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15.06.15 Soil Microorganisms contribute to plant nutrition and root health.

Soil micro-organisms provide an essential function in nourishing and protecting plants. They also play a crucial role in providing soil, air and water services that are absolutely critical to human survival. Understanding this linkage allows better nutrient management decisions.

This information here comes from an article published in Better Crops, developed by the  International Plant Nutrition Institute at the beginning of this year by Mark S Coyne and Robert Mikkelson. To read the full article please click here.

Sustainable crop production is essential to a healthy and adequate food supply. At first glance a healthy crop reveals only the above ground plant; the roots that support the visible plant are seldom seen. However these plant roots grow in an incredibly complex environment which is teeming with billions of soil organisms, particularly bacteria and fungi, which play a crucial role in promoting health and maintaining an adequate supply of plant nutrients for crop growth.

As previous blogs have shown, we are nowhere near knowing all about what goes on within the soil and the details of all the interactions that take place. It is understood that plants modify their soil environment by exuding large amounts of carbon from their roots. This zone in the soil where the roots are becomes a hotspot for the biological populations that live in the soil. Adding carbon to the soil surrounding the roots leads to a huge increase in the number of micro-organisms living within and outside the roots.

As soluble carbon is released by roots, micro-organisms are stimulated and colonise the soil surrounding the roots. This can result in competition for nutrients because plants and microbes rely on the same essential nutrients for growth.

Below are some of the key interactions between soil microbes and plant nutrition in a diagram and explained in more detail underneath.


Nutrients are converted to plant-available forms

Living organisms have a crucial role in controlling the transformation of plant nutrients in soil. In most soils nitrogen, phosphorus and sulphur are present as various organic compounds that the plant can’t use. Micro-organisms play a crucial role in regulating the conversion of these organic pools into plant available forms. This conversion takes place through numerous mechanisms. Various management practices including tillage, irrigation, residue management, using manures and the addition of specific biological inhibitors or stimulants and innoculants can be used to influence these important microbial processes.

If these biological processes aren’t accounted for in soil / nutrient management, then excessive nutrient loss or plant nutrient deficiency with a significant reduction in crop yield / quality can result.

Nutrient recovery is enhanced

Nutrient recovery has an intrinsic relationship with mycorrhizal fungi. The small diameter of the fungal hyphae allows greater access to soil pores than roots alone which gives the plant better utilisation of water and nutrients and maintaining root sorption activity in older parts of the root.

Mycorrhizal fungi can increase the supply of various nutrients to plants (including Copper, Iron, Nitrogen, Phosporus, and Zinc) in exchange for plant carbon. The boost in Phosphorus uptake provided by Mycorrhizal fungi is especially important for crops with high P requirements. Mycorrhizal fungi can also release various enzymes to solubilise organic phosphorus and they can extract soluble P from the soil at lower concentrations than plant roots are able to do alone.

Nitrogen fixation is facilitated

Certain specialised symbiotic bacteria can fix atmospheric N2 into ammonium based compounds for plant nutrition. The most important of these organisms for agricultural plants are from the species Rhizobuim and Bradyrhizobium.

It is estimated that N2 fixation provides between 10 -20% of the N requirement for cultivated crops and between 25-40% of the entire annual reactive N in the world.

Improved soil structure promotes root growth

An often overlooked contribution of soil microorganisms to plant nutrition is their enhancement of soil physical properties. Good soil structure enhances plant root growth and results in greater extraction of water and nutrients.

Individual soil particles are bound into aggregates by various organic compounds (especially polysaccharides) released from soil microbes. Glomalin, which is a protein released by mychorrizal fungi and is in the green picture at the top of the page, sticks soil particles together and improves overall soil structure. The more aggregation in soil, the greater the porosity which often leads to greater soil aeration and water storage capacity.

Pathogens are controlled

There is a growing appreciation of the link between soil microbes and plant pathogen control. Soil bacteria that produce siderophones can deprive pathogenic fungi of iron. Various antibiotics have been identified on soil that can suppress pathogenic organisms. Rhizosphere organisms can compete with pathogens for attachment to the plant root and essential nutrients for growth.

