What lies below: how soil bacteria fight off sticky roots

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.

The hows, whys and wheres of composting…

By Alida Robey

I have had some intriguing responses to my previous post on composting– most commonly “Hurry up and tell us how to do it!” ; so without further delay, I give you the why, where and (most importantly) how of composting….

Why compost?

There is so much more to composting than simply meeting our own personal needs.  For me, the global urgency is such that I would have us label all shop bought fruit and veg: WARNING: Not composting will lead to the depletion of our soils! Here’s why:

Compost helps regenerate soils and improve soil structure

Current agricultural practices suck nutrient out of the soil. The resultant produce has less nutritious value than in previous generations, [1] meaning we are needing to eat more to get the same nutritional benefits. [2] Commercial fertilisers are designed to promote maximum growth, not necessarily superior nutrient content of the fruit and vegetables produced. Nor do these fertilisers benefit  soil structure and health. The fibre of compost added to soil helps improve water retention and also helps moderate temperature extremes.

It provides a slow release of nutrients (especially nitrogen)

Unlike synthetic fertilisers, compost adds a bank of biological activity to the soil, which encourages beneficial worms and helps to make significant quantities of nutrients (such as nitrogen, phosphorous and potassium) bio-available slowly over time.

Composting keeps organic waste out of the landfill

About a third of household waste is likely to be kitchen-generated organic matter. Composting it yourself reduces increases in your council tax by saving some of the huge costs of domestic waste collection transport and disposal. Also, organic matter in landfill produces methane (a greenhouse gas  that contributes to global warming) and nitrogen-rich leachate (pollutes rivers and streams).

Composting transforms plant material, food waste and other organic matter into humus or compost, which is a richly nutritious soil-like material with the added benefit of microorganisms that help plants take up  the goodness in the soil. In other words, it turns otherwise smelly, unwanted waste into something really productive and pleasant to handle.

Where to compost

A community composting bin in the Shelton Community
Garden in Shelton Stoke-on-Trent, Staffordshire.
Photo credit: Joshua Whiton via Wikimedia Commons

The traditional means of composting is a bin, a heap or an enclosure in a sunny spot in the corner of a garden.  However, you can do some very effective composting even without a garden of your own:
Community composting bins require one or two people to maintain but can receive compostable materials from a community. The compost can then be used for community gardens or by individuals in the community . They can be located in parks, communal gardens, unused corners, on the edge of school grounds and other public/semi-public spaces. 
Wormeries are a wonderful alternative for those in apartments or with limited external space.  A wormery is usually a small stack of trays, which is home to a colony of compost – eating worms (NOT earthworms) that will convert most kitchen waste into wonderfully nutritious ‘worm wee’ and worm castings that can be used to feed indoor or outdoor plants or given away to friends and neighbours to use on theirs.

How to compost

This is what I consider to be the basics.  Once you have tried some of this and found it’s not going as badly as you had imagined, then I suggest you access some of the online information that will help improve your productivity. 

What goes in?

Veg peelings & fruit
Coffee grounds, tea bags, egg shells – crushed by a crunch of your hand
Cardboard (torn up no larger than a standard envelope), tissues, loo roll tubes & waste paper – shredded or scrunched up.
Especially welcome are egg boxes (ripped up a bit) and the contents of  paper shredders
Grass-cuttings (so long as you haven’t used weed-killer) and discarded pot plant contents including old compost and dead flowers
Plant prunings – chopped up to help decomposition
Weeds –  so long as they are not in seed, otherwise you will have them sprouting merrily back in the soil.
OUT (of compost bins but IN for wormeries)
Pasta, rice, couscous
Beans, pulses, lentils, cereals
Bread, chapatis, biscuits etc
Plate scrapings
Cheese and dairy products
Meat, fish and bones
Cooked potatoes
The reason many of the items above are excluded from compost bins but not wormeries is their attraction for vermin.
OUT (of everything)
Cat and dog poo from animals that have been wormed.

Location, location, location

A typical compost available from
local councils.

For general composting, find a warm sheltered corner preferably reasonably accessible so you are not put off taking stuff there.  Set up your means of containing your compost, a compost bin or bins is the easiest, but a boxed-in area or even just a pile will do.  Your local council may, like Bristol, sell plastic compost bins and deliver them, all for as little as £12-15. You need to bear in mind that you will need to be able to turn the contents occasionally and that worms need access from below.

The great compost bake-off

Underlying the composting process is the chemical transformation of carbon materials (shredded paper, straw, vacuum cleaner dust, leaves, egg boxes, egg shells) and nitrogen materials (grass clippings of untreated grass, weeds, kitchen scraps, coffee grounds) into a whole new product – compost.  It is a bit like baking a cake where the ingredients are deliciously transformed by mixing and baking.  We can control the conditions in our compost to encourage the materials to decompose faster and effectively (i.e. to produce a really good cake rather than a baked lump of goo).
The other factors your composting recipe needs to include are a mix of particle sizes that assist aeration and hold enough (but not too much) moisture.  As with the cake, the mixing and aerating are important success factors between it just working and it being great. If it’s getting smelly, add more carbon materials and aerate it more frequently by turning it over.
Depending on your method, the transformation process can take just a few months.

Layer dress

Start layering your contents, bearing in mind the need to mix carbon and nitrogen items (roughly 2 carbon:1 nitrogen, but adjust according to whether it seems to look and smell healthy).  And just keep adding, remembering that it will all break down a lot smaller. I prefer to have 2 or 3 bins, and empty them out completely from time to time, retrieving the made compost from the bottom and piling the rest back into one bin. This can be a lot easier than turning the contents of individual bins. You can keep one bin of nearly decomposed compost at the ready for when you want to use it in the garden.
Happy composting!

