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Beneath Our Feet

The Marvel of Soil Biodiversity

By Leo M. Condron, Professor of Biogeochemistry, Lincoln University, Canterbury, New Zealand

This article appears in the Autumn 2017 issue of New Zealand Turf Management Journal

We have been granted permission to share this article in full.

Click the image on the left to view the full article. Tags: 

Illustrating Soil Life

Image by: Katelyn Weel

By Katelyn Weel, artist, Gransherad, Norway



I first discovered the beauty and elegance of microscopic creatures as a student of Environmental Sustainability at Lakehead University in Orillia, Ontario.  During my studies,  I  worked as a research assistant analyzing protozoa and diatoms in natural freshwater biofilms.

In 2013 I left Canada and started working at VitalAnalyse in Norway, where I observed soil in the microscope and started learning about soil life as it applies to agriculture. Despite having studied environmental sustainability for four years, until I started this work I really had no idea about what was going on in the soil. Once I started to learn just how complex and intricate below ground ecosystems are and how little we really know about them, I developed a much greater appreciation for soil, and I started to see the need for a very different approach to agriculture.

In my role at VitalAnalyse, I occasionally help lead public workshops, seminars, and demonstrations about life in the soil. During these events, I have noticed that the smallest things most people can easily relate to are usually mites or springtails that can be seen with the naked eye. If it requires a microscope, it starts to feel abstract. Even solid and detailed images taken from scanning electron microscopes are clinical looking, alien, out of context, or simply too “sciency” for most non-academics to connect with. If only we could take pictures of rotifers, protozoa, and bacteria in their natural habitat with regular cameras, to simply observe them as we would any other animal with our own eyes.

I decided to try using my imagination and my experience with the microscope to illustrate what it might look like if we could simply shrink down and observe rotifers, flagellates, ciliates, and other soil organisms face to face in their natural habitat.

In each drawing, I aim to demonstrate some of the complexity and diversity of soil ecosystems, including small details you might not notice at first glance, such as tiny flagellates, bacteria, or threads of fungi in the background. I want to illustrate the organisms in a way that they are both realistic and beautiful, and to draw the viewer into the mysterious world beneath us.

Image by: Katelyn Weel

Testate amoeba
Image by: Katelyn Weel

The drawings have been well received here in Norway. I’ve realized that there is a lack of illustrations like this in our field, so I am reaching out to let more people know that these drawings exist, and I’d love to do more.

My gallery of soil life illustrations can be found here. There are more drawings in progress, and the site will be updated as I continue adding to the collection. I hope that my artwork can help more people connect with soil biology, and bring them a little closer to the invisible and underappreciated world of microbiology that is so important to our everyday lives.


Chasing rabbits: How do soil communities respond to herbivore mammals? Part II

Rene van der Wal, ecologist at University of Aberdeen,
surveys the plant community on Isle of May.
Photo by: Walter Andriuzzi

By Walter Andriuzzi, Postdoctoral Fellow, Colorado State University


In the previous post I described how herbivore mammals, from rabbits to cattle, can affect the soil food web, and how difficult it is to find general patterns across different places. Here I summarize what we found in a meta-analysis of field studies that had compared soil communities inside and outside exclosures (plots of land that were fenced to keep herbivores out).

First, the effects of herbivores depend on climate. For example, soil respiration rate is lower with herbivores than without in subarctic ecosystems, whereas in temperate ecosystems it is higher with herbivores than without. Second, the effects of herbivores vary between trophic groups in the soil food web, and between soil biological functions. For example, unlike respiration, soil microbial biomass and nitrogen mineralization rate do not respond consistently to herbivores in either climate type, whereas they both tend to decline when herbivores are present under arid climates. In subarctic sites, root-feeding nematodes are negatively affected by herbivores, whereas predatory nematodes appear to do just as fine.

Third, the effects of herbivores vary also within trophic groups in the soil food web. Take for example two of the most widespread and abundant groups of soil animal decomposers, oribatid mites and springtails: the former decrease in abundance when herbivores are present, whereas the latter do not show a consistent response. Fourth, the effects of herbivores depend on the herbivore species, in a way that can be at least partly predicted based on their body size: the smaller the herbivore, the more likely its effects on the soil organisms to be neutral, or even positive (that is, increasing biological activity or abundance of soil organisms); the larger the herbivore, the more negative its effects tend to be.

How do our results compare with previous theory? An established framework predicts that herbivore presence has positive effects in the highly productive systems, and negative effects in poorly productive systems. However, the results of our meta-analysis support these predictions only in part. Herbivores have negative effects in low productivity biomes, for example in tundra, but most highly productive systems also exhibited negative effects of herbivory on belowground communities. The big exception was soil respiration in temperate grassland. Moreover, we found that climate is more important than vegetation type; and that herbivore identity and body size are also important.

In our meta-analysis, we did observe that responses tend to shift to negative with increasing body size, and an explanation may well be physical disturbance. A more recent framework of belowground responses to herbivory focused on the role of large herbivores on soil compaction. In fine-textured soils, trampling by cows reduces soil pore size and limits oxygen and/or water availability, leading to declines in mineralization rates. We could not test the importance of soil texture in our meta-analysis, because too few of the available studies quantified it rigorously.

Conceptual model of how herbivore size and climate determine
the effect of herbivores on the soil community.
Modified from Andriuzzi & Wall 2017

Based on our results we developed a conceptual diagram which partly integrates those previous frameworks, by envisioning gradients of herbivore body size and/or climate limitations. Small herbivores, for example the rabbits on the Isle of May, may have limited effects on soil biological activity, or even enhance it by fuelling the soil food web with their excreta and/or more palatable plant resources. Large herbivores, for example cattle (especially if at high density), may lead to physical disturbance such as compaction (because of trampling) and exposure of soil to erosion and atmospheric agents (because of great reduction of plant cover) so the net response belowground is negative. Likewise, with a temperate climate herbivore presence could promote soil biological activity, though not to a great extent if the system is productive enough (as likely was the case on the Isle of May). In ecosystems more limited by aridity, cold, etc., herbivore presence begets the opposite response due to its physical effects on soil. All this is a simplification - different groups of soil organisms may not respond in the same way – but it offers a mechanistic framework to make sense of our findings, and to generate new hypotheses to test.

There are several areas with limited data that challenge the applicability of our general frame work.  There were very few studies from the tropics that we could include in the meta-analysis. As a result, while we know a good deal on the effects of reindeer on soil organisms in subarctic tundra, we know next to nothing on those of elephants and impalas in African savannah. Another major surprise was how little some major groups of soil organisms have featured in herbivore exclusion experiments. Protists, which are essential in the soil food web, are lacking altogether from the meta-analysis; earthworms, which have huge effects on soil and plants, were also poorly represented. I hope that our meta-analysis will spur new research to understand how herbivores change their ecosystems not only aboveground, but also belowground.


