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Written by Joel Williams

Soil Biology – two words that have become commonplace in the lexicon of the farming community in recent years, and rightly so. Biological interactions are of course as important as the physical and chemical interactions that make up the fascinating medium we call soil. Among all the groups of organisms that live in soil, there has been a particular growing focus on the microorganisms; interest in which gained significant traction as we began using more powerful tools to study them – genetic and molecular tools for example. As we began to unearth the world of the soil microbiota, we quickly realised just how vast and complex this underground universe really is – certainly much more so than previously thought. In dealing with this complexity, one branch of research has shifted attention away from the soil to study the microorganisms that are associated with plant tissues – enter the plant microbiome.

The plant microbiome – also known as the phytomicrobiome – refers to the groups of microorganisms that are intimately and directly associated either on or within various plant tissues. The number and diversity of organisms that make up the plant microbiome is a fraction of what is found in the bulk soil, hence the emerging focus on studying this less complex plantassociated ecosystem. Please note, I use the words ‘less complex’ very cautiously here – arguably, there is nothing ‘less complex’ about it at all apart from having less diversity and density of organisms.

I’m sure most readers will be familiar with the below ground community of microbes known as the rhizosphere but the above ground plant habitats are collectively known as the phyllosphere. These microbial communities consist of bacteria, archaea, fungi, viruses, algae, and occasionally nematodes and protozoa (these latter two are much more common down below in the rhizosphere but less so above ground). Bacteria are by far the most commonly found microbe above ground in terms of both numbers and diversity. All of these microbes that associate with the plant are either acquired from the environment (soil and atmosphere) or they are inherited from the mother plant via the seed.

Within each of the plant associated habitats, some microbes live inside the plant tissues (endophytes) while others will remain outside of the plant, living on the surfaces (epiphytes). There is some overlap between the microbes that associate on various plant parts, but surprisingly, many of the species are totally unique and distinct from each other, fulfilling very specific roles and functions within each of their micro-habitats. Let’s briefly explore some of the different regions of the phytomicrobiome:

Root microbiome – often referred to as the rhizosphere, this is of course the microbes who associate with plant root systems. Arguably the most well studied of all plant microbiomes, the organisms in the rhizosphere play particularly important roles for nutrient acquisition, plant immunity and resilience during environmental stresses.

Shoot microbiome – the microbes that dwell in shoot tissues appear to be more closely related to the species found in the soil highlighting the soil as an important primary source of organisms which colonise the plant. The endophytes found in the shoot are highly mobile within the plant and are also commonly found in the seed – forming part of the seed microbiome for the next generation.

Leaf microbiome – the leaf microbiome has been shown to influence photosynthesis and transpiration hence playing a vital role in plant development, particularly under difficult climatic and weather conditions.

Flower microbiome – our understanding of the microbial communities that uniquely associate with flowers is far less when compared to other above ground plant habitats. This is particularly due to the fact that these attractive habitats receive more regular visitation by a diverse range of insects who facilitate transfer of other beneficial and pathogenic microbes; as well as inadvertently leaving a fingerprint of their own insect-associated microbiota. As you might guess, the organisms associated with flowers have been implicated in influencing plant reproductive success – they have even been shown to use flower scents (volatile organic compounds) as a food source and additionally induce distinct changes in the expression of a plants floral scents.

Seed microbiome – like other parts of the plant, the seeds are also colonised with a diverse group of microbiota. At the end of reproductive development, the organisms on and within seeds act as a reservoir for the next generation and typically establish as endophytes in next years offspring. Functionally speaking, the seed microbiota release a range of metabolic substances that enhance germination and establishment as well as plant performance and productivity under stressful conditions. We will return to the seed microbiome in the next issue of Direct Driller and will expand on this article with a deeper dive specifically into the role of the seed microbiome.

Altogether, the plant microbiome directly and indirectly influences plant performance, productivity and can support low input production systems. Direct mechanisms that support plant growth include nutrient supply via solubilisation from soil reserves or biological nitrogen fixation, as well as production of plant growth promoting hormones. Indirectly, plants can also recruit specific microbes to help them overcome various biotic and abiotic stresses – such as activation of beneficial microbes who can suppress pathogens or improve drought resistance.

There is an increasingly prominent nudge towards reducing fertiliser and pesticide use in agriculture from both top-down (policy) and bottomup (consumer driven). There is significant potential in the use of DIY or commercial microbial inoculants to support this transition, however, many challenges remain regarding improving product consistency in field conditions. Central to achieving this is the need for a deeper understanding of the ecological processes and mechanisms that underpin the plant microbiome assembly and function. Addressing these knowledge gaps will no doubt help provide the necessary tools to support agricultures transition toward ecological and productive sustainability.

