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Soil and root microbiome: discovering the grapevines greatest weapon

Following a recent article in which I expressed concern regarding the lack of evidence-based practise at the core of biodynamic winemaking, I spoke with Keith Edward’s of Mise en abyme. We discussed in more detail what exactly I’d like to see result from the discussion sparked around the legitimacy of biodynamics. My answer was simple. I’d like to see the wine industry champion rigorous, evidence-based farming centred around maintaining healthy soils and fostering diverse, resilient ecosystems. Though still not throughly understood, it is commonly accepted that microbiome is essential in upholding the fabric of life. Our gut, mouth and skin each host their own unique microbiome community whilst healthy soil microbiome remains crucial for the growth and longevity of crops and wildlife. Nurturing this symbiotic relationship between a community of bacteria, archaea, viruses, fungi and protozoa is a core tenet of biodynamics. However, a number of studies have shown biodynamic preparations to be ineffective in improving soil health metrics. In this article, I explore microbiome in more detail and discuss working, evidence-based practises aimed at strengthening and diversifying soil microbiome.

The microbiome

Root microbiome is the diverse, dynamic community of microorganisms associated with plant roots. Plant roots provide unique environments for a diverse collection of soil microorganisms, including bacteriafungi and archaea. The microbial communities around the root and in the rhizosphere are distinct from each other and from the microbial communities of bulk soil, although there is some overlap in species composition. Research suggests that plants may, in fact, self-select their own microbial communities, different plants planted in the same soil only metres apart display entirely different microbial communities.

Beneficial soil microorganisms include bacteria which fix nitrogen and promote plant growth including mycorrhizal fungi, protozoa and certain biocontrol microorganisms. The mycorrhizal mutualistic association is an astonishing display of natures self-sufficient potential. The mycorrhizal relationship provides the fungus with nearly constant and direct access to carbohydrates, such as glucose and sucrose. The carbohydrates are translocated from their source to root tissue and on to the plant’s fungal partners. In return, the plant gains the benefits of the mycelium‘s higher absorptive capacity for water and mineral nutrients, partly because of the large surface area of fungal hypha, which is much longer and finer than plant root hairs, and partly because some such fungi can mobilise soil minerals unavailable to the plants’ roots. 

Poor microbiome (left) v robust microbiome (right)

Unaided plant roots may be unable to take up nutrients that are chemically or physically immobilised; examples include phosphate ions and micronutrients such as iron. Immobilisation can occur in soil with high clay content, or soils with a strongly basic pH. The mycelium of the mycorrhizal fungus can, however, access many such nutrient sources, and make them available to the plants they colonise. Immobilisation also occurs when nutrients are ‘locked up’ in organic matter that is slow to decay, such as wood. Some mycorrhizal fungi act directly as decay organisms, mobilising the nutrients and passing some onto the host plants.

Early research indicates that a strong, diverse root and soil microbiome is paramount to sustainable and rewarding agriculture. Until recent advances in sequencing technologies, root microbes were difficult to study due to high species diversity, thus understanding is in a stage of relative infancy. However, existing peer-reviewed research clearly indicates that healthy and diverse root and soil microbiome increases nutrient uptake, disease, drought and salinity resistance, resistance to toxicity and resistance to insects.

In summary, robust soil and root microbiome supercharge the plant’s natural ability to survive, prosper and yield quality fruit. This symbiotic relationship supports sustainability and longevity thus reducing the need for pervasive, costly and ongoing interference. For a rigorous exploration of available understanding and future direction of the role of soil microorganisms in plant mineral nutrition, Jacoby et al. have covered the topic in great detail.

Harming microbiome

Pessimistic estimates vary, the UN claims there to be around 60 years of harvests left whilst UK ministers have placed the figure at around 30-40 years. Much of this is sensationalism, soil experts agree that setting an end-point for agriculture is nigh on impossible and any estimates are likely unrealistic. That being said, most experts agree there are real threats to many agricultural soils around the world.

Reviews show that prolonged, intensive and indiscriminate use of agrochemicals adversely affects soil biodiversity, agricultural sustainability, and food safety, bringing in long-term harmful effects on nutritional security, human and animal health. Most of these agrochemicals negatively affect soil microbial functions and biochemical processes. The alteration in diversity and composition of the microbiome can be unfavourable to plant growth and development either by reducing nutrient availability or by increasing disease incidence.

