Friday, 27 January 2017

Epigenetics in the Garden


When this caterpillar metamorphoses into a butterfly it retains an unchanged genome
Epigenetic's can claim to be the biggest biological advance in the last twenty years and new implications in plant and animal biology become apparent every day. Scarcely anything that happens to the plants and organisms in our garden is not epigenetically controlled.

What is epigenetics?

I am indebted to Nessa Carey’s fine exposition in her book ‘The Epigenetics Revolution’. It becomes heavy going as you turn later pages but never have I read such clear explanations.

In simple terms epigenetics is about how and when genes impart their information. In a sense the term ‘gene’ is too crude a term in reading DNA. When the human genome was first fully encoded scientists were amazed that gene numbers barely reached twenty five thousand. This is slightly less than a rice plant and a small fraction of paris, the woodland weed! (The latter being as yet the biggest genome that has so far been counted).


The Paris japonica genome is fifty times bigger than a human one

The really significant numbers are that in humans, for example, we are coded by about three billion base pairs of genetic code. The number of cells in our body are measured in trillions. Every single one of these cells is shaped and performs under epigenetic influence.

Every cell in our body contains a complete set of the genetic code in our genome and yet most of the code is not expressed in the individual cell. The code is not turned on. For example the information specific to making a liver cell is not turned on in a skin one!
A dramatic illustration of epigenetics in action is the development of a new embryo in the womb. The first divisions from a human embryo are undifferentiated  and potentially can divide to create any human cell. Once epigenetically tagged their divisional destination might be for ever predetermined. A primordial skin cell might only ever divide to produce skin. Some cells such as neurones once laid down might never divide again and yet serve us for the rest of our life.
Some cells are more versatile and may permit change. A great challenge in this new science is to discover cells that retain their versatility and to explore ways of returning certain cells to the undifferentiated state. Already significant advances have been made. To replace our body’s damaged cells by generating new ones is for certain medical conditions a holy grail.
Reading the script
A genome might be regarded as a script rather than recipe. It is reassembled from one sexual generation to another as male and female components combine but essentially it retains the same structure. In asexual reproduction it barely changes at all. The actual genome script is, at the present level of understanding, not changed at all by epigenetic action. What does change is its interpretation.
‘Genes’ are epigenetically turned off or on by a process of tagging. You may have read about temporary methyl, ethyl and histone attachments to the genetic machinery. The presence of a tag might mean genetic code is switched on or off - or some partial combination. Some tags remain a lifetime or longer, some tags are ephemeral. In the life of a cell some tags might be on or off like a yo yo.
An aspect of epigenetics that has caught the public imaginations is that in some cases the modified action of genes by the process of tagging can be passed on from one generation to the next. Has Lamarck’s theory of the inheritance of acquired characteristics been reinstated as a source of genetic diversity? Seemingly not, but long term epigenetic change is not without significance.
Normally at birth a new germ cell’s tagging is wiped clean. We now know in some cases this does not happen and the environmental influences on one generation are passed on to the next and in some cases beyond.

What initiates tagging?
Significantly the environment. The environment in the womb, the environment within the body and the effects of the surrounding world. 
In truth almost anything might drive the process of tagging. All the cells of the body working together constantly effect one another. The action of pathogens, symbiotic entities, physical damage to cells, pheromone signals from afar are all included. 

Relevance to the gardener 
I have intended setting down a few thoughts about epigenetics in gardening for some time and reading Nessa Carey has emboldened me to to do so.

I need to explain that many plant cells retain pluripotency (the ability to differentiate into any new cell) throughout the plant’s life. Pluripotent cells occur in the primary meristems at the shoot and root tips and in the secondary meristems such as cambium. These cells as well as reproducing themselves in their undifferentiated form can differentiate into any plant part. Plants unlike most animals can completely renew themselves - either as  extension growth or when detached as new entities. We gardeners call the latter vegetative propagation. Even simple cells like parenchyma can become pluripotent.
Scientists exploit the regenerative abilities of plant cells in meristem culture.

You might say cells of the stem are stem cells in respect of rooting!