References

1. Understanding phytomicrobiome: A potential reservoir for better crop management. (2020). doi: 10.3390/su12135446

2. Phytomicrobiome for promoting sustainable agriculture and food security: Opportunities, challenges, and solutions. (2021). doi: 10.1016/j.micres.2021.126763

3. Plant microbiome: A reservoir of novel genes and metabolites. (2019). doi: 10.1016/j. plgene.2019.100177

4. Toward Comprehensive Plant Microbiome Research. (2020). doi: 10.3389/fevo.2020.00061

5. Microbiome selection could spur next-generation plant breeding strategies. (2016). doi: 10.3389/ fmicb.2016.01971

Written by Dominic Amos, Crops Researcher at the Organic Research Centre

As based on information found on Agricology (www.agricology.co.uk)
Reducing tillage and chemical inputs can be beneficial for soil and the environment, so could a permanent clover understorey acting as a ‘living mulch’, moving towards a perennial soil cover, offer a practical solution to reducing inputs and having more sustainable cropping systems?

This is the question being investigated by a group of arable farmers attempting to implement the system for input reduction through an Innovative Farmers Field Lab. Inputs in this case could be agrochemicals and fertilisers or tillage and diesel, depending on the current farming system. These are the two starting points of the group who are either already practicing long term conventional no-till looking to reduce chemical inputs or established organic farmers looking to reduce tillage. There is an imperative from both perspectives but whilst both farming systems can learn from each other, the challenges for each of making an alternative system work are quite different due to the respective starting points.

What is a living mulch?

A living mulch (LM) system includes aspects of several common farming practices and concepts such as cover cropping, intercropping, undersowing, and mulching, with the system building upon these approaches with full integration as a cropping system. In practical terms it requires the establishment of a perennial forage legume to provide protection for the soil as a (semi-)permanent ground cover common to perennial cropping systems such as top fruit or viticulture. It is rarely used in annual cropping systems due to the competition with the cash crop so the question is, is it compatible with annual arable cropping? The LM approach differs from the well-known organic reduced tillage systems with the roller crimper pioneered by Rodale where the idea is to terminate high biomass cover crops to provide a dead mulch that helps suppress weeds for establishing cash crops. In truth this system relies on certain climatic conditions generally not experienced in the UK.

Services and benefits

The LM system can be expected to deliver a number of key ecological services to the agroecosystem including nitrogen (N) accumulation, weed suppression, enhanced soil physical characteristics (and trafficability), soil protection, catch cropping function, self-regulation of pests and disease, increased soil fertility and increased biological diversity. At this stage it is also worth considering that many organic farms already have weeds that provide some of the ecosystem services but with less control over species, so the mulch could be thought of as a ’designated weed.’¹

The two key services that need to be delivered for a LM system to best contribute to agricultural productivity are weed control and N supply.Living mulches offer a potential alternative and sustainable strategy for these two provisions, although the amount of N made available for the cash crop and level of weed control will be greatly influenced by management and by the season. Conventional notill systems may require supplemental N fertiliser to maintain crop yields. These two services offer an insight into the complexity of the system and the trade-offs (not necessarily unavoidable). There is a strong correlation between the mulch biomass and weed suppression and N accumulation services but high biomass will offer stronger competition against the cash crop. 

This management balancing act between cash and cover crop growth throughout the season is the fundamental challenge to a working LM system – in order to harness the benefits of this permanent cover whilst limiting the risks to productivity. If enhanced soil health, increased biodiversity (above and below ground) and reduced emissions can also be delivered, then a more sustainable and resilient farming system is the prize on offer. There is a word of warning at this point since much of the research already conducted in this area including recent work at Stockbridge Technology Centre through the DIVERSify and TRUE projects demonstrate large and potentially unsatisfactory grain yield losses from arable LM systems that will require careful thought and management to make successful.

Enhancing beneficial interactions and managing competition

The ecological concepts that underpin the cereal-forage legume system are known as niche complementarity and facilitation and the system works on the principle of functional diversity. In theory this means the two ‘parts’ of the system work in harmony but in practice, particularly from the organic perspective, making the system work has proved elusive. This is a complex issue but a key factor is the interactions of the cash and the cover crop, and the ability to manage and manipulate the competitive advantage of the cereal. In fact, from an agroecological perspective, boosting the cash crop and weakening the cover crop at key times in the growing season is a real challenge especially since, as previously mentioned, weakening the mulch actually contradicts its key service provisions. Small doses of N fertiliser and herbicides can selectively weaken the clover and hand the competitive advantage to the cereal but of course these options are unavailable for organic farmers.