In recent years, conscious farmers have ushered in a shift away from widespread, long-term and over-application of pesticides and herbicides. Studies have shown severe effects on soil ecology that may lead to alterations in, or the erosion of, beneficial plant probiotic soil microflora.

Industrial agriculture can be particularly troubles, mono-cropping, the practice of growing the same crop on the same plot of land, year after year, depletes the soil of nutrients, reduces organic matter in soil and can cause significant erosion. Mechanical tillage and the use of heavy farm equipment can cause both soil compaction and soil erosion. Soil compaction is often caused by heavy farm machinery and tilling when soils are too wet. Compaction leads to poor water absorption and poor aeration which further lead to stunted root growth in plants and smaller yields.

Erosion can be caused by many different factors, but poor soil management, including tilling, has been known to cause significant erosion over time, as can practices such as not planting cover crops in winter and not mulching. In a recent article, I discussed the efforts of Piedmontese farmers working to negate erosion. 

It’s all too easy to pontificate over ‘modern agriculture’, and to denounce it based beliefs of what ought to be. As Stephen Skelton MW points out ‘since the 1920s, the use of modern farming methods, machinery and improvements in planting material has vastly improved yields, thus lowering the price of food and increasing the availability, in both type and season, of what we eat. In 1960 we spent 17% of disposable income on food, today it is 9.5%.

This achievement is only a touch short of a miracle, many millions of people have been lifted out of absolute poverty over the last 8 decades and whilst one can certainly point to an array of unforeseen circumstances (long-term soil fertility being one) arbitrary moral relativism and blaming science is poor sportsmanship. Modern agriculture solved a profound humanitarian problem, sure there are practices which require review, but we ought to express more than a little humility pre-judgement for it can be argued our very existence and prosperity is in part owed to modern agriculture.

The failure of biodynamics

I’ll spend as little time as possible talking about biodynamics, given that I have already expressed my thoughts in great detail. However, in his brief rebuttal to my piece, Craig Camp mentioned soil microbiome a total of 8 times, it’s clear that this topic is at the heart of his affinity with biodynamics. Craig spoke of ‘the secrets of naturally building the microbiome‘ of how biodynamic preparations are intended to ‘rebuild soil microbiome‘ and of soil microbiome and mycorrhizae being the ‘hot topic of modern agri-science

There’s little debate about whether soil microbiome should be at the forefront of viticultural discussions, whether the topic is yield, grape quality, soil health or sustainability, microbiome appears to be the glue which holds it all together. But let’s be clear about one thing, if the aim of biodynamics, in any form, is to improve soil microbiome it fails miserably.

In summary, peer-reviewed research provides little evidence that biodynamic preparations improve soils, enhance microbes, increase crop quality or yields, or control pests or pathogens. Reviews also establish that the additional costs associated with formulating and applying the preparations represent an economic loss when compared to organic farming.

Studies found no significant differences between soils fertilized with preparations 500–508 vs non-biodynamic compost. Other studies confirm a lack of efficacy on soil fertility from preparations 500–507. Organic matter in organically treated soils has been shown to be higher than that in unmanured soils treated with biodynamic preparations 500–504. Similarly, studies reported enhanced soil life in organically managed fields compared with those under biodynamic management.


Studies observing the effect of biodynamic preparations 502–507, specifically meant for use on the compost, reported a consistently higher pile temperature and more nitrate in the finished compost using these preparations. In contrast, researchers have found that biodynamic preparations reduced both compost pile temperature and nitrate concentration. Craig entirely misunderstood the importance of these findings, it was not that I misunderstood the intention of the preparation it was to highlight that no consistent outcome was achieved.

Researchers have consistently found no differences in microbial activitybiomass, or fungal colonization in biodynamically treated soils compared with organically managed soils. A single report of greater dehydrogenase activity in biodynamically treated compost linked to greater microbial activity has been observed. When added to organically grown crops, biodynamic preparations have been uniformly ineffective. Compared with organically managed systems, additions of biodynamic preparations did not affect yields of cover cropsforage grasseslentilricespeltsunflower, or wheat

Based on both available literature and rational deduction it seems evident that any improvement in soil health observed under biodynamic farming ought to be attributed to the organic elements of biodynamics, increased time spent in the vineyard, self-selection and uncontrolled variables. If we are to take soil microbiome seriously we ought to stop romanticising pseudoscience and look to the established literature and serious work of scientists and farmers who have established practical, sensible methods to improve soil microbiome.