Chasing rabbits: How do soil communities respond to herbivores? Part I

Terror of the undergrowth:
A young rabbit on the Isle of May.
Photo by: Walter Andriuzzi

By Walter Andriuzzi, Postdoctoral Fellow, Colorado State University


June 2011. I am standing near the edge of a vertical cliff above the Atlantic Ocean. Two puffins glide and land gracefully on the rocks despite their almost comically short wings. I am on the Isle of May, a wind-swept Scottish island with some of the biggest colonies of marine birds in Europe. Not far from the guano-streaked cliff there is a small plot of land enclosed by a fence. This is an exclosure, and its task is to keep out the rabbits that graze the vegetation on the island with the efficiency of a lawnmower. The grass outside, punctuated by cushions of forbs like Silene uniflora and Armeria maritina, is ankle-high; inside, the grass brushes my knees. And this is not the only difference. Outside the exclosures, the ground is littered with rabbit faeces, which fertilizes the soil. The plants grazed by the rabbits undergo changes in their chemical make-up, and tend to release more carbon into soil as root exudates. The rabbits also change the environment physically: with a reduced plant cover, the ground is more exposed to atmospheric fluctuations; and of course, rabbits make burrows. Unsurprisingly, excluding rabbits is a big deal for the plants. But what happens belowground?

This is a question that ecologists Richard Bardgett and Rene van der Wal have investigated since the early 2000s. They set up these exclosures on the Isle of May to test the idea that the effects of herbivores on a soil biological community depend on the fertility of the system. The Isle of May is an ideal natural laboratory to test this framework, because it has two levels of soil fertility: near the seabird colonies the soil is enriched in nitrogen of marine origin (courtesy of the birds’ guano and ammonia), whereas in the middle of the island it is not. And yet, three years after the exclosures had been established, rabbits had the same (weak) effects on the soil food web regardless of whether the plots were close to the coast or not.

In 2011, as a master’s student of van der Wal, I seek to find out if things have changed eight years since the experiment started. As a proxy for the soil food web, I study the nematodes, microscopic roundworms that live in the water films between soil particles. They occupy almost all trophic levels belowground: there are nematodes that feed on bacteria, nematodes that feed on fungi, nematodes that feed on microalgae, nematodes that feed on plant roots, and nematodes that feed on nematodes. Because they are so diverse and extremely abundant, they have a big impact on ecosystem functioning; in turn, of course, they are affected by what happens to the plants and the soil where they live. And yet, once again we find only small differences in the soil food web inside and outside the exclosures, despite obvious differences in plant biomass and plant diversity.

One of the exclosures on the Isle of May.
Photo by: Walter Andriuzzi

The difference between what happens above and below ground is in no way peculiar to this experiment. Many other studies found surprisingly weak effects of herbivore mammals on soil fauna and microbes. Other studies found big effects, but not in a consistent direction: in some herbivores increased the abundance of soil organisms or the rate of soil biological processes, while in others the opposite was observed. In an attempt to better understand general patterns in belowground responses to herbivory, I recently performed a meta-analysis, an analysis of results from numerous previous studies, on herbivore-plants-soil interactions to find global commonalities in how soil organisms and the biological processes they regulate respond to herbivores. Stay tuned for the next post to discover what I found out!


Belowground visions of life: Soil makes Art: exhibition and mural in April 2017

A handsome mite.
Image by: Ed Reynolds

By: Dr Tancredi Caruso, School of Biological Sciences and Institute for Global Food Security, Queen’s University of Belfast


In the past, worldwide and across cultures people knew that soil plays a critical role in supporting our life cycle. In modern urban environments, too many still think that soil is just dirt. Ed Reynolds, an artist supported by the Leverhulme Trust, and I (a soil ecologist) will be trying to overturn that view to show the kaleidoscopic beauty of the biological universe called soil. We believe that art is the key to make people aware of the beauty and importance of soil biodiversity in our life. We will soon exhibit our work in Belfast: on 1st and 22nd of April 2017 we will have two events taking place respectively at the Ulster Museum and the Girdwood Hub in Belfast, Northern Ireland. Meanwhile, the project has also illustrated Soil and War, a chapter from Richard Bardgett’s book Earth Matters (Oxford University Press): you can read more about that here.

Emerald springtail
Image by: Ed Reynolds

Soil biodiversity is vital to humans!
Image by: Ed Reynolds

The project will have a conclusive mural event: Northern Ireland murals have become iconic, reflecting local cultures and history, but very often also the divisions caused by the Northern Ireland conflict (also known as the Troubles). Especially in Derry and Belfast, the last decade has seen the replacement of sectarian murals with new murals that aim to rebuild deteriorating relationship across communities. Here, we aim to rebuild the deteriorating relationship between humans and soil, and for this reason we have decided to realise a mural in the middle of Belfast: we want to offer an artistic vision of soil to deliver a message of peace to all cultures in the world. A workshop with children from various backgrounds will take place in April (exact date yet to be decided) and the mural will then be painted. The walls have been identified, and details will follow soon: in the next post, we will show you the mural idea...stay tuned!

Transformation of beetle larvae
Image by: Ed Reynolds


The supply of Soil Functions in European Soils

By: Rachel Creamer (Wageningen University, Netherlands) and Francesca Bampa (Teagasc, Ireland)

Why do our Soils matter?

Visualization of Sustainable Development Goals with
ecosystem functions supporting all goals.
Credit: Azote Images for Stockholm Resilience Centre

The Sustainable Development Goals were established in 2015 by the United Nations to to end poverty, protect the planet, and ensure prosperity for all. There are 17 goals in total and each goal has targets to be reached over the next 15 years. Recently the Sustainable Development Goals were rearranged by the Stockholm Resilience Centre to highlight the importance of soil, land, water and climate as they underpin all the remaining development goals. Soil is essential for society as a whole, as it provides us with our food, raw materials for fuel, clothing, as well as an environment in which we can flourish as a cultural society.

Soil is specifically mentioned in four of the 17 Goals only, these include; No. 2 dedicated to Zero Hunger in the World, No. 3 on Good Health and Well-being, No. 12 on Sustainable Production and Consumption and No. 15 Life on Land. While soil was not considered in the original text of the goal No. 13 Climate Action, the agreements made at the Paris Climate COP 21, in November 2015 highlighted the role of soils in Climate Action as well, in particular for carbon sequestration.  

In Europe, there has traditionally been a focus on soil functions and threats, rather than soil health. In 2006, the Thematic Strategy for Soil Protection was developed looking at the role of soils in society. This document highlighted the main soil threats (compaction, erosion, salinity, acidification, landslides, loss of biodiversity, sealing, decline in organic matter and contamination) and also the positive message of the functions that soil supplies to society (substrate for plant growth, habitat for biodiversity, nutrient cycling, carbon sequestration and cycling, water quality and regulation, platform for infrastructure and store for archaeology). Following the Soil Strategy, a European Legislation was developed looking at minimising the threats to soils and enhancing soil protection. This was named The Soil Framework Directive. However, this Directive was never accepted by all member states, with the focus on soil threats and was removed from policy discussions in 2014.

Therefore, the approach now is to look at the role of soils from a positive perspective and show what soils can do for us as a society and how we can sustainably manage this precious resource. 

What do we want from our soils?