Farmer-led trials with Innovative Farmers

There are several areas that are being explored by farmers through the field lab:

1. Mulch species and establishment

2. Cash crop species and establishment

3. Mulch management (both externally and in crop)

Mulch and crop species selection

Different combinations of approaches are being tested with the farmers – utilising their knowledge of the context of their farms and systems and taking wider considerations into account to choose the most appropriate options for them. This will facilitate the peer to peer exchange and progress on living mulch best practice. In the field lab trials the farmers have used a mix of wild white and smallmedium leaf clover recommended by Cotswold Seeds, that has been selected to remain prostrate and provide persistence but with limited longer term competition against the crop. The clovers were established through undersowing into cereal crops in spring 2020.

Direct drilling cereal crops into the pre-established stand of clover took place last October with winter oats and rye selected for their competitive abilities. How and when, or even if, to manage the mulch is a key question being explored. There are opportunities to mow or graze before drilling the cash crop, or even during the foundation phase of cereal growth in the late winter. One of the most interesting questions is whether the mulch needs to be selectively managed later during the growing season and how this might be done? An option being considered is inter-row mowing, though commercial equipment is not yet available.

In conclusion

This fine balance of managing and manipulating the dynamics of a cash and cover crop to the advantage of the cash crop whilst maximising the services from the cover crop is what in the end will determine the successful implementation of what is on paper a sustainable and resilient way to farm the land – albeit one that will require a system redesign approach. In the end the system will rely on the knowledge and ingenuity of the farmers and the peer to peer learning to turn the theory into successful practice.

Agricology is an independent collaboration of over 40 of the UK’s leading farming organisations sharing ideas on sustainable farming practices. We feature farmers working with natural processes to enhance their farming system, and have a wide range of farmer videos on our YouTube page. We also share the latest scientific learnings on agroecology with the farming community from our network of researchers. Our website hosts over 400 articles on different agroecological practices. Subscribe to the newsletter or follow us on social media @agricology to keep up to date and share your questions and experiences with the Agricology community.

Written by Tom Chapman, Head of Regenerative at Innovation for Agriculture

How would we design agriculture now, in the 21st Century, if we were starting from scratch? What would we do differently, given what we know about regenerative agriculture and about farming with, not battling against, nature? Would we continue with the same cropping, the same machinery, the same fertiliser & spray regime and the same field layout or would things be radically different?

We should all know the five golden rules of soil health, but it never harms to reiterate them. They are:

1. Always keep the soil covered and protected from the elements

2. Keep a living root in the soil at all times

3. Avoid both chemical and physical disturbance of the soil

4. Avoid monocultures, diversity is essential

5. Integrate livestock into your system

Starting with a blank canvas, the farming system that most closely meets the above rules is a perennial crop of forage plants interspersed with trees and shrubs and grazed by a mixture of ruminants, monogastrics and poultry. However, humankind has a massive (and some would say disproportionate and unhealthy) demand for grains so we need to find a way of integrating the growing of these into our ‘new’ farming systems. Unfortunately, perennial grain crops still appear to be many years from commercial reality, so we need to find a different way to tick the soil health rules using annual cropping.

A number of farmers in Australia are growing crops drilled directly into longterm permanent pasture, giving it the obvious name of ‘pasture cropping’. As the grasses start to slow in growth and become dormant in the autumn, these pasture croppers drill their cereal crops directly into the sward. In early spring the combinable crop grows away from the grass, shading the latter and slowing its growth. After the crop is harvested in mid to late summer, sunlight can, once again, penetrate to the forage understorey and its growth accelerates.

They accept that the grain yields from the system will be lower than we currently achieve, but they also know they can, effectively, doublecrop it, moving their grazing animals onto the grass understorey once the grain crop has been harvested. The wonderful thing about the system is that it captures much more sunlight: No more bare earth, lacking in green leaves to photosynthesise and produce sugars. Consequently, they are seeing tremendous improvements in soil health. Root exudates feed the soil life, year-round; grazing livestock convert the crop residue and forage plants into plant food; humus levels rise; and the land becomes vastly more fertile.

There are a number of farmers here in the UK who are experimenting with this technique. At the moment forage rye is most popular, so not strictly a standard combinable crop, but its ability to continue to grow at low temperatures and its tall growth habit, relative to the grasses, means they are having some success (I drilled a mixture of forage rye and vetches, last autumn, directly into permanent pasture and am watching its development with great interest).