Certain differentiated cells in a simple plant stem are able to generate root cells when we take stem cuttings. On the other hand there are fewer examples of plant root cells having the ability to produce stems. Some of the exceptions can be quite a nuisance when they appear as suckers! Such roots with the capacity for pluripotent action are the basis for root cuttings. 

Gardeners and ecologists have been reading for some time about research showing plant genes been turned on or off. Not infrequently we read how plants from a distance warn their neighbours with pheromone signals of the presence of a parasite or predators. Supplied with this information a plant mounts it defence - as diverse as producing distasteful tannins, growing more spines, producing natural toxins or even sending out its own signals to beneficial predatory insects.
All these defences come at a cost to the plant’s resources and being epigenetically ‘switched off’ when not needed is part of a plant’s good housekeeping.

I sometimes get irritated about researchers pontificating about the significance of genes being working or not. I have previously indicated my irritation when two years ago researchers on biochar demonstrated significant growth improvements by using biochar as a growing media and yet damned this material by reporting the plant genes that fight pathogens were switched off. I suggest you might expect them to be switched off if the plant was thriving without them.
In actual practice plants grown in the field using biochar and indeed in historic terra preta produces very healthy plants indeed.

My clivia has never been healthier since being potted into charcoal


Phenotypes
Scientists recognise that a single genome can in different environments  produce different ‘phenotypes’. (A phenotype can be recognised on the basis of an organism’s external features). In animals different phenotypes produced from the same genome might be as different as a caterpillar and butterfly or as ephemeral as the colour of a fur coat in the Winter.

Different phenotypes of genetically identical plants is not uncommon and are epigenetically controlled. Certain aquatics look very different if growing on dry land rather than in water. 
Plant leaves on the same plant vary in shape, size and chloroplast density dependant on whether grown in full light or shade or varying temperature. Its all epigenetic.

Varying phenotypes are a characteristic of juvenility. A young beech tree retains its leaves in Winter whilst an old one doesn’t unless it has been kept young by clipping. Brenda’s son did not recognise the flowering ivy in his new garden. It looks so different to the juvenile kind.
Some conifers permanently retain their juvenile phase and this is a source of dwarf forms.

This variety of hamamelis unfortunately retains its dead leaves.

Peter Williams’ picture shows ivy in its mature form

I wrote recently about hard and soft growth. Surely this is epigenetically controlled?

A well researched epigenetic phenomenon is a plant’s response to cold in relation to flowering and the timing of seed germination. Vernalisation (preparing for Spring) controls for example a plant cell’s ability to differentiate flowers. Scientists have identified how genetic tags control this phenomenon. Extreme in its sophistication it combines classic epigenetic phenomenon such as  environmental stimulus, delayed timing, long lasting action and at the end of a season ‘scrubbing’ tags clean.

In animal studies there is great interest in developing profitable pharmaceuticals that encode epigenetic actions. I wonder if ever there will be chemicals sold to promote flowering?  At least that might stifle the garden pundit’s feeble resource of suggesting you give your none flowering plants a dose of potassium!

Queen bee

Royal Jelly is epigenetically potent
Another remarkable example of phenotypically distinct organisms that share exactly the same genome is the thousands of worker bees and their very few sisters that become queens. 
Widely researched their epigenetic story is now almost unravelled. 
The ruling queen after several fertilisations by drones on her maiden flight settles down to a sedentary existence of as long as eighteen months and in that time lays tens of thousands of eggs. Thousands of females will be genetically identical (Not all the bees, distinct fertilisations will give rise to different clones and the very few males have their own special duty).

The epigenetic destiny of sisters is controlled by their nutrition. For the first two days from hatching all females are fed with ‘Royal Jelly’. This substance is produced by specialist workers - themselves phenotypically gifted to exude this material. Future queens continue to be fed Royal Jelly for the rest of their life.
The content of this material is a complex rich mixture and contains epigenetically active components. Crucial genetic elements in the growth processes have now been elucidated, methylation enzymes have been identified and it interesting to note that to become a queen a specific gene is turned off.

Must tell the others

Apparently in bees there is another well examined example of epigenetic activity that involves a worker’s memory of food sources classically communicated in the famed ‘waggle dance’. Not only does it need to remember it needs to forget a previous site. It’s all in the tagging.