We must first decide what are the main soil functions that we want the soil to deliver? In an agricultural context, this is primarily to provide food, fibre and fuel – whether that is cereals, beef, milk, biomass crops, or wood etc. However, in the production of food, we must also ensure that we do not diminish the capacity of the soil to also carry out the other soil functions necessary to ensure sustainable food production. This dual optimisation of both agricultural supply and the capacity of the soil to meet environmental requirements can be at times challenging.

Soil provides many functions including clean water,
agricultural production, biodiversity, and nutrient cycling.
Credit: Schulte et al. 2014

What do we mean by soil functions? In agricultural systems, we consider the following functions that the soil supplies:

  1. Primary productivity - providing maintenance for the growth of food. feed and fibre, this includes; root support, water and air through the soil structure.
  2. Cycling of external nutrients – capacity of a soil to absorb and store and slowly release nutrients to crops over time.
  3. Water purification – ability of a soil to remove excess nutrients and pollutants from water before it reaches the water source.
  4. Carbon storage and cycling – capture and cycling of carbon sources from the atmosphere and plants, that carbon then provides strength to the soil structure and nutrient reserve.
  5. Biological habitat – provides a home to the largest diversity of biological organisms on the planet. These soil organisms drive most of the processes that take place in soil.


Managing our soils lives at the heart of farming systems. So understanding what functions our soils are best at delivering is essential to get the best from our land. While all soils are capable of delivering on all functions, some soils are better than others at specific soil functions. That is traditionally how we decided where to grow which crops, which areas to leave to nature and which soils are suited more grassed based or forest land use types.


Managing our soils across a range of scales

Every day, farmers make decisions on how they manage their land and soil, including decisions on fertilisation, ploughing, reseeding, weight of tractors, application of pesticides, herbicides and insecticides, etc. At the same time, national and European policy makers make long-term decisions on how to manage their soil resources at larger scales, such as how to work towards meeting greenhouse gas emission targets through optimising carbon sequestration in soils.

Therefore, the contemporary challenge for researchers and stakeholders is to link the decision making on land management across scales, so that the practicalities of how farmers make decisions on a daily basis is reflected in policy formation.

We cannot expect all soil functions to be delivered simultaneously to optimal capacity, but with careful decision making we can optimise our soils to provide multiple functions. In reality not all functions can be optimised to their full capacity at the same time, as the conditions required to deliver one function may be in contrast to those to deliver another function. A good example of this, is the requirement for nutrient cycling which may compete with the with the ability of the soil to support the function habitat for biodiversity, where external inputs include sewage sludge derived materials, which can have a significant impact on the soil biology. However, in many cases multiple functions can work in synergy together and in most scenarios three out of five soil functions can be optimised together.

European landscapes, Top: Terraced fields, credit: Rusu Teodor, USAMV Cluj
Lower left: Agricultural field, credit: Eckhard Pieper, LWK Niedersachsen
Lower right: Irish Soil Information System project (Teagasc, Ireland)

Mapping and Assessing Ecosystem Services:

In addition to the soil functions approach, there is an increasing focus on mapping and assessing soil based ecosystem services. The Food and Agriculture Organisation of the United Nations (FAO) defines soil based ecosystem services as; “Ecosystem services are a way of putting a value on biodiversity by looking at what it does and how we value the function that the soil performs”.

MAES (Mapping and Assessing Ecosystem Services) is part of the Action 5 deliverable of the Biodiversity Strategy. The Directorate General for the Environment of the European Commission are currently in a process of developing guidelines for the mapping and assessing of soil ecosystem services. These guidelines will be provided to Member States within Europe, who will be asked to identify and map the soil ecosystem services within their country.


What the future holds for soils in Europe

While there is no current legislation for the protection of soils in Europe, there is certainly increasing recognition of the role of soils in society. There is a lot of on-going research which is identifying the role of soil functions and how we can optimise the supply of these functions in a sustainable manner. One such project is the LANDMARK project, funded by the Horizon 2020 European Research Funding. This includes representative scientists, advisors, land managers, and policy makers from across Europe, China and Brazil. This project is looking at the role of soil functions at three different scales:

  1. Local scale – to help farmers optimise the soil multi-functionality on their farms
  2. Regional scale – to identify how soil functions vary across the different climatic zones of Europe and how we measure soil functions.
  3. An assessment of policies that can ensure that we ‘make the most of our land’, from both an agronomic and environmental point of view at a global scale.


For more information on LANDMARK see:


The choice of agricultural landscape has an influence on crop (and soil) health

A young pistachio orchard (foreground) in a larger
maize cropping system on the banks of the
Orange River, Prieska, South Africa.

By Prof. Schalk vdM. Louw, Centre for Plant Health Management, University of the Free State, Bloemfontein, South Africa.

This article appeared previously in the Ons Eie magazine, April 2007


Agricultural landscapes are by implication complex adaptive systems, tailored by anthropogenic interference. The relationship between structure and function, e.g. trophic structures, diversity - productivity connections and nutrient fluctuation patterns of such landscapes is fundamental in their organization, whether self-driven or regulated. In cropping system landscapes, we are obligated to understand the processes that influence the abundance, richness and diversity of biota that impact on plant health and ultimately crop yield.

Crop health management therefore requires that, amongst others, an understanding is developed on how the architecture of landscapes influences pest population dynamics and their interaction with the surrounding environment, natural enemies and agents of control. Agricultural landscapes, on whatever scale, implies habitat fragmentation to a lesser or larger degree and we need to understand the implication of such events with regard to ecosystem processes.

Understanding the processes which drive agricultural landscapes, especially in semi-arid regions, is a prerequisite towards analysing patterns, which in turn lead to sound policy and management decisions. This article therefore makes the point that, in general, crop system analysis in the context of diverse agricultural landscapes across South Africa is lacking and needs to be addressed. The main research question derived from this, in turn, is in which manner spatial (i.e. shape, size and structure) and temporal (i.e. seasonality) features of agricultural landscapes and the crop value chains emanating from them, link to the population dynamics and trophic structure of insects and other biotic agents.

Understanding the population dynamics and trophic structure of insects in crop agroecosystems is vital in the sustainable management of such systems. However, this would be an incomplete picture of the actual scenario, should the diversity, identity and architecture of the particular landscape within which these systems fall not be taken into consideration. Bring into the equation the fact that agricultural landscapes are always under the pressure of anthropogenic influences at different scales and the issues suddenly become intricate. What follows below is a breakdown of the array of direct and indirect factors that influence the identity of agricultural landscapes within which crops are cultivated and which have a bearing on their value to the farmer/producer and ultimately the end-user.


A holistic approach

Fundamental would be that the management of landscapes influenced by humans be geared towards the enhancement of biodiversity and ecosystem function. This must be regarded in the context that agricultural landscapes in an area unavoidably result in fragmented habitats, which, in turn, are the drivers of complex localized processes and community structures. Biodiversity, as such, is an organizing principle in agroecosystem management, since it determines the degree of relative stability in a disturbed environment. Landscapes planning should therefore protect and enhance biodiversity and support ecosystem processes of succession, energy flow, and hydrological and nutrient cycling. In this context gaps should be bridged between agricultural policy, land-use and biodiversity indices. A further objective   should be a marriage between the approaches of social scientists and ecologists when providing relevant advice.