Practical farming for healthy soil microbiome

Opposed to seeking to discredit existing literature in the hope of future studies affirming a priori beliefs. Or seeking obscure, abstract reinforcements to support outdated, pseudoscientific beliefs it seems to be infinitely, and immediately, more beneficial to promote and share an understanding of practical, evidence-based solutions shown to reinvigorate and reinforce soil health.

Cover crop is a crop of a specific plant grown primarily for the benefit of the soil rather than the crop yield. Cover crops are commonly used to suppress weeds, manage soil erosion, help build and improve soil fertility and quality, and control diseases and pests. Cover crops are typically grasses or legumes but may be comprised of other green plants.


A meta-analysis of current research (60 field studies) up to 2019 show that cover cropping significantly increased parameters of soil microbial abundance, activity, and diversity by 27%, 22%, and 2.5% respectively, compared to those of bare fallow. Further research indicates that multi-mix treatments, as opposed to single-mix cover crop, are better at maintaining overall microbial composition and diversity. A plethora of literature has reinforced the importance of cover crop, not only in viticulture but in tree crops and other plant life.

Tillage is the agricultural preparation of soil by mechanical agitation of various types, such as digging, stirring, and overturning. There is a growing movement toward reduced or zero tillage in an effort to promote healthy, nutrient-rich fertile soils. In a three-year study, researchers demonstrated that tillage decisions played a major role in shaping microbial community structure, and in influencing additional environmental, ecological and agricultural soil parameters. Numerous other studies have demonstrated similar results. That being said causal mechanism is not well-established and the benefits of reduced tillage could be related to reduced compaction.

The most relevant human-induced causes of soil compaction in agriculture are the use of heavy machinery, tillage practice itself, inappropriate choice of tillage systems, as well as livestock trampling which all reduce pore space and aeration. Use of large and heavy machinery for agriculture often causes not only the topsoil but subsoil compaction. Compacted soil is economically damaging to farm business efficiency, as it results in reduced crop yield and increased fertiliser and energy input requirements. Several studies have also shown compacted soils to lack beneficial microbiology, particularly ectomycorrhiza, a form of symbiotic relationship that occurs between a fungal symbiont, or mycobiont, and the roots of various plant species. Less compacted soils have also been shown to be more resistant and resilient.


There are a number of ways to reduce soil compaction (covered in detail here) including but not limited to avoiding wheel traffic and tillage of wet soils, using wider tires, minimising tractor weight, maintaining the minimum tire pressure needed for acceptable tire life, avoiding using oversized equipment, and combining field operations to make fewer total passes.

Conventional agriculture may target plant pathogens through the use of pesticides/fungicides, with a potential side effect of reducing soil microbial community diversity and evenness. Whereas, organic agriculture may seek to control plant pathogens through competition and/or antagonism by utilizing treatments that promote a more diverse and even microbial community such as the addition of varying types of organic matter or more creative practises such as vine skirts. Further work has explored available research on practical farming practises and their effect on soil microbiome.


For plants to access recalcitrant soil-borne nutrients, they are dependent upon the metabolic activities of soil microbiota. Despite the experimental challenges, scientists argue that many important factors have been identified that will enable us to understand the mechanisms governing dynamic plant-microbe interactions. We know that although the soil is the major determinant of the microbial community associated with plant roots, plants have a significant effect on taxonomic assembly. Continued progress in our capability to collect and analyze exudates will be important for assessing the molecules plants use for communication with soil microbes, and also the pathways the microbes use to decrypt these signals.