There is still much more to learn about how soil micro-organisms improve the health of plant root systems and overall nutrient efficiency.

Effect of fertiliser on soil microbial communities

Any management practice has the potential to influence soil microbial communities in positive or negative ways.

Short term, the effect of addition of mineral fertilisers on biology will be negative and will cause temporary osmotic stress. Long term experiments with wheat from Rothamstead show that adding mineral fertiliser over a longer term did not significantly influence the diversity of the bacterial population or two genes specific to important N transformation.

Other literature has shown that mineral N fertiliser application was associated with an average 15% increase in microbial biomass and 13% increase in soil organic carbon, compared with unfertilised control soils. They found that increases in microbial populations were largest in studies with at least 20 years of fertiliser. But it also showed the importance of pH, with soils with an acid pH (less than 5) having a negative affect on biological populations.

Soil micro organisms interact intimately with plants to stimulate productivity by supplying essential nutrients in a soluble form. Healthy plants stimulate the microbial community of the soil through the root exudates they secrete and the organic residue they leave behind.

Source: Soil Microorganisms contribute to plant nutrition and root health, Mark Coyne and Robert Mikkelsen.

12.06.15 Beneficial soil fungi boosted by organic farming with reduced tillage

The biodiversity and abundance of arbuscular mycorrhizal fungi - important soil organisms that can help plants to capture nutrients - is greater in organically managed soils with reduced tilling compared to conventional methods, a new Swiss study suggests. This illustrates the impacts that land management practices such as ploughing can have on soil biodiversity and the ecosystem services it provides.

Soil organisms are important for nutrient cycling, and there has been some suggestion that their decline may increase the need for artificial fertilisers. Arbuscular mycorrhizal fungi (AMF) are found in the roots of most land plants, including agriucltural crops, and can help supply nutrients to the plants. However they can be vulnerable to some agricultural practices such as ploughing or tilling, which disturbs the top layers of soil.

For this study researchers compared the AMF communities in the clay soils of seven sites, all in close proximity to each other in a Swiss Valley. Four of the sites were long-term, organic field experiments, each site divided into sub-plots to compare the combination of different management options of the land: Two tillage systems - reduced and normal tillage, and two fertilisation regimes - applying farmyard compost and slurry or slurry only. One of the other three sites was organically managed grassland, while the other two were cultivated using conventional farming practices - normal or semi-reduced tillage, and the application of mineral fertilisers on both sites.

For all seven plots, the researchers took soil samples from four layers - top soils (0-10 cm and 10-20 cm deep) and undisturbed sub-soils (20-30 and 30-40 cm deep). The researchers also cultivated AMF communities in pots from soil taken from six szites. The pots were planted with seeds from four different plant species and kept in a greenhouse for 20 months.

The results show that although the researchers found that fertilisation regimes affected the AMF communities in the seven sites, tillage practices had a stronger impact. The number of AMF species collectively identified through field samples and the soil cultivation experiments was greatest in the grassland site, at 38. This dropped to 33 species in the two reduced tillage organic sites, 28 in the one of the conventionally ploughed organic sites and to 28 in the conventionally managed site with normal tillage. Overall, 32 species were found in the conventionally farmed site with semi-reduced tillage.

Furthermore, the number of spores and diversity of AMF species was highest in the top soils of the grassland, next highest in the top soils of the two experimental plots where reduced tillage was used and lowest in the two experimental plots that had undergone normal tillage. Normal tillage disrupts the extensive spread of hyphae, fine strands of the fungi that form in the top soil layers, affecting spore production. Across all sites, the number of spores and different AMF species were lower in the bottom layer (30-40cm) than in the top layer.

AMF diversity was also higher in reduced tillage plots compared to normally tilled plots. Some AMF species are better adapted to the effects of ploughing than others and may dominate AMF communities in normally tilled soils, reducing their overall diversity.

Together these results show that organically managed soils can produce diverse AMF communities that will benefit plant nutrition, productivity and health and enhance sustainable practices.