If we were to adopt this practice more widely in the UK, and to do it with mainstream wheats, barleys and oats, would we see a return to the tallergrowing varieties of yesteryear? Plants that could rise above the grasses growing at their base would capture more sunlight, as well as making harvest easier. They would also have to be deeper rooting, to out-compete the grasses below ground. The improving natural fertility offered by the healthy soil is likely to lead to stronger plant stems which, combined with the slightly lower yields, means lodging risk would be lower than we experience with tall plants in our current farming regime.

There is a downside to the above plan, from a regenerative point of view, in that the annuals being sown are still a monoculture, albeit sown into a (hopefully) diverse sward. Would our ‘designed from scratch’ farm truly be drilling monoculture crops, or would it be drilling a range of different crops – grains, pulses and legumes, oilseeds and brassicas – into the same field? This would be the ‘herbal ley’ of the cropping world. The mixed crop would have a varied leaf architecture, to maximize the amount of sunlight it intercepts. The roots would differ too, with some surface feeders and some reaching deep down into the subsoil, bringing up water, minerals and other nutrients as well as adding organic matter at depth. The diversity would host an amazing array of beneficial organisms and fungi, all working to improve the soil still further.

Designing such a farm from scratch, though, would also mean designing from scratch the way we harvest our crops. A traditional combine harvester probably wouldn’t be able to handle a range of different-sized seeds. Now I’m no mechanic – those who know me will ascertain that I’m a true ‘dog and stick’ farmer (though without the dog!) – so will leave predictions of what the new harvesting machine would look like to those with more of an engineering bent. Could such a machine do the harvesting, the cleaning and the sorting of seeds in one go, or would the mixed crop need transporting back to a specialised threshing and dressing machine at the farm?

Shrubs and trees would also feature in our ‘new model farm’. Silvoculture can already be seen on a number of farms with fruit and nut trees forming alleys wide enough to allow a sprayer or fertiliser spreader to pass through. Typically these are in straight lines, though with GPS and autosteer, do they need to be? It would be much more natural to have sweeping curves to our cropped areas, reducing wind flow and creating microclimates across the land. There could be a mixture of hedges, grazeable shrubs and trees, some for firewood and some for fruit and nut production. Certain tree species even fix nitrogen!

Would we be able to throw away our sprayer and fertiliser spreader on our ‘new’ farm? Monocultures are like commuters on the London Tube: one person coughs and they all catch a cold. Likewise in your fields, a stray fungal spore, or a swarm of insects and the whole crop is decimated. Growing a ‘herbal ley’ of arable crops in a permanent pasture sward would mean disease would find it incredibly difficult to spread, just as insects would have a tough time targeting their preferred host plant.

The mixture of plant species, in conjunction with the animal grazing, would mean the crop is also self-fertilising. We already see this with foragebased herbal leys and never seem to need artificial fertiliser to make them grow. Nitrates in water, nitrous oxide emissions polluting the air, such things could be consigned to the annals of history, were we to follow this path.

Putting the engineering challenges to one side, a mixture of crops, surrounded by trees and shrubs, all growing in a permanent pasture field that is grazed by cattle, sheep, pigs and poultry for part of the year ticks all the soil health rules. Soil is continually covered, there are always a diverse mixture of living roots in the ground, which isn’t disturbed (either by machine or by chemical), and the livestock dung, urinate and salivate onto the fields to stimulate the soil biota. Cash crops are harvested each year and the land also produces beef and lamb for sale.

Sunlight would be captured all year round, pumping energy into the system, minerals would be cycled and recycled, both in the acidic root zone and by the growing quantities of soil fungi and bacteria, and the water cycle would start to function properly, with surplus rain captured and held by the carbon in the soils to tide you over the dry periods, rather than running in sheets over the land and out to sea, carrying precious topsoil and nutrients as it goes.

We are all weighed down by the baggage of our existing paradigms, and many will say the above is just fanciful, but could it be the future, if we started with a blank canvas?

Watching the live feed from NASA last week as the rover ‘Perseverance’ touched down on Mars was a quite spectacular achievement. A planetary alignment, or confluence, of millions of externalities came together to achieve something marvellous, along with a generous helping of rigorous planning and attention to detail.

Sometime a series of events can surprise you in every way. Just recently a series of events unfolded which form the basis of this article. The first instance was when someone posted on TFF a slide from a webinar which appeared to show that ploughing was good for the soil. Intrigued by this I found a recording of the webinar and proceeded to watch with interest. The researcher presenting the webinar made no such claims about ploughing, quite the opposite, it was suggested that to increase SOM we needed to move away from intensive cultivations. As per usual communication was the loser, and I suspect a lot of people went away feeling rosy as they knew that cultivation was again ok.