This Post Has 24 Comments

  1. Stephen Skelton

    You write: “Reviews show that prolonged, intensive and indiscriminate use of agrochemicals adversely affects soil biodiversity, agricultural sustainability, and food safety, bringing in long-term harmful effects on nutritional security, human and animal health.” But “reviews” will also show that since the 1920s, the use of modern farming methods, machinery and improvements in planting material, has vastly improved yields, thus lowering the price of food and widenting the availability, in both type and season, of what we eat. In 1960 we spent 17% of disposable income on food. Today it is 9.5%. I have worked in farming since 1971, and know farms who use large machinery, cultivate their soils, use fertilsers, pesticides and herbicides, and make a living out of their land, and whose land, despite all these practices which “adversely affect” the land, still keeps delivering AND shoiws no signs of suffering the “harmfull effects” that “reviews” talk about. Just saying – modern farming is not all bad news.

    1. wordonthegrapevine

      I actually entirely agree, originally I had written a paragraph in the piece which defended modern agriculture and science, given its fundamental role in alleviating the hunger of many millions of people, however, I deleted it last minute, perhaps I should have left it in upon reflection,

  2. Stephen Skelton

    I wasnt attacking your views, just hoping to get some comments from those who are always attacking modern farming, without having any practical experience of it.

    1. wordonthegrapevine

      I’m going to reinsert my original paragraph defending modern agriculture and quote you, I think it’s important my personal opinion is obvious. I entirely agree with you on the topic of modern farming, whilst there have been some unforeseen consequences, what it has achieved is difficult to even comprehend in the context of human prosperity.

  3. Thomas Molitor

    Hi Joshua,

    First time blogging on your site. Part of a vineyard’s biome, of course, are viruses. I’m working on an article on the Serine/Syrah grape from Cote-Roti. Jean-Michel Boursiquot, one of the preeminent French ampleographers, said he thought that Serine was in fact Syrah that had been affected by a certain set of viruses, which was responsible both for its putative defects but also for its originality and excellence.

    Sometimes a winegrower removes some of the original genius characteristics along with the problematic traits. In other words, the virus is the treasure.

    1. wordonthegrapevine

      Thanks for checking my blog out, Thomas, really appreciate it. Great points about pathogens, the extent of the symbiotic relationship in soils is fascinating, I’m looking forward to doing more work on the topic. Please do share your work with me when it’s complete, I’d love to read it.

  4. wordonthegrapevine

    I would recommend you read my piece on biodynamics, I’ve included a relatively comprehensive literature review. I don’t have the time to debate BD back and forth, it gets boring because I never hear anything other than anecdote. The current science is clear, BD preperations are ineffective. Until somebody can prove otherwise, people’s stories won’t change my mind unfortunately.

    Many of the best winemakers are also not interested in biodynamics, so quoting winemakers who are biodynamic doesn’t indicate any efficacy of biodynamics, that’s a misnomer.

    You’re welcome to share any studies you’d like to share.

  5. Thomas Molitor

    I did read Pam Strayer’s postings but the postings have disappeared. I have no previous knowledge of BD so I don’t “have a dog in the fight” as we say here in the States. The profile I’m working is a very famous vintner here in the States and I posed the question of BD to him, and he replied, “I studied BD for several years, was in a group with Mike Benziger and Alan York, and I’m a believer in the efficacy of BD. I don’t, however, think one can make a scientific case for it, but, as its adherents (correctly) claim, the vines are healthier and the wines are imbued with more life force.”

    He goes on tho say, “I would disagree with the contention that BD does not positively effect the microbiome. There have been studies that have shown BD enhances microbial complexity in soils – both in diversity and in actual number of species.”

    He ended, by saying, it’s expensive to do BD farming and my pocketbook no longer has the luxury to do so.

    1. wordonthegrapevine

      I can’t spend all of my time debating people’s personal opinion on biodynamics, I’d be here all day. Instead, I roll with the science, and that’s very clear as it stands currenrly, BD preparations alone are ineffective, it appears much more likely that the organic elements are what benefit the soil, along with other practical regenerative farming method.

      It’s an oxymoron to believe something is effective but to not be able to make a scientific case for it, then to say there are studies which show it’s effective.

      There are shit biodynamic wines and great biodynamic wines, it’s not a panacea. It’s disingenuous to say wines made under biodynamics are simply better because they’re biodynamic, not true at all.

      I’ve included a literature review in my biodynamics piece, I’ll stand by that until there’s evidence to the contrary.

