The scientifically-attuned readers of this journal will be well ahead of the general public in awareness and understanding of the human microbiome. This life-sustaining population of micro-organisms is something that each of us carries round in our gut, body cavities and urogential tract. But word is spreading thanks to emerging coverage by lay media, including the recent BBC Radio 4 Food Programme’s ‘That Gut Feeling‘, presented by the elegantly surnamed Dan Saladino [1].

Over the period 2008-2012, the Human Microbiome Project [2[1]] has “characterized the microbial communities found at several different sites on the human body. The project has examined the role of these microbes in human health and disease.

“Over 1,300 reference strains isolated from the human body have been sequenced. Three hundred healthy adults between the ages of 18 and 40 were sampled at five major body sites: oral cavity, nasal cavity, skin, gastrointestinal tract and urogenital tract.” Since completion, this great work has spawned a new generation of research exploring the obvious question, what next?

Meanwhile, in the plant and soil science community, scientists setting out on a similar quest to their human health pathfinders have established the Earth Microbiome Project ( bold ambition is “to characterize global microbial diversity for the benefit of the planet and mankind“, no less. The immense scale of this project is outlined in a TEDx talk by University of Chicago Professor Rick Stevens [3[2]].

Meanwhile, writing in The Scientist, specialist science author Amy Coombs has said, “Like humans, with their complement of microbes that aid in everything from immune responses to nutrition, plants rely on a vast array of bacteria and fungi for health and defense… but plant biologists are only beginning to scratch the surface…”

Even so, it is known that just one teaspoon of soil contains up to 50,000 species of micro-organism: bacteria, fungi, protozoa, nematodes, mites and microarthropods. On a larger scale, Prof Stevens calculates that 1kg of soil contains more microbes than there are stars in the entire known universe.The numbers are colossal: 1030 microbes in 1kg soil, which is 106 (i.e. one million) times more than 1024 stars. Slightly more down to earth here in the UK, soil scientist Dr Martin Wood of Earthcare Technical Ltd says the typical total quantity of microbial biomass is the same as 12 adult sheep per hectare.

Simplistically, the larger any locality’s soil microbiome, the healthier the soil; or perhaps the healthier the soil, the larger the microbiome. Either way, healthy soil is more productive that unhealthy. Aside from nutrient content, Dr Wood suggests parameters that determine soil health include organic matter content (>3.5% organic carbon), no capping, no compaction, earthworms (c.25 per spadeful), porous, aerated and moist not waterlogged, all of which create the conditions required for a healthy and vigorous microbiome.

Based on all this, a reasonable hypothesis is that, in parallel with growing awareness of the human microbiome’s value to lay people, the same will happen in farming and agri-science about the soil microbiome. Even today, despite our lack of knowledge, one certainty is that there will be no catch all solution.

More relevant is the approach made so successful by Sir Clive Woodward with his 2003 Rugby World Cup squad or Sir Dave Brailsford with Team GB and Team Sky in cycling. Respectively, these are summarised as one per cent improvements in 100 areas or the aggregation of multiple marginal gains. And herein lies the direct relevance for this journal’s readers who, of course, are connected directly with soil health via manures from the animals they medicate or feed.

Some such connections are already well understood, particularly associated with anthelmintic (wormer) treatments for grazing livestock. In only about 17 days, grazing cattle produce their own weight in dung; for sheep, the figure is about 25 days [5[2]]. Of course, dung pats and sheep droppings decompose over time and make a worthwhile contribution to soil organic matter and nutrient content. But without the action of an invaluable group of insects, the breakdown of dung on pasture would take much longer and grassland productivity would be much reduced. In fact, dung beetles can save the UK livestock industry, and individual farmers, serious money.

The UK has more than 40 native species of dung beetle, according to Pembrokeshire-based Dr Sarah Beynon, senior research associate of the University of Oxford [6[3]]. “By tunnelling and breeding within dung, feeding on it and burying it below ground, dung beetles play an essential role in its breakdown and decomposition,” she explains.

A healthy dung beetle population can create a long list of benefits to soil health and pasture productivity including:

  • Increased soil fertility and grassland productivity
  • Improved soil aeration and reduced compaction
  • Reduced pasture fouling and rejection, and therefore better grass utilisation
  • Less need to harrow and so time saved, with diesel use and tractor hours reduced

“Without dung beetles, faeces from just 12 cows would cover a hectare completely in one year,” Dr Beynon adds. She warns how dung beetle populations “appear to have decreased dramatically” in the UK, and that some wormers and other parasiticides can be toxic to them. “To ensure dung beetles continue working for our benefit, we must look after them,” she urges. “To protect dung beetle populations, only medicate animals with a level of parasite burden that justifies treatment.”

Still at the mucky end of livestock farming, there is also the spreading of stored manure and slurry. At face value, these can make a worthwhile contribution to soil nutrient and organic matter levels. But many samples of slurry in particular are far from benign, explains Liz Russell, a specialist in biological conditioning applications for agriculture at Envirosystems UK.

“Typically over the winter storage period, fibrous material will float to the surface and create a crust through with light and oxygen cannot penetrate,” she explains. “Below this, small particle solids form a sludge at the bottom, with a liquid portion above it. Anaerobic microbial activity creates acidic, septic and foul smelling conditions in both the liquid and sludge layers.