A few days I was watching another webinar listening to notable practitioner and teacher of ‘Regen Ag’ espouse that ploughing in a regen ag system is ok because every farm and every situation is different. At this point I went and found something better to do than listen to pointless nonsense. I’ll admit that the first pillar of Conservation Agriculture (CA) makes reference to ‘minimal soil disturbance’ and not ‘no soil disturbance’, but does it really allow for maximum disturbance? I know that we all want to be flexible. Flexibility within the confines of the system is allowed, but ploughing is well and truly stepping out of the system, and for what? I would argue there is no gain from rotational ploughing, in fact I would go further and suggest that each rotational ploughing destroys the very biologically active system we are trying to create.

The clock has been reset to zero and you have to start all over again. It should be noted at this point when I refer to ploughing or cultivation I am referring to any intensive cultivation such as subsoiling, ploughing, combined single pass machines with legs and discs, powers-harrows etc.

The final event happened shortly after the aforementioned webinar where I happened to hear James Alexander of Primewest being interviewed on Radio 4’s ‘Farming Today’ programme. James mentioned some research that had been carried out on his farm comparing the net carbon gains of his organic system compared to his Regen Ag system. Knowing James a little I contacted him to find out more about the work undertaken and the results. Upon speaking to James it became clear that the real eureka moment had been completely lost in the short clip played on Farming Today.

Cultivation, as we all know, plays a considerable part in carbon release from the soil. The research, undertaken by Charlotte Cook of Indigro Agronomy, using the Cool Farm Tool to calculate net carbon release and sequestration, revealed exactly what I was anticipating. It is important to note at this point that if you are not practising Conservation, or Regenerative Agriculture then cultivation is an important part of your overall establishment strategy. We are not against cultivation per se but are focused on achieveing the benefits of optimising cultivation inputs.

From the data in table 1 it can be seen that for all metrics, except fuel use, the regen ag system has a higher carbon output than the corresponding organic, in particular the massive spikes from the manufacture and use of nitrogen fertilisers. This does not come as a surprise as I am sure we are all familiar with the large energy demand during manufacture of fertiliser N and resulting carbon–loss from soil once the nitrogen is applied. All of this does not paint Regen Ag in good light until we turn our attention to the broader picture with the inclusion of cover crops into the calculations, shown in table 2.

Here we can see that the action of including cover crops along with reduced soil movement through zero-till has significantly altered the picture. The carbon stock change per hectare now shows a large net sequestration of 8.7 tonnes/ha for the regen-ag system. This is over 3 times the sequestration achieved compared to a production system where intensive cultivation is employed. This tends to agree with some research from the US which showed that soil ploughed to 11 inches released 30 times more CO2 than undisturbed soil in the following 24 hours.

I am not trying to pit organic against conventional production, far from it, but it’s a useful comparison to show that our choices are not always straightforward. It also very much depends upon your viewpoint on the use of pesticides. The most important point of all of this is that we have to learn to reduce our tillage practices as much as possible if we really want to benefit our soils and the wider environment. Similarly we are going to have to become a lot more focused on our use of nitrogen fertilisers.

While we may be able to reduce our dependence on them partially I am not certain we can ever maintain our current level of output without them in some degree. Our use of nitrogen fertiliser is probably on borrowed time, and we really need to focus on how we can use this resource much more efficiently, or at the very least begin to cut N rates back. A production system based around CA principles should allow us to do this, for as we build soil carbon, we are naturally building soil nitrogen. We also need to ‘grow’ more of our own nitrogen through better rotations and better soil health.

 Good soil health can be measured by indicators such as soil bulk density and porosity, water infiltration and air movement, good levels of soil organic matter and biological activity, reduced loss of soil, nitrogen and phosphorus into ground and surface waters. We know intensive tillage negatively affects all of these parameters and every time we plough we effectively reset the clock on achieving the aim of functioning soil. It could also be argued that by doing this you are never going to see the real financial benefits of regen ag and functioning soil biology if you cannot reduce the level of cultivation you employ. So with good planning and attention to detail it is possible to employ a production system which does not rely on the damaging effects of cultivation, and the wider environmental issues that cultivation can create. But ultimately are we happy to allow the promotion of #ploughing in conjunction with #regenag? Or does this detract from the message we are trying to convey?

My warmest thanks must go to James Alexander of Primewest & Charlotte Cook of Indigro for allowing me to use their research. I must also stress that I have used their research to support my own particular viewpoint and may not necessarily be what the authors were intending to show.