  6. Thomas Molitor

    “The wines are imbued with more life force.” How can you scientifically measure that? On the palate side with wine, we’re talking about subjective taste. On the scientific side, I am reminded of Linus Pauling who went to his grave vehemently defending the health efficacy of Vitamin C. But my microbiologist buddies say, “Where’s the data?”

    As to Strayer’s assertion regarding the Tablas Creek experiment, “after blind tasting of grapes” the BD grapes were clearly “better tasting,” – again my microbiologist buddies would say, “Where’s the data?”

    1. wordonthegrapevine

      You can’t measure it because it means nothing, to one person ‘life force’ simply translates to nothing, it’s a subjective anecdotal position. But the reality is there are MANY bad biodynamic wines and many good, so it’s simply not true that biodynamics makes wines better independent of other variable.

      His anecdotal tasting experiment is all well and good, but that’s his experience, not reflective of the bigger picture, as I have already pointed out, there are many bad biodynamic wines, so it’s likely numerous other variables control quality, not BD preperations.

      BD is a romantic notion but not one which is effective in any objective sense of the word.

  7. Dan Perrelli

    Are you familiar with Champagne de Sousa Mycorhize Blanc de Blancs? My understanding is that about 1200 bottles are produced annually from a small plot of Chardonnay ‘infected’ by a particular root fungus. In general practice, when the fungus can’t be eradicated, producers have replanted. The flavor profile of this BdB is very savory, not typical. I love it.

  8. Thomas Molitor

    Hey, Dan, thanks for the post referencing Champagne de Sousa Mycorhize Blanc de Blancs. Never had the wine but now am intrigued to do so. I’m working on a profile of a vintner who incorporates Mycorrhiza practices in his vineyards.

    Mycorrhiza is a symbiotic association between a fungus and a plant. The plant (in the vintner’s case “the rootstock”) produces sugars by photosynthesis and supplies them to fungus, and the fungus supplies the rootstock water and mineral nutrients, such as phosphorus, taken from the soil. The aim is to bump up the expression of terroir relative to the grape variety.

  9. Thomas Molitor

    My understanding is vinifera is unable to suck up minerals (apart from potassium) so is dependent on Mycorrhiza for transfer of minerals. Biochar, non use of fungicide, helpful for Mycorrhiza proliferation. A healthy microbial population supports expression of terroir.

  10. Pam

    This is a study that found micorrhizal fungi decreased 53% with the use of herbicide in vineyards.

    The lovely grower champagnes by Champagne de Souza inculding the one mentioned above, were all featured at the 2018 International Biodynamic Wine Conference in San Francisco (which I ran for Demeter USA).

    I am always amazed at how affordable the fabulous Champagne wines from this and other growers are. Terroir champagne is the way to go! And Caroline Henry’s book Terroir Champagne is a great guide to the territory.

  11. Pam

    Also if you read the wonderful new book by Merlin Sheldrake on fungi – Entangled Lives – you will learn that plants used fungi for thousands of years as roots until plants grew roots of their own, so their symbiotic relationship is long lived indeed.

  12. Jake

    A general comment: As a current grower in Napa, I see the whole spectrum of farming including conventional, dry farmed, organic, and biodynamic. From my experience, I think farming responsibly and improving the overall health of ones vineyard/soils is finding that happy medium between all of these methods. We drive our farming decisions and practices by our own data collection and the scientific community.

    What I often see is ranches “pigeon holing” themselves into farming one way or another, rather then taking the best of each method and using them in a practical way.

    For example:

    1. I often see what I would consider “over-tillage” in organic and dry farming because such managers have very few options for weed management, so how good is this for soil health (as well as release of sequestered carbon)?

    2. Additionally, having to apply organic fungicides (sulfur) every 7 days leads to increased soil compaction.

    3. Often times, certified organic pesticides are not targeted/specific, often resulting in the killing off of pests AND beneficials.

    So I would argue that there are farming practices that are detrimental to vineyard and soil health in ALL philosophies of farming, not just conventional. I think you have to look at the best available tools available and use them to create a sustainable system (both above and below the soil). As a current example. with the pushback we are getting from the wine industry in general about the use of herbicides, my farming company has began assessing seeding grass/insectary blends UNDERVINE as a way to mitigate weeds, provide a habitat for beneficial insects, increase biodiversity, reduce tillage, and hopefully improve soil health.

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