Further resources about composting:


[1] World Economic Forum (14 Dec 2012) What if the World’s Soil Runs Out? Time 

Why doesn't everyone compost?

By Alida Robey

Composting was an inherent part of how we lived when I was growing up – nothing was wasted.  Food scraps went to the chickens, kitchen and garden waste to one of several  compost heaps and leaves were piled into a pit for future leaf-mould.
Today,  I live in a flat with a small decked courtyard. I have access to five compost bins in an area of communal gardens in Clifton (Bristol, UK); this means with almost no effort at all the only rubbish I produce is recycling and an occasional black bag of non-recycleable inorganic waste. I don’t even have to keep a compost bin at home. And still each week along my road I see quantities of black bags destined for landfill spilling out onto the pavement with fruit and veg and greenery.  Given the years I have spent trying to coax friends and neighbours in different locations to compost, this scene is a heart-rending weekly reminder of my lack of success in this personal campaign!
So when I was camping a few weeks ago, and had ready access to a group of highly educated and motivated young people, I decided to get some clues as to just why, I have had such disappointing results!  Just what is it that gets in the way of perfectly sensible people doing a perfectly sensible thing, which is so crucial for soil regeneration?
The group I talked to all had higher education degrees of various disciplines; they ranged in age from 22 to 43 and three of them were parents of young children; one is a science teacher and one has a mother who is a professional gardener; one has parents who spend their weekends on the allotment.  I was hopeful of finding motivation and some enthusiasm and knowledge.  I set forth with a few simple questions to find out just what their position was on the matter of composting.
Whilst this group may not be representative of anything remotely statistically significant, it did illuminate some interesting gaps in knowledge and understanding.
Composting is critical for regenerating soil.
Photo courtesy of Joi Ito, Flickr Creative Commons

What is composting?

I thought I had better start by finding out whether we were talking the same language. It was something of a shock to find that indeed we were not! To one individual it meant putting food waste in the council bin, while others provided me with a highly scientific portrayal of the biological process with little appreciation of the practicalities and its application in the garden;  one respondent assumed compost  was useful only for growing vegetables and another that it created a ‘sludge’ to go on the garden.  They had parts of the composting story but were unable to say accurately what should/should not be included in making compost and expressed no appreciation of the need to compensate for soil depletion on a localised or a more global level. 

Where did you learn about composting?

I had spent some years in New Zealand where our local Council bombarded us with information leaflets, subsidised the purchase of composting bins and where volunteer projects seemed to be run in many junior schools. The Council itself distributed free ‘worm wee’  to employees which it had generated from wormeries fed from kitchen canteen waste.  I assumed that most children these days (whether in New Zealand or Britain), were growing up well primed by the education system to look after the planet. 

Yet, it seems as if the school system had failed to equip my group of young interviewees with the basics. While some people’s composting knowledge had been passed down from relatives or acquired on the internet, many couldn’t recall exactly where they had learned about composting. ‘I learnt about it at school, not actively, just picked it up along the way,’ said Dom.  It would seem as though composting skills are acquired rather passively.

Do you compost?

It was time to get to the heart of the matter.  Not one of them had made and used compost.  One was in the process of filling a compost bin and had not yet generated usable compost. Even use of Council –provided and collected food bins was hit and miss.

Why don’t you compost and what would it take for you to do so?

It was clear from the responses that they all felt they had to have a vegetable garden or allotment for it to be worth their while to compost.  As Helen, who does have a fair sized garden said,  ‘I’m not big into gardening.’  What took me by surprise was the response of Adam, a 43 year-old father who votes for the Green Party and is interested in global environmental issues. He saw green waste going into the landfill as ‘harmless’ – ie non-toxic, without appreciating that it should be being actively used to replenish depleted soils. He had no real sense that global issues were in any way within his scope to influence, starting  in his own back garden.

Food scraps ready for the compost. Photo courtesy of
szczel, Flickr Creative Commons.
I had expected some antipathy to ‘smelly’ processes seen by many as attracting vermin or a strange but common wariness of having to handle worms. Not so this group. They didn’t feel there was anything stopping them composting,  but had no idea why they should do so and what they might be able to use it for, let alone how they might confidently go about it.
So where did this leave me?  I have to admit I was fairly despondent thinking of this as the next generation of gardeners and in charge of our fragile planet.
It struck me that these young people, though versed in some of the technical aspects of c
omposting, lacked any real sense of the practical processes and applications for compost. Nor did they have a sense of urgency about soil depletion and regeneration. While some of my fellow campers were able to explain the nitrogen cycle and complexities of bacterial decomposition, they couldn’t, for example, tell me what to put in the compost.
We are failing to equip school leavers and tertiary graduates with the basic core skills at their easy disposal for generating our rapidly depleting soil and minimising waste, let alone motivating them to do anything about it. In a world that exudes a sense of helplessness in the face of global trends we have not succeeded in showing them even the basics of what we can all realistically and fruitfully be doing towards the health of our planet, our communities and our own households, parks and gardens. In my next post, I’ll write about how and why we should be composting in our urban communities.

Alida Robey has a small gardening business in Bristol. For several years in New Zealand she worked with others to support projects to establish composting on both domestic and a ‘city-to-farm’ basis.