Brave New World
New Scientist last month reported in a major feature that there were huge developments in plant epigenetics just round the corner. Many of the developments will relate to yield and pest and disease control in Agriculture. What comes to farming gets passed on to horticulture and one day we might see at the garden centre epigenetic products that change the colours of flowers.
Much of the epigenetic action in potential farming products revolves around a switching mechanism that involves RNA interference. Like all the above examples there are no permanent changes to the genome.


Respite for the bees?
The bees will be pleased that an epigenetic product that controls varroa mite has been announced to be in its final stage of development

Relevant links

I get precious about my biochar

I now now wonder if soft growth involves epigenetic change

More about varroa mite

paris genome

Tuesday, 17 January 2017

The benefits of mulch

Much ado about mulching


Mulch is a thin cover on the soil surface. Mulch gets thin cover in the horticultural press too. Reporting is very shallow.
You probably know that mulching makes plants grow better, conserves water, looks good, insulates the soil and can suppress weed. You might add that it protects the soil from erosion in heavy rain and keeps the mud splashes off the strawberries.
For many gardeners that is sufficient but you won’t get away with so little today. As is my wont, I want to dig deeper!
Except I don’t dig. A  perceptive student once inquired why as I am so keen on minimum cultivation I don’t just put a mulch on top of the soil and get a cavalcade of further advantages. He was right of course, it was a very shrewd insight. Although I have often rather snidely declared that the main advantage of mulching is to prevent the over enthusiastic gardener disturbing the soil it might actually be true.
As I so often promote the benefits of none cultivation I will spare you that today!

I bark mulched last May. Three cubic metres delivered from a local nursery £120

Mulching materials
The actual properties and gardening merits vary with the material. The very best for water conservation are gravel and stones. Include in this list larger rocks and un-cemented paving. How often do you hear that clematis likes a ‘cool root run’ under stones. Partially true. The active principle is that loose stones and gravel do not intercept water and even light rain nearly all penetrates through. Like most mulches, as intended, they do reduce direct evaporation from the surface. Permeable plastics and substances such as polythene add to the list of good water conservers. 

Bark mulch gives all year round cover
Mulches are usually fairly long lasting surface materials although those such as bark and wood shreddings need topping up every few years as they slowly degrade. Discuss with the rabbits and moles the permanence of stone chippings.


Peter was mulching last week (I think this post reminded him!)
We also use the term mulching to include surface organic materials such as farmyard manure and garden compost. In actual fact these materials are usually intended to be incorporated by the worms and only remain at the surface for a while. Manure mulched rose beds annually topped up might last the whole year. Lawn mowings and Autumn leaves are perhaps a half way house in this crude classification. Mulching as a very effective means of adding organic matter is not really my subject today.

I will use my plastic scarifier to sweep the leaves off the the grass path on to my borders

Weed control 
Other than plastics, mulching against existing established perennial weed is almost useless. The weeds will love the mulch as much as the plants. We will say nothing about gardener’s attempts to smother perennials with newspaper and cardboard!
Against weeds coming from seed mulch’s measure of control is really quite useful. It seems to be generally agreed that mulches need to be about two inches thick to stop weed seed germinating. This cover will be enough to suppress light levels at the soil surface to inhibit germination and enough to prevent emergence of small seeds. It won’t help very much with seed that blows onto the surface or is shed in situ (shame on you).
In my own case the thinness of my wallet reduces the thickness of my mulch. My weeds are well enough controlled by my glyphosate spraying and I actually want many of my garden plant to sow themselves around. (This is why my mulches never overlay plastic - I want my garden plants to self seed).

Hand weeding anyone?

My Scilla biflora feely seeds itself around
This cyclamen would have not sowed itself if the gravel was under-laid with plastic
People tell me that weeds that do sow themselves in mulch pull out very easily!
This year I newly mulched a large part of my borders with bark. This was to pacify Brenda who can’t stand the liverwort! 
The freshened up borders looked very nice.