Source: Science for Environmental Policy, 11th June 2015


10.06.15 Natural England, State of current knowledge on soils

At the end of last month, Natural England released a document looking at where science and research is with regards to knowledge on soil and soil management.  The document sets out Natural England's assessment of the evidence relating to their soils and how we conserve and manage them.  It assesses what we know already, areas that are currently being researched and what we don't know yet.

When looking at soil biodiversity, the common consensus is that there is still much to discover in terms not only of the millions of organisms that live there, but also how they interact with each other and aid key processes in soil that help us grow profitable crops.  The information in the report is broken down into different sections and the messages below deal specifically with what we know about the life beneath our feet.

What we currently know

Soils are habitats for millions of species ranging from bacteria, fungi, protozoa and microscopic invertebrates to mites, springtails, ants, worms and plants. 

A single gram of soil can contain a billion bacterial cells from up to 10,000 species (Torsvik et al, 1990, 2002).

Soil organisms are involved in delivering all the main supporting and regulating ecosystem services (Turbe et al, 2010) including:


  • food and fibre production
  • soil formation
  • flood risk management
  • water quality
  • climate control
  • waste and pollution processing
  • nutrient cycling

Soil biota are strongly influenced by land management (Stockdale et al, 2006), what we do as farmers impacts on soil biological populations

Agricultural land management practices which reduce disturbance and increase / diversify organic matter inputs will most likely benefit soil biota and their function (NE, 2012)

Soil biodiversity reflects above ground plant diversity (Wardle), but can be highly variable over short distances and times.

Soil organisms are arranged in food webs or varying complexity with internal feedbacks (Bardgett et al 2005). If organisms don't like the conditions they can effectively go to sleep for a long time (but stay there). We don't really understand the true requirements of most soil organisms.

The vast unexplored biodiversity of soils will be economically important in such areas as medicine, industry, agriculture and environmental bioremediation - the possibilities are endless!

Soil biodiversity has been largely ignored by conservationists (Usher, 205) the topic has often seen to be too complex to address.

Areas that are currently being researched

The extent to which soil diversity is important to soil function and resilience - resilience as a concept and how well the soil can function in different conditions has been the subject of many discussions (including among the FCCT team!). There are such a vast range of functions that occur in soil and some can be done by different organisms and some (for example nitrogen fixation) are more specific to certain groups of organisms.

The impact of climate change on soil communities and their function

How to best integrate soil biolgoy into farm advice (can we produce tools which accurately assess biological activity and health, or are we still counting worms?)

The extent of variation in many soil organisms across soil types and their interdependence with vegetation and management - soil pH is a major determinant of soil community composition

Whether it is possible to deliver measurable improvements in agricultural or environmental functions as a result of management to enhance soil biota in UK farms.

Whether DNA barcoding can be linked to genome data to identify and characterise soil communities.

What we don't know

A basic knowledge of most soil organisms - out of over 11 million species of soil organisms, an estimated 1.5% have been named and classified (Turbe et al 2010).

The range of soil species occurring in the UK - increased genetic barcoding will help

The distribution abundance and population trends for almost all of our soil dwelling organisms.

The habitat management requirements for conservation of most soil organisms (including their requirements for undisturbed sites).  How do we know the extent to which soil organisms benefit from conservation?

Specific circumstances where soil innoculation is worthwhile to encourage the beneficial function of mycorrhizae, rhizobia or other beneficial organisms in agriculture.

How to interpret soil biological measures to link them to desired soil function, conditions and services - Defra have shown that soil life and its functions are sensitive indicators of change, but we don't know whether they can be benchmarked to provide subtle information on soil functions to inform soil management or set targets.

This information is only from the section of the report looking at soil biodiversity.  There are also sections on:

  • the soil itself
  • soils and society
  • soils and landscape
  • soil carbon and greenhouse gas flux
  • soils and land management
  • sustainable land use in relation to development
  • soils in climate change adaptation
To read the full report click here.