Space and time are basic entities in ecosystem analysis. Thus, analysing landscapes and their biotic inhabitants in terms of spatial and temporal dynamics is crucial in providing an informed perspective. In this context landscapes patterns arise which originate from exogenous (e.g. climate) and endogenous (e.g. competition) processes and feedbacks.

A holistic approach to investigations of this nature is always a strong recommendation, since it provides insight into system self-organization. Any deviation, which is out of sync with the optimal functioning of the system, is an interference which could jeopardize sustainability. In harsher, semi-arid regions this could have far reaching effects with regard to establishing new/underutilised crops which are required to address different utilisation commodity groups.


Porosphere soil from a wheat field, western
Free State province, South Africa.

Landscape fragmentation and insect population dynamics

There are implications of insect populations in habitat fragments. In such a scenario the sequence of events are: crop cultivation > natural habitat destruction > sharply contrasted habitat mosaics > threat to biodiversity > collapse of trophic structures. The implication of such a scenario is that populations of beneficial insects collapse, whilst detrimental / pest insects are boosted. In other words, fragmentation sensitive species could be influenced in terms of trophic position, population dynamics variability and vagility. There are also further ramifications that relate to pure habitat loss, fragment size and shape, fragment isolation, fragment quality, edge effect and landscape structure.

A further crucial landscape ecology issue exists in terms of the temporal frameworks link for above ground – below ground multifunctional linkages between organisms. This is not only an important barometer for soil health and ultimately crop health, but also for microbial-insect-plant interactions. Interaction strength levels, on the whole, matter very much in landscapes and determine their complexity. Overall the specific biome and regional setting of a particular landscape is the ultimate determining factor of soil and crop health integrity.

In fragmented landscapes habitat edge effects (i.e. greater species richness and abundance in the transitional zone between habitats than in the habitats themselves) also reveal interpretive complications and may be the foremost explanation of many of the negative effects arising from fragmented habitats. One such negative effect is that habitat edges can serve as ecological traps, whereby an anthropogenic change in an organism’s environment leads individuals to use misleading cues of habitat quality. Specifically the size and internal habitat of a fragmented patch and its relationship with ‘edge effect’ needs further investigation.  Fragmentation affects populations along a number of routes that relate toedge effect, i.e. area identity, degree of isolation and area age.


Soil quality and the role of bioindicators

Another important factor in agricultural landscapes is soil quality. Insect herbivory, as part of the trophic structure of a particular landscape, increases litter quality and decomposition indices and as such influences ecosystem nutrient cycling and accelerates the production of soil organic matter. It also acts as a persistent control mechanism for ecosystem processes.

If bioindicators can be identified in a system in this context and used to indicate disturbances in an environment, the relevance emanating from this could be significant.  In terms of sound management strategies, analysing insect structures in heterogeneous environments (landscapes) to determine optimal diversification in systems, can act as an important guidance towards establishing environmentally acceptable pest management strategies.



Ecosystem services are the benefits that humans (society) obtain from ecosystems. Agricultural landscapes and their soils also provide multiple ecosystem services, the successful management of which depends on the recognition of the relationships between the processes and the structures that maintain a healthy system. Although science continuously yields new environmentally friendly agricultural practices and techniques, the sustainable development of a system will ultimately depend on a farmer’s ability to understand and utilize these advances.


For more on soil health in South Africa and the Soil Ecosystem Research Group (SERG) go to


Plant diversity speeds-up belowground recovery

By Ryan Klopf (Virginia Dept. Conservation and Recreation), Sara Baer (Southern Illinois University Carbondale), Elizabeth Bach (Colorado State University), and Johan Six (Swiss Federal Institute of Technology)


“Prairie was, in fact, a community of plants and animals so organized as to build, through the centuries, the rich soil which now feeds us.”  -Aldo Leopold, Prairie: The Forgotten Flora (1942)*

Tallgrass prairie restorations planted with high plant diversity (left) and low plant diversity (right)
Photo credit: Ryan Klopf

The tallgrass prairie of the U.S. Midwest is one of the most endangered ecosystems in the world, with >99% of the ecosystem converted to cultivation in some states.  Restoring farmland in the Midwest back to tallgrass prairie has been of public interest since the days of Aldo Leopold.  Much of this restoration work, however, has focused on reconstructing native plant communities with the assumption that animals and ecosystem functions will follow in time. Many land managers have also questioned whether their efforts to restore diverse plant communities has added benefit to soil recovery from the long legacy of agriculture. Ecologists have conducted many studies to test whether biodiversity influences ecosystem functioning (e.g., aboveground productivity). Most tests, however, been performed at small scales with controlled numbers of species in relatively simple plant or aquatic communities (e.g., <20 species).  Many of these studies show that higher biodiversity has a positive effect on ecosystem functioning, particularly aboveground. The application of this theory to the practice of ecological conservation and restoration at large scales and under less controlled conditions has been limited. To fill this application gap, we measured the rate of belowground recovery in former agricultural fields restored to high diversity prairie and low diversity grassland (Klopf et al. 2017).  

Soil from a high plant diversity restoration.
Photo credit: Elizabeth Bach


The fields used in this study were restored using two different approaches.  One set of fields were restored through the USDA’s Conservation Reserve Program (CRP), a federal program that pays landowners to convert marginal crop land to perennial vegetation. A main goal of this program is to reduce and prevent soil erosion.  As such, fields restored to prairie through the CRP program generally include <10 plant species.  Previous work has shown the low diversity CRP approach can increase soil carbon storage over decades (Baer et al. 2002, 2010).  The set of fields used in our study were restored by The Nature Conservancy, with the goal of reconstructing diverse tallgrass prairies communities to protect rare plants and animals.  As such, these restorations are planted with >30 locally collected native prairie plant species and actively managed using frequent fire to reduce weeds (non-native plants).  All fields were located on similar soils within a two county region of Illinois, USA.  Fields under both practices ranged in age (time since restoration) from 2-22 years.


Our findings showed that restoring and managing for more diverse plant communities can improve recovery of belowground biology and functioning in predictable ways. Specifically, we found greater accumulation of roots, more predictable recovery of soil microorganisms (bacteria and fungal biomass), more rapid improvement in soil structure (less compaction), and less nitrogen available for loss from the system  in prairie restored and managed for high plant diversity relative to the low diversity grassland plantings.  Thus, the hypothesis that biodiversity promotes ecosystem functioning is relevant to large-scale conservation and restoration practices on the landscape. 


Read the original manuscript here:

Klopf RP, Baer SG, Bach EM, and Six J. 2017. Restoration and management for plant diversity enhances the rate of belowground ecosystem recovery. Ecological Applications 27: 355-62.


Additional reading:

Baer SG, Kitchen DJ, Blair JM, and Rice CW. 2002. Changes in ecosystem structure and function along a chronosequence of restored grasslands. Ecological Applications 12: 1688–701.