An insulating layer. Be careful what you wish for
In general a mulch’s insulation might be thought to be a good thing if it keeps soil warm in Winter and cool in Summer. 
Not all mulches are insulators and plastics are only thin layers. Some colours are good heat absorbers and/or emitters. The relationship between day and night temperatures might be just as significant as those between seasons. It might for example be a difference between crop failure and success if night air above mulch is too cold and fruit blossom is frost damaged.
It is really quite complicated - what do you want? If a Winter laid mulch keeps the soil colder this might be thought to be a bad thing. On the other hand if my frost delicate Dicentra spectabilis emerges a little later I will be very pleased.
In practice in normal UK conditions I ignore potential exceptions, lay mulches at almost any time of the year and in terms of heat transfer hope they are beneficial!

Three case studies about soil temperature
*In my earlier post about gravel mulching a lady wrote in that in her tropical climate gravel got too warm in the hot Summer sun. I must say that on our subsequent holiday in Costa Rica I did not notice this effect on the weeds growing in the hotel’s gravel roads! On the other hand the dry sand on the beach was too hot to walk on. I imagine in such climates the soil is much cooler under stones and although hot for a plant to clamber over keep roots happy?

*A neglected exploitation of mulch’s insulation is putting an extra layer over dormant tender plants such as dahlias in Winter. The mulch might even be extra soil!
This year we had five months of spectacular colour of dahlias overwintered in the ground - it had been a very mild Winter. To increase my chances next year I have carefully folded over the large frost-dead tops of the dahlias and supplemented that with a layer of my miscanthus prunings and scattered amongst it mole soil from the lawn! I will remove it all in March! It does look a mess but the dahlias are worth it.

 Dahlias advertise my vulgar taste next to the road
The mulch will have confirmed my reputation

This mulch was an accident
I have only limited hopes for my effort! Insulation might be successful if Winter cold comes in short sharp spells.
If we get a prolonged period of penetrating frost there will only be a very small benefit. With only a very small heat source from deep soil my mulch will be of very little value in stopping the soil freezing.
As an analogy in our extreme 2010 Winter the inside of my unheated greenhouse was as cold as outside. Your own Winter coat only keeps you warm because of the heat from your body. Blog sleuth and myth buster Robert Pavlis writes about this phenomenon when he tested soil insulating cones.

The best insulation for your dahlias is to plant them very deeply at original planting!

 *When I went to see Peter he showed me the graphs he had drawn when he wrote his PhD thesis. They showed how soil surface temperatures fluctuated throughout a sunny Summer’s day. It is really quite astounding. Most mulches would dampen such fluctuations although thin plastics might increase them.

Drawn by hand before computer graphics, Peter measured soil surface temperatures on successive Summer days.
(Ignore the two horizontal lines)
Water retention
My old Head of Department, a soil scientist, contended that mulches contributed very little to soil water conservation and I used to argue that they did.
I thought before finalising this section I would have a word with soil scientist Peter Williams and found that he was not very enthusiastic either. He emphasised that never-the less he thought mulches in the round were a very good thing.  He went on to mention that he had recently assessed the soil moisture under the mulch in his garden after heavy rain that had followed a dry period and found that very little water had penetrated through. Mulches reduce water evaporative loss from a soil surface but they sometimes intercept rain before it can penetrate in.

At that point I scrubbed my text for this section and started again!

I think a key attribute of a water conserving mulch is that it should let water pass through without soaking it up! I have long argued that none absorptive materials such as gravel and to a lesser extent coarse bark act like a one way valve for light rain that otherwise would evaporate away.

A significant thing to understand is that an un-mulched wet soil surface becomes dry very quickly in drying weather. It rapidly becomes its own mulch in terms of water retention and soil surface evaporation stops. It will start again only when the soil is re-wetted and in the case of light showers the water will be very soon gone. 
Gardening books will correctly tell you that the best time to put on a new mulch is when the soil is already very wet. I put this to Peter and he explained that although the water retained by such a mulch would be a very useful equivalent of perhaps half an inch of rain that this was not very much in relation to the soil’s total available water content.
Leaving gravel and plastic aside, I think a mulch’s greatest contribution to soil water relations might be to keep the soil surface ‘in play’ in dry weather. When a dry un-mulched soil has reached the stage of ‘self mulching’ it is dry several inches down. In that zone root water absorption and such as mycorrhizal activity will temporarily shut down. Considering that the most fertile soil is usually at the surface this is not a good thing. Peter added that such dry surface soil can also get harmfully hot on a warm Summer’s day (see his graph).