“Clearly, spreading this on farmland makes a beneficial contribution of plant nutrients and organic matter, but also innoculates soil with a high loading of anaerobic microbes washed into the ground in an acidic soup.”

To assess the impact of this, Envirosystems has been involved in a research project with Lancaster University. One aspect was a respirometry test to measure carbon dioxide production from soil samples as an indicator of its biome’s metabolic activity. Two different cattle manure slurries were added to soil samples and assessed. One was innoculated with a commercially available microbial and enzyme cocktail to stimulate aerobic respiration and oxygenation (label SB on the graphic), and the other untreated (label S).

The project report confirms a consistent increase was found in cumulative carbon dioxide concentration from soils across the experiment, consistent with respiration of carbon during the soil incubation, and that the highest respiratory activity was observed from inoculated slurry [7 ].

The research also conducted phospholipid fatty acid analysis (PLFA) as an indicator of microbe proliferation in the soil samples, also finding a higher level in soil treated with the inoculated slurry.

EnviroSystems UK’s involvement in this research was prompted by anecdotal reports from farmers about plentiful fresh pasture grass being ignored by hungry high yielding cows. Herd manager and ruminant specialist Dave Lievesley [8[1]] says, “it’s deeply frustrating to watch cows turned out onto fresh grass and not see them put their heads down to graze – and it’s not as unusual as you may think.

“What’s even more disconcerting is that it’s happening more on farms that take great pride in their grassland management and are used to growing bumper crops of grass. Yet successful farming is totally dependent upon the soil.

“It’s every farm’s biggest asset but for at least 40 years the importance of a farm’s soil profile has been ignored by the management practices that have been promoted to farmers.”

Lievesley believes a lot of metabolic issues that dairy cows now suffer are directly linked to shortcomings in soil biology that supports the grass and conserved forages they eat. On a number of farms, he credits biological aerobic slurry conditioning and a corresponding reduction in bagged nitrogen fertiliser with transforming pastures from “plenty but unpalatable” into “lush and irresistible” over a five year period.

Moreover, EnviroSystems UK managing director Liz Russell reports that biological conditioning prevents crust formation in slurry stores and helps create uniform consistency from surface to the bottom. “This means minimal stirring is required before spreading, reducing markedly the workload and fuel consumption involved,” she explains.

“Clearly, this reduces costs and helps improve the farm’s carbon footprint. However, over the long term, I’m convinced that the value of improving the soil microbiome will dwarf these more immediate gains.”

Of course, it could take at least a decade to prove this and publish the peer-reviewed evidence. Meanwhile, encouraged by Dave Lievesley’s evangelism, a steady trickle of farmers are conducting their own farm-scale trials in pursuit of one of Sir Dave Brailsford’s marginal gains.

They are also employing Second World War US Army General George S Patton’s strategy that a good plan executed now is better than waiting for a perfect plan to be ready [9[2]].

Green bedding questions and other options for dairy cow cubicles

From time to time, interest in the use of recycled manure solids (RMS) – ‘green bedding’ according to some – reappears in the dairy sector, not without controversy. For a balanced view, guidelines dated 18 December 2015 have been published by AHDB Dairy (website address at bottom of article).

In summary:

1) Wales – not allowed.

2) Scotland & England – allowed subject to defined procedures, including 14 legal requirements. Must comply with Red Tractor assurance, which includes a self-assessment of risk, an annual vet’s review (both using RT template), copies of both kept on farm for showing to RT assessor, and informing RT that RMS is being used3) RMS as bedding material continues to be under review and its conditions of use may change.

The stimulus, of course, is recurring interest in reducing costs while matching the strengths and overcoming weaknesses of other materials. Sand is popular for cow comfort and being inert and therefore inhospitable to mastitis pathogens, but not all slurry systems can cope with it.

Clearly, straw is readily available for anyone willing to pay the going rate, which flucuates markedly with supply and demand, but chopping consumes fuel and staff time. Even when chopped, straw is low absorbency. Wood shavings offer better absorbency, but are expensive. As long as sawdust has been screened to remove large splinters and even nails, it offers good comfort and moderate absorbency. Shredded paper has been tried in the past but suffers from high cost and low absorbency. Dried paper pulp blended for additional bulk with sawdust is gaining users for ‘blotting paper’ absorbency and good cow comfort.

Of course, all options demand a standard set of conditions: Store in a dry place, use plenty, keep clean and top up daily, and periodically clean out completely and start again with 100% fresh material.

RMS information source:

Written by.. Phil Christopher BSc Agric

Knowledge transfer assistant at EnviroSystems UK Ltd, developer of innovative biological conditioning applications for livestock farming.
Previously dairy herd manager, farm management consultant, press & publicity officer, PR contractor to vet-pharma and Agritrade companies.
Member of the Guild of Agricultural Journalists, Royal Association of British Dairy Farmers (RABDF), Linking Environment and Food (LEAF), National Sheep Association, British Grassland Society.
Owner and sole employee at Red Rock Publicity Ltd. Co-Owner and Marketing director at