Baer SG, Meyer CK, Bach EM, et al. 2010. Contrasting ecosystem recovery on two soil textures: implications for carbon mitigation and grassland conservation. Ecosphere 1: art5. OPEN ACCESS

*This handwritten essay is included in:  Sayre, R.F. 1999. Recovering the Prairie. University of Wisconsin Press. Madison, Wisconsin



Globally, a wealth of local knowledge of soil biota exists

Categorisation of farmers’ knowledge of soil
biota, based on the ‘knowledge-practice-belief’
complex in ethnoecology. From Pauli et al. 2016

By Natasha Pauli, Lecturer in Geography in the UWA School of Agriculture and Environment, University of Western Australia


The 2016 publication of the Global Soil Biodiversity Atlas presented a compelling depiction of soil biology to a wide audience. The need for the Atlas is reflected in the fact that soil biodiversity is undervalued by society, and rarely considered within policy frameworks to protect either soil quality or biodiversity. However, this relative lack of interest in soil biological health does not hold true across all segments of society. If you were to go and ask someone who makes their living from the land what they know about soil health and soil biology, you may get a far more informed answer (as discussed last month by Hannah Birgé).

My interest in what farmers know about soil biota was sparked in the hills of Central America, while investigating the spatial distribution of soil fauna in a smallholder landscape in remote Honduras. Ultimately, I wanted to know whether the soils beneath particular trees that were left within cropping fields attracted soil animals, with flow-on effects for soil quality. There were dozens of species of trees to examine and the topography and soils were highly variable - it was difficult to know where to begin! We decided to start by asking the farmers what they knew - and what they had to say was fascinating, reaching far beyond simple descriptions of which parts of their farm supported the greatest density of earthworms (read about it here).

As I soon learned, while these types of questions may be asked in the field, they are often not deemed worthy of in-depth investigation or publication. The volume of literature on farmers’ knowledge of soil organisms pales in comparison with that on scientists’ knowledge of the topic. Even the field of ethnopedology (which is concerned with local ecological knowledge of soils) has tended to emphasise the identification, mapping, management and use of different local soil types within agroecological systems, with little enquiry on the living components of soils. Historically, social scientists and soil biologists have worked together infrequently. So, does this lack of information on how farmers view and use soil biota reflect an actual dearth of knowledge, or simply an understudied field of enquiry?

To address this question, I worked with colleagues Professor Lynette Abbott at the University of Western Australia, Dr Simoneta Negrete-Yankelevich at INECOL Mexico, and Dr Pilar Andrés at CREAF, Spain to undertake a systematic, worldwide review of peer-reviewed and high quality grey literature on local knowledge of soil fauna in agriculture. Our review, published last year in the open access journal Ecology and Society, turned up 60 studies that highlighted some aspect of farmers’ understanding of soil fauna, drawn primarily from Africa, Latin America and Asia, with a handful from the USA, Europe and Australia. Our findings show that there is a potentially rich body of knowledge on soil biota, but one that is rarely elicited.

Illustration of farmers’ perceptions of the effect of soil invertebrates on components of a smallholder farming system in Honduras. Redrawn from Pauli et al 2012 for the Global Soil Biodiversity Atlas.

There was a very broad range of ways in which farmers understand and use soil fauna. The most common example was the use of particular taxa (usually earthworms and beetle larvae) as an indicator of soil quality, cited in around two-thirds of studies reviewed. There were also many instances of local observations of species’ ecology, behaviour and life history, as well as exquisitely detailed taxonomies of invertebrate life. Some authors documented management practices such as deliberately using the action of soil fauna to improve soils for cultivation, by encouraging the activities of ants and termites to improve soil structure and increase organic matter content on marginal land. Soil invertebrates can also have cultural and spiritual significance, which influences how people perceive these organisms.

Farmers are rarely deliberately or deeply consulted by researchers on their knowledge of soil biota, soil ecology, or soil ecological processes. We encourage soil biologists to work together with social scientists to explore this important topic. In particular, researchers should explore not just observations of soil fauna, but

Map of the location of 60 reviewed studies on farmer knowledge of soil biota.
From Pauli et al. 2016

how these organisms are considered in agricultural activities, and the belief systems and cultural values that influence agricultural systems and perceptions of soil life. Our review found very few studies on local knowledge of fungi, rhizobia, or soil microbes, with most existing research limited to visible organisms - this is another area ripe for further exploration.


There are very important reasons why soil biologists should do more to understand how farmers use and value soil life. A deeper understanding of this topic can lead to more effective development of collaborative extension programs, policies and management initiatives directed at maintaining healthy, living soils. We give some examples in the paper of how this has occurred in smallholder and broadacre systems from Mexico, Nicaragua and Australia. Giving farmers the tools to measure elements of soil biological activity in their own fields can empower them to undertake their own experiments and analysis, and ultimately support adaptive and sustainable management of agricultural landscapes.


Further reading:

Pauli, N., Abbott, L.K., Negrete-Yankelevich, S., Andrés, P. (2016) Farmers’ knowledge and use of soil fauna in agriculture: A worldwide review. Ecology and Society 21, 3.

Pauli, N., Barrios, E., Conacher, A.J. and Oberthür, T (2012) Farmer perceptions of the relationships among soil macrofauna, soil quality and tree species in a smallholder agroforestry system of western Honduras. Geoderma 189-190: 186–198.


Understanding the role of biodiversity in our soils

Soil profile, Irish Soil Information System
Photo by Brian Reidy

By: Rachel Creamer (Professor, Wageningen University, Netherlands), Dorothy Stone (Leeds University) and Paul Massey. This article was originally published when all three authors were working at Teagasc, Johnstown Castle, Wexford, Ireland. The article was published in Organic Matters Magazine in 2013.


Soil Biodiversity encompasses a huge array of life on the planet. In some cases, 5 tonnes of animal life can live in one hectare of soil.5 The variety of soil biodiversity is also quite astounding ranging from bacteria, which are from 1-100 μm in size (i.e. completely invisible to the eye) through to the macrofauna which are on average 2 mm or larger in size and can be easily seen, such as earthworms, ants, woodlice, centipedes etc. The size of an organism is extremely important as this controls its life cycle and its impact on the soil functions. While an individual bacterium is tiny, it fits into minute spaces and there can be 3,000,000 to 500,000,000 bacteria present in 1 g of soil.  The role of soil biota in the soil is essential for everyday functions and ecosystems services to take place such as water filtration, nutrient cycling, organic matter breakdown, development of soil structure, plant growth and pollination.

In terms of agricultural production, the intensification of management systems has led in some cases to reduced soil biodiversity due to increased mechanisation, addition of chemical based fertilisers and application of mono-culture systems. The organic farming approach acknowledges the key role of soil biodiversity in the production of food and fibre. However, in order to maintain yields in low input organic systems, every single addition needs to be used as efficiently as possible.  As little of the nitrogen from a green manure, or carbon from the ploughing back in of stubble, should be lost.  To ensure that none of these additions are lost, it is essential to achieve as diverse a below-ground community as possible. The more diverse the biological community i.e. more species, sizes of organisms, feeding habits, life cycles etc the more potential to capture and cycle nutrients within farm and therefore provide an added source of nutrition to the organic production system.