If roots come right up to the surface and into a mulch so much the better

My Sternbergia lutea is growing in the gravel

Cosmetic value  - disguise. I have my own problems when I try to grow ferns on my hydrophobic sandy soil! I plunge ten litre pots to give me a watering lip. 
Things people ask.
Do mulches such as wood chips deplete the soil of nitrogen?

One might counter with the question, how could a layer at the surface do so? 
It can! Most of the decay of woody mulch is a result of fungal action. Fungus mycelium grows down into the soil to draw up nitrogen to maintain a suitable carbon/nitrogen ratio.
The good news is that the nitrogen extraction is very small and for most practical purposes can be ignored.
Not so if woody mulch is worked into the ground. If it is a problem it can be corrected by a light dressing of a nitrogen containing general fertiliser.



Peter’s recent three inch mulch of composted mowings and leaves won’t deplete nitrogen 
Can fresh wood chips, bark or shreddings be used without composting?

There might sometimes be slightly toxic content of fresh material that might damage very delicate plants.
In practice with my well established sturdy perennial borders if I find an arboriculturist anxious to rid himself of a lorry load of his shreddings I ask him to dump them and I use them straight away.

Is a gravel mulch suitable for herbaceous borders?

Not if your border is the kind where you are aways transplanting. I personally prefer bark for a herbaceous border
On the other hand I love gravel mulch around free standing specimen herbaceous plants - and shrubs too

Links

My previous post on mulching
Hardcore gardening

Saturday, 7 January 2017

Cathi’s grass verge, prologue to Year 2

This series started with my post on eliminating ground elder and nettles.

Daffodils and tulips in late May 2016

Ever dreamed of impossible things before breakfast? Here are seven.
  • Establish a garden feature without prior soil preparation
  • Eliminate ground elder that has been thriving for years and covers half of a 250 square metre site. A gardening programme recently described it as the most persistent ground cover ever. They said it was brought in by the Romans…
  • Introducing garden plants before all the ground elder is gone
  • Convert an existing coarse grass sward that has been invaded with ground elder to fine fescue
  • Establish a grass ground cover by sowing and planting that is only fescue. 
  • Ensure the grass is eventually exclusively none creeping Chewing’s fescue with garden plants in between
  • Never need to mow the said feature

This is my dream - no not a nightmare. I have already written four posts about it. Go to ‘Cathi’s grass verge’ in my theme column to follow Year 1 - or follow the links below!

May 2015 shortly before the first spray

If you consider glyphosate the work of the devil read no further. Cathi’s verge is under a glyphosate maintenance regime. I am there with my knapsack sprayer to both eliminate the established weeds and spray any new ones as a regular routine - just like all my other gardens. Whether a plant is a weed or a wanted plant will change as time passes and priorities move on. You can have too much of a good thing.

A different philosophy
You might have noticed that for me developing a garden feature sometimes takes a long time. My cemetery gardens took more than half a decade. Gardening by evolution, not revolution I call it. Cathi's verge will have been three years before it is something special and that won’t be the end. Brenda’s son Stephen would have moved house very much sooner!
For a gardener like me who carries out any gardening task at ninety miles an hour my patience might seem strange. Even my no dig method in my vegetable garden takes few years for the best of its numerous benefits to shine through.
As one who might advocate to a new gardener methods that give immediate returns to gain motivation I personally prefer the long term.
I have when necessary made small garden features for clients in the proverbial day. At home a quick turn round time is not for me.


It was a little scruffy at crocus time last year

A patient approach is essential if a new garden contains established perennial weed. A dear lady showed me her very expensive perennial  border overgrown with ground elder and couch grass. She asked me what she should do. I wanted to say “don’t start here’.