So what this highlights, is that although we have made progress in certain areas, there is still a load of stuff that we don't know.  A lot of previous research has looked at the physical and chemical characteristics of soil and managed to miss out the biological perspective. However what we now realise is that in order to manage soils in a sustainable manner which allows us to grow profitable crops that yield quality produce, we need to manage all three aspects of soil.  Neglecting the biology is like trying to dry washing in the rain, you'll get there eventually but its so much easier when the sun shines. To read about managing soil and FCCT's soil carbon project please click here.



08.06.15 Insecticides - new best practice advice from the Voluntary Initiative

The new insecticide advice highlights four foundations of best practice: identification of environmentally sensitive areas on the farm, following an integrated approach, using pest thresholds as a decision making tool for treatment, and ensuring treatment is made safely and accurately.  Following this advice alongside the Voluntary Initiative's Integrated Pest Management Plan (IPMP), or similar tools will help farmers and sprayer operators minimise  the environmental impacts of insecticides and safeguard the future use of plant protection products.

VI Chairman Richard Butler said 'I try to use insecticides only when absolutely necessary and will use the new VI insecticide guidance to minimise risk.  I also take account of advice from my agronomist and use these revised business thresholds for specific insect pests, which I find very helpful when deciding when it is necessary to spray.

David Ellerton from Hutchinsons praised the VI's insecticide advice: 'Following these simple guidelines will help the farmers and operators I work with to minimise the risks of their crops being affected by pests and helps give them the confidence to make the right decision about when to resort to the use of insecticides by checking thresholds.'

To find out more, download the Voluntary Initiative's guidance document 'Insecticides: Best Practice advice for farmers and operators.' Hard copies will be available at Cereals and the Highland Show.

Source: NFU

05.06.15 Greenhouse gas mitigation practices - England Farm Practices Survey

The information below comes from the recently released Greenhouse Gas mitigation practices - England Farm Practices Survey 2015.   Compiled by Defra and the Office for National Statistics the document contains the results from the February 2015 Farm Practices Survey which focused on practices relating to greenhouse gas mitigation.  

Where does the data come from?

The survey is usually run every year and collects information on a range of topics usually related to the impact of farming practices on the environment.  This release includes the results from the survey run in February 2015, which largely focussed on practices relating to greenhouse gas mitigation.  There was a range of topics covered including nutrient and manure management planning, the uptake of farm anaerobic digestion, fertiliser, manure and slurry spreading and storage, farm health planning and livestock breeding and feeding practices.

The results and data come from a questionnaire that was sent to approximately 6,000 holdings in England.  The sample was targeted by farm type and size, and the response rate was 44%.

Below I have highlighted some of the key points that (when I read it this morning) stood out to me.  If you want to read the full report please click here.

Nutrient management

If you have been a regular follower of some of the FCCT blogs you will be well aware of the fact that nutrient management planning is one of the keys to farm profitability.  Knowing crop requirements, and taking account all input sources to arrive with a balanced supply will not only help to target nutrient applications to crop growth and minimise over application (saving money), but also reduce the amount of nutrient that is sitting in the soil and not utilised (with the associated GHG emissions and pollution risk).


Manure and slurry storage and application

Calibrating fertiliser, manure and slurry spreaders can help to improve input efficiency and reduce GHG emissions.  How manures and slurries are stored and applied has an effect in the amount of nutrients that are available to the growing crop (thus saving you money on bagged fertiliser), and also affects the potential for GHG emissions and the release of ammonia  to the air. 


Grassland management

Grass is often described as 'the cheapest feed,' however the way that it is managed has a massive effect on its productivity and feed value.  Efficient grassland management hinges on how efficiently we convert the grass we grow into milk or meat (what we get paid for), and some of the methods that are often used are the inclusion of clover in temporary grass leys or the use of high sugar grasses.  When looking at the effect on GHG emissions, high sugar grasses improve the efficiency of animal production (this lowering the amount of GHG per unit of product, meat or milk), and clover will fix nitrogen from the atmosphere into the soil and be available for the growing crop.


Farmer attitudes to emissions and their importance

The data from this section looks at the importance that farmers place on greenhouse gas emissions when making decisions about their farms.  The data also shows which, if any, actions farmers are taking to reduce emissions and their motivations.  


For more information on this and to read the report please click here.



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