There are some key groups of biology which are important in the delivery of these soil functions these include; bacteria and fungi (due to the large number present in soil and their role in decomposition of organic matter), nematodes (which are well know for the suppression of plant diseases and regulation of nutrient cycling) earthworms which are the “engineers” of the soil and are responsible for the large scale movement of soil particles and organic matter in the soil that define soil structure. 

The biological community structure in soils is quite similar to how all animals live on the planet. Different species live in different parts of the soil, some in water films, others in air spaces and the feeding strategies (known as a food web) are very complex. The food webs that exist below ground (a chaotic interlinked tangle of organisms that eat dead organic material and the organisms that in turn eat them), are more efficient and resilient to stresses like drought or disturbance if they have a complex structure, with many pathways for nutrients to move along as they are transformed from waste material to a form that crops can use. Within these foodwebs certain species are quite important as they feed upon other species or are fed upon by others. These species are vital for the flow of nutrients through the system. The presence of these keystone species helps us assess potential problems in the soil. In this article, we will discuss the role of nematodes and earthworms as case studies as they are considered a good bioindicators (show changes in soil health) due to their central role in foodwebs and soil structure.

Omnivore Nematode
Plant-feeding nematode,
Dolichodoridae tylenchorhynchus
Plant-feeding nematode

Nematodes are aquatic animals and within soil (“free-living” nematodes as opposed to “marine” nematodes or “plant parasitic” nematodes), live in the thin water films around soil particles and within soil pores1.  It is estimated that there are between 40,000 and 10,000,000 species of nematodes2 and there can be up to a million individuals per m2 in soil3.  Sometimes called “roundworms”, these small invertebrates (0.2 – 2.5 mm long) are impossible to see in soil with the naked eye, though they are visible when they are extracted into water, where they look like short thin white hairs. Nematodes are too small to affect the structure of soil in the way that earthworms can4, but they have the potential to contribute massively to the efficiency of nutrient cycling and thus the amount of carbon, nitrogen and other important elements available for crop growth.  When nematodes are present in soil at a high level of biodiversity, they contribute to the complexity of these nutrient cycling food webs.  They are able to do this because they feed on a wide variety of different sources within the soil.  Each species of nematode has specialised mouth parts, therefore some nematodes can eat bacteria, others feed on fungi, there are some nematode species that only eat plants and others that have the ability to eat all of these things (see diagram below for the different mouth parts associated with the different feeding types).  There are also predator nematodes that prey on other nematodes and sometimes even other soil fauna such as enchytraeid worms.  This ability to provide so many varied and different connections between the pathways along which nutrients are cycled mean that nematodes are an intrinsic and important group of species for maintaining soil fertility.

Earthworms at work

Earthworms are considered the farmer’s friend, as they are essential for the maintenance of soil structure. As I explained in my last article maintenance of soil structure should be one of the main considerations for any organic farmer, as it influences so many other functions in the soil such as nutrient availability, seed propagation, rooting, drainage etc. There are three main trophic groups of earthworms;

  • Surface living (epigeic) worms – which feed on litter and manure and break these down on or near the surface of the soil;
  • Night feeding (anecic) worms which have vertical burrows which come up to the surface from 30- 50 cm down, these include the well known Lumbricus terrestris species and they feed on the surface decomposing plant material which they pull down into the permanent vertical burrows;
  • Soil-eating (endogeic) worms – these worms make horizontal burrows by eating the soil as they move through the soil and excreting it to fill the space as they move through. The bacteria living in the guts of these worms transform the nutrients in the soil material making it more available on excretion. 

While a lot is known about the role of nematodes and earthworms in our soils, much of the soil biology is not yet understood for it’s role in soil functions. We also have very little understanding about which species are present where. Therefore, there is a great need to further our knowledge on this and to understand what baseline is required for a healthy biodiversity in soils of different land use types to deliver the functions we require as a society. Teagasc is involved in a large scale European project (Ecofinders) which is looking into this and will report on the variety of soil biology found in different land-uses across Europe and how some of these species are important for the delivery of soil functions as listed above.

Farmers & scientists examine a soil profile

Additional Resources

1Ecology of Plant and Free-Living Nematodes in Natural and Agricultural Soil, Neher D.A., Annu. Rev. Phytopathol, 2010, 48: 371-394

2The Role of Nematodes in Ecosystems, Yeates G.W., Ferris H., Moens T., Van Der Putten W.H., In Nematodes as Environmental Indicators, Ed Wilson J.W., Kakouli-Duarte T., 2009, CAB International, London UK.

3SSU Ribosomal DNA-Based Monitoring of Nematode Assemblages Reveals Distinct Seasonal Fluctuations Within Evolutionary Heterogeneous Feeding Guilds, Vervoort et al., PlosOne, 2012, 7:10

4Ecology of Plant and Free-Living Nematodes in Natural and Agricultural Soil, Neher D.A., Annu. Rev. Phytopathol, 2010, 48: 371-394

5European Atlas of Soil Biodiversity (available in English & French)



Why nature restoration takes time

A unique insight into the full soil community network By Elly Morriën and the EcoFINDERS team

Soil organisms have an important role in aboveground community dynamics and ecosystem functioning. However, most studies have considered soil biota as a black box or focussed on specific groups, whereas little is known about entire soil networks. With a consortium of colleagues from Europe, in the EU-funded EcoFinders project, we show that during the course of nature restoration on abandoned arable land a compositional shift in soil biota, preceded by tightening of the belowground networks, corresponds with enhanced efficiency of carbon uptake.

We examined a chronosequence of semi-natural grasslands in The Netherlands on sandy-loam soil that were abandoned 5-10 years ago (Early), 20-28 years ago (Mid), and >30 years ago (Long-term). In mid and long-term abandoned field soil, carbon uptake by fungi increases without an increase in fungal biomass, about 10% is fungal biomass and 90% is from bacteria, or shift in bacterial to fungal ratio. In previous studies on the same chronosequence, researchers showed that fungal biomass did not increase with time since abandonment, whereas they expected fungal biomass to increase with time since abandonment. The question remained what is the functional contribution of soil fungi to soil food web development and functioning. We discovered that already at an early stage in succession half the amount of carbon that flows from plants into soil is taken up by the soil fungi. After 30 years, that share has risen to three quarters of the plant-derived carbon stored in the soil. By labelling the carbon atoms, we were able to follow the carbon flow into the soil food web. In this way, we could link the organisms to their corresponding functions in the community. This linking has never been done before at such a large scale.

These results advance our view of soil community development and consequences for ecosystem development and vegetation-soil feedbacks in terrestrial ecosystems. The implication of our findings is that during nature restoration the efficiency of nutrient cycling and carbon uptake can increase by a shift in fungal composition and fungal activity. Therefore, we propose that relationships between soil food web structure and carbon cycling in soils need to be reconsidered. Fungal/bacterial biomass ratio’s may explain part of the processes, but understanding of the whole process requires considering the activities of these organisms as well. These results may be applied in future nature restoration activities, but perhaps they can also be used in order to promote the sustainability of agricultural soils.