I have enjoyed myself right from the very start of Cathi’s project. Pleasure for me comes from technical progress, making decisions, popping plants in and all the signs of beauty unfolding. For the first five months of Year 2 (2016) with the already established snowdrops - they have been there for years - and the succession of bulbs planted the previous Autumn the verge looked really quite lovely. 
In addition for the later part of the year without the messiness of cutting long grass back I have had a taste of the Summer and Autumn flowers I have planted. Last year’s small plants planted late 2015/early2016 will become something special this year 2017.
.
As I write now in early January it looks nothing special. At this moment superficially half grass and half soil its just another scruffy mud splashed verge.

The new feature carries an extremely low budget. Most of the plants are garnered from my garden. It has actually taken very little time measured in actual hours worked.  Most of the time has been dreaming, planning and blogging about it!  Planning is In my head not on paper and is made up as I go along!

You might discern that my planting is a little haphazard


With my methods fashionable and normally necessary - but to me painful - reduction of soil fertility is not needed.

Catching up - summary of posts published so far

1. My first post in this series currently appears in my top ten hits and has been read to my amazement 35,000 times. Perhaps it is that the title includes ‘nettles’ which is such a common problem. In point of fact the nettles were well gone by the time the first season was over.

2. In my second post I followed the weed control to the end of the first season 2015. In the first year in addition to glyphosate I used MCPA which is known to give a relatively quick kill of nettles.
I attempted a comparison of using just glyphosate with a glyphosate/MCPA combination and at the end of the season I could discern no difference. Since then I have abandoned any variation of treatment and just use minor modifications of the routine glyphosate  spraying I normally do.

I could have elected to take out this ground elder from the grass with MCPA. The selective action would not kill the grass

The endemic snowdrops were inevitably amongst the clumps of ground elder. Three weeks after this picture it would be possible to spray all over without damaging the snowdrops

Snowdrops last year

3. In a later post  I introduced the heretical notion that I was going to start planting before completely eliminating the ground elder. Maintenance would be made easier if I limited my planting to bulbs and other upright monocotyledons - but not exclusively so. I think it was here that I mentioned that at least for the next two seasons the pretty June carpets of dandelions and buttercups albeit restricted would be allowed to continue close to the road.

4. My last post was more a statement of ambition and detailed my previous experience with growing fescue grass as a plant in my other gardens and included pictures of the monocotyledon plants I had then started planting.  I have now sourced seed of pure Chewings fescue. To me it is a beautiful none creeping grass.


You can see how it is fairly easy to spot treat the ground elder with glyphosate because It is still a distinct series of intact plants

Step to the future and see how the garden developed through 2016
At the present time these two posts have yet to be published (one is written and I have all the pictures). These will have appeared by early Summer and the first will be next month. I will insert the links on publication. 

A kind of disclaimer
Although I am confident my methods work for me - I have used them before but not altogether - I think I ought to give you a warning. I don’t expect many of you will attempt all those ‘impossible’ things I listed in my preamble today! I would like to encourage gardeners to think ‘out of the box’ but unless you are very experienced in chemical weed control following me too ambitiously or perhaps imprecisely might lead to disaster!

In particular it needs to be emphasised that to completely eliminate ground elder using glyphosate takes repeated applications over three years. It is somewhat irresponsible of me to tell you that I am planting certain plants before it is gone.
When roots of ground elder infiltrate the root mass of most conventional herbaceous perennials all is lost for permanent elimination unless you are highly skilled with a sprayer. For most gardeners the only resource is to lift the perennial when dormant and to divide the perennial into small enough pieces to remove by hand every single ground elder root - even washing roots away! Effectively you are re-propagating your herbaceous plant by division.
My anticipated complete control of ground elder is only possible because of the upright nature of the monocotyledon plants I have chosen, my plant placement, and that surviving ground elder has not been chopped to small pieces by attempted physical removal. I am prepared to invoke ‘force majeur’ and sacrifice the occasional plant - but it has not happened yet.

My normal advice to gardeners with a new weedy site is get rid of all perennial weed before planting perennials. For many common weeds such as couch grass, docks, nettles and  - it may surprise you - bindweed, it will take up to or no more than a season. For such as ground elder very much longer! Elsewhere I write about control of other difficult perennial weeds which can be found via the search box or my theme column
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