entering the system, the column should theoretically continue to maintain a healthy microbial ecosystem for many months.
Waiting to develop: Over time, students at Red Maids’ hope
to see their Winogradsky columns develop into a stratified
system. This will provide a visual example of various modes of
metabolism and zonation in the microbial world. The
mesocosm shown in this image is several months old. 
Conditions at the bottom of the column are highly anaerobic with a high sulphide concentration ideal for the growth of sulphate reducing bacteria, green sulphur bacteria and purple sulphur bacteria. Moving higher in the column, with conditions becoming more aerobic and a reduction in sulphide concentration, we can expect to see the development of purple non-sulphur bacteria, iron-oxidizing bacteria, heterotrophic bacteria and cyanobacteria. 
Of course none of this would be possible without the kind assistance of the Botanic Garden staff, who waded into freezing winter waters to collect the mud. The Red Maids’ School is very grateful to have established this connection, and hopes that it too will blossom over time. 

Dr Jacqueline Campbell has a PhD in physics from St Andrews University and twelve years of editorial experience working for the Institute of Physics Publishing and as a freelance journalist. She now works as a science technician at the Red Maids’ School.