LINK to open access article:


What’s in a name? “Soil health” as defined by farmers, managers, and scientists

By Hannah Birgé, PhD candidate in the School of Natural Resources and The Nebraska Cooperative Fish & Wildlife Research Unit at University of Nebraska


Most of us generally know what’s meant by “soil health”. The problems emerge when we try nailing down its specifics. What makes a soil in Nebraska quantifiably healthier than a soil in Antarctica? What variables reveal a farming practice to be destroying a soil’s health? As a land manager, how can I adjust aboveground practices to improve my soil’s health?

With so much soil heterogeneity across space and time, and so many diverse human demands and perceptions of soil ecosystem services, is operationalizing “soil health” an impossibly fast moving target?  Perhaps. But the term is now commonplace in the lexicon of practitioners ranging from small town farmers to federal scientists guiding national policy. A more precise definition of soil health can shift the concept of “soil health” from where it currently resides –firmly in the abstract –so that it can fulfill its lofty potential in applied contexts. And keying in on a better definition for soil health likely matters: for producers to meet the demands of population growth by 2050, they must increase agricultural output by 70%, intensifying current agricultural operations, converting non-agricultural lands to row crop agriculture, and relying on soil in remaining non-agriculture lands to provide essential ecosystem services –all while contending with additional, interacting, drivers of global change. Yet undesirable side effects and soil feedbacks exist that, if ignored, could undermine the long-term capacity of this large-scale transition to sustain people and nature. Developing a general method that could be applied by practitioners to capture local changes in soil “health” would be an invaluable asset during this transition. 

A first step towards establishing working definition of soil health is simply to assess how its operators use the term. So I asked farmers, scientists, state and federal agency personnel, and land managers to describe soil health, in their own words. Their annotated answers are at the end of this blog.

Here are the key take homes from all of the answers: nearly all respondents recognized the central role of soil organic matter/soil carbon to soil health, and they all described a soil system with integrated physical and biological components as being “healthy”. None of the definitions mentioned a specific value or rate of change for any single variable that a practitioner could measure to better elucidate the “health” of their soil. Each one described an integrated system that gave rise to emergent properties –much like human health. Important and immeasurable.  In other words, this exercise didn’t progress “soil health” towards some operationalizable metric, or even clarify the definition in a meaningful way. But it does reveal something important about how we perceive the soil as managers, farmers, and scientists. There is a growing recognition that the biological and abiotic components belowground are vastly more complex than previously appreciated, and that incorporating soil ecological knowledge into management decisions is essential for meeting long-term objectives. Stewards and scientists of the soil may be a long way from developing a general method for assessing soil health, let alone landing upon a single definition, but that doesn’t mean the exercise of trying isn’t yielding vital benefits along the way.



I first met Art Tanderup in summer 2014. You might recognize his name if you’re from Neligh, NE (pop. 1,599) or if you followed the XL Keystone Pipeline fight and Cowboy Indian Aliance, of which he was/is a vocal leader. Art and his family have a picturesque farmhouse surrounded by gently rolling rowcrop farm fields, and flanked by sturdy modern outbuildings (I should know; I hunkered down in one during a brief tornado). In reply to my query, Art sent me this over Facebook: “In an era of increasing world populations, the challenge is becoming one of increasing quality food production. That challenge begins with building soil health. The first step is to move agriculture to a no-till farming system. Along with that is planting cover crops. These practices keep carbon in the ground as the soil thrives with active worms, microorganisms, and open space for oxygen and water. The ground cover created by not tilling and cover crops creates mulch for new crops to emerge in. The mulch slows weed growth, prevents run off and keeps the soil cooler in the heat of the summer. As the cover crop roots decompose, root channels are created for the new crops. The entire process also increases organic matter in the soil. Incorporating livestock production into a no-till operation can enhance soil health.”


I also reached out to the Nebraska Corn Growers Association, and received a response from Clay Govier, a 5th generation (!) farmer who runs a corn and soybean operation with his brother near Broken Bow, Nebraska. If you haven’t had the chance to experience the beauty of the United States’ heartland (interstate 80 does not count), Broken Bow should float to the top of your list. He told us that, “To me, soil health means caring for the organisms that live in the soil as much as I care for the cash crop we're growing.  Soil health means balancing the soil's minerals to give the microbes a balanced diet just as we feed ourselves a balanced diet. Healthy soils lead to healthy plants that don't need fertilizers or fungicides to survive. To have healthy soils you must have good soil biodiversity. Healthy soils grow healthy food.” Clay also captured the tension that arises from uncertainty surrounding the feedbacks between short-term crop yield gains and long term soil functioning and noted that “most farmers try their best to be good stewards of the land they farm, but are overcome with the amount of information they receive from sources (i.e. large ag, chemical, fertilizer, and seed companies)”.  It’s equally true that managers of natural lands and soil scientists deal with similar uncertainty and doubt –more information about the soil doesn't always lead to knowledge or better decision-making (brief plug here for my paper and corresponding blog post entitled Adaptive Management for Soil Ecosystem Services).


I also received a response from a colleague’s father, Dave Schiltmeyer, who runs a corn and soybean operation in Elgin, Nebraska. His emailed response: “Good soil health means that I will have good plant structure from the beginning of the growing season to the end of the growing season. Good soil structure means good plant structure, which then means good water retention, and finally that turns into good yields and good test weights from my crops.”



Back in November, Dr. Bill Shuster, Research Hydrologist United States Environmental Protection Agency, and I were discussing the conundrum of “soil health”.  Bill researches how various soil types influence green infrastructure in urban settings and I was interested in how he considered soil health. After some thought, he emailed this to me: “Soil health is a consilient, dynamic state of affairs in which organic matter is of sufficient content and quality to energize nutrient cycles within a mineral matrix that itself lends support to root systems and soil fauna, and is hospitable and economical with regard to air and water fluxes.”


Scott Wessel is a private lands wildlife biologist with Nebraska Game and Parks out of Norfolk, NE. I work closely with him on my Ph.D. research to examine how hidden soil feedbacks influence management outcomes. I think about soil a lot. Scott thinks about soil more than he used to, but when I texted him to ask how he defined soil health his first reply was “did you mean to text me!?”. When I assured him that yes, I did, because soil is the literal and functional foundation of all terrestrial ecosystems, and last I checked he worked with wildlife in Nebraska, which is far from major oceans. His response, via text message: “Soil health to me is probably best defined on normal to poor scale of form and function. Are the pieces still there and functioning ‘normally’ in relation to everything else of interest to the manager? For the “everything else” group I’d guess value would be driven in most cases by perspective.”


Chris Helzer is the Director of Science for The Nature Conservancy of Nebraska. I reached out to him and we had a brief discussion about the problematic nature of the term “health” and how loosely it’s applied to so many contexts. He agreed to offer up a brief definition when I explained that my article was partly a discussion of this problem. Chris’s definition is as follows: “Soil health refers to the capacity of interacting living and non-living soil components to support diverse and resilient plant and animal communities and ecosystems.”



Dr. David Angeler is an Austrian scientist working in Sweden with expertise in complex systems science and the application of ecological theory to land management. I reached out to him wondering if he could deliver a punchy, quantifiable definition of soil health, and his first reply was as follows:  “the term ‘health; has been debated in ecology because it is pretty vague.  If there is a healthy soil what does a sick soil look like :-)))” I followed up, telling him about this piece and asking him, if he had to, could he possibly define soil health. The second time around (David is a great sport), he gave me this: “Soil health is the ecological condition of soils wherein structural and functional attributes allow for the maintenance of critical ecosystem processes, both in the soil itself and in other ecosystems that directly and indirectly depend on soils. Healthy soils are ultimately necessary for ecosystem service provisioning to humans.”


Dr. Jenny Soong is a soil scientist and postdoctoral researcher studying the effect of environmental gradients on soil carbon and nutrient dynamics in the tropics.  She emailed me this reply from her laboratory in Belgium: “To me, soil health should take into account the various ecosystem services that soils provide, including nutrient recycling, carbon storage, water filtration, habitat for biodiverse biota, resistance to erosion, etc. while also taking into consideration some degree of resilience of stability. Of course that's very general! What that means in context is fully dependent in both place and time.” 


When I asked Dr. Rich Conant of Colorado State University (and my old master’s adviser) what he thought was meant by “healthy soil” he told me, “You know it when you see it.” Apt!


Soil Health and an Era of Ecological Experimentation in Agriculture

By Steven Rosenzweig, Ph.D. student, Department of Crop & Soil Science, Colorado State University This blog post originally appeared on the HumanNature blog from the School of Global Environmental Sustainability at Colorado State University.  It is the first in a series of global perspectives on the concept of soil health.  

Curt Sayles is doing something radical in his part of the world. There are only a handful of farms like his in eastern Colorado. Purple flax, yellow sunflowers, and every conceivable shade of green – it’s a welcome sight to see some color in a landscape of brown wheat and fallowed fields.

Curt grew up farming the conventional way. Farmers in Colorado grow wheat every other year, alternated with a year of fallow, where the land lays bare to store up rainwater for the next wheat crop. It’s been that way ever since the Dust Bowl in the 1930s. But at 60, Curt is experimenting with a greater diversity of crops than conventional wisdom would suggest is possible in his climate, which is famous for wildly variable weather and multiyear droughts. He grows a mix of six different crops at once that his wife and son-in-law move cattle through to graze. He grows this forage mix in rotation with other crops like rye, corn, sunflowers, and millet. And he’s completely eliminated fallow, a daring move for a farmer without irrigation or much rain. It’s not easy trying something new in plain sight of judgmental eyes.

“I quit going to the coffee shop because [other farmers] look at you like you're… I mean you may as well have flown a UFO in because they think you're crazy,” he says.

But Curt is inspired to farm differently. After a trip to Dakota Lakes Research Farm in South Dakota, a group that’s been pushing boundaries in agriculture since the early 90s, Curt became a different kind of farmer. And he’s not the only one who is making changes. Curt is swept up in an excitement that is inspiring thousands of farmers and ranchers around the country to try a new approach. Agriculture is on the brink of another revolution.

A New Vision for Agriculture

Farm-to-table, local food, organic – they all seek to tie the consumer to alternative agriculture. These strategies have societal merit, but they haven’t yet inspired the large-scale changes necessary to repair the hostile relationship between agriculture and the environment. Agriculture needs a vision that improves the land.

That is what the concept of soil health promotes. It seeks to foster a regenerative approach to farming and ranching.

The mindset in conventional agriculture is all about simplification, and it has a singular focus on maximizing this year’s crop yields. It loses sight of the agricultural system as, well, a whole system. You mined your soil organic matter and there are no nutrients left? Buy some more fertilizer. Never mind that building organic matter will not only feed your plants, but also prevent erosion and store more water.

In contrast, soil health is inspired by the way native ecosystems function. It appreciates the whole system. Soil health a philosophy that guides a farmer’s management, such that every action taken on the farm seeks to adequately feed and protect the living organisms in the soil, thus unlocking the enormous potential of soil microbes to release nutrients, create soil structure, build organic matter, and confer drought and disease resistance to plants. In practice, this mindset is realized through four simple principles: minimize soil disturbance, maximize diversity of plants, animals, and soil organisms, keep a living plant root growing as long as possible throughout the year, and maintain residue cover on the soil.

For Curt, these principles are transformational. He eliminated tillage so he doesn’t disturb the soil. By integrating livestock, crop rotation, and a diverse forage mix, he maximizes diversity. And by eliminating the fallow year, he extends the amount of time with a living root in the ground, and maintains residue cover on the soil.

But there is a reason he is only one of a handful of people farming this way in his region. Curt is taking a big risk.

“It’s like a fight all the time.”

Many of the practices associated with soil health have been more quickly adopted “out east,” as Colorado farmers refer to the Midwest, but their adoption has been slower in drier climates. Successfully eliminating fallow or growing a diverse forage mix is much trickier with less water, and no one has developed the recipe for success in eastern Colorado. As a soil health pioneer in this region, Curt realizes it’s not easy.

“Show me the book and formula and I’ll just go do that. Well, there is no book and there is no formula. We're trying to find things that work here. You know winter pea, does that work here or not? It's like a fight all the time. Nothing's easy.”

But without farmers like Curt pushing the limits of diversity, dryland agriculture would be forever confined to one or two crops and years of bare land. Without anyone willing to get rid of fallow, no one would ever know whether it is truly a necessity, or a relic from the years following the Dust Bowl. It would be an admission that there will always be erosion in agriculture, and that the soil is as good as it’s ever going to get.

But soil changes slowly, and it will take time to tell if Curt’s changes have worked. Now, more inspired than ever, Curt is worried he wont have enough time to complete all of his experiments.

“We’ve opened a whole new chapter. I have lots to learn. My biggest fear now is, I'm sitting here at 60. I maybe have 10 more harvests… That's all I've got left. I wish I'd known 20 years ago what I know today.”

Curt’s success with the soil health approach is more important to the Movement than he may realize. In one of the driest and most volatile climates in the country to be a non-irrigated farmer, the obstacles to Curt’s success are greater than just about any farmer in America. If he can make soil health work in Colorado, it will work anywhere.

But the pressure doesn’t rest solely on Curt’s shoulders. He has a close network of other farmers in his region who are undertaking a variety of creative and daring changes on their own farms. Many other farmers and ranchers throughout the US and beyond recognize that soil health may be the way of the future. Universities, government agencies, industry, non-profits, and international experts are responding to the farmers’ excitement to usher in an era of ecological experimentation in agriculture. The age of soil health is here.



Soil Restoration and Global Sustainability

by Elizabeth Bach, Executive Director, Global Soil Biodiversity Initiative, Colorado State University

Restoration of ecosystems, and soil in particular, took center stage at the 22nd Conference of the Parties (COP22) for the UN Framework Convention on Climate Change.  Restoration and stabilization of soil provides numerous benefits to communities and the environment, advancing numerous Sustainable Develop Goals including supporting life on land, climate action, sustainable communities, clean water, and reducing hunger.  Three key reports unveiled at COP22 focus on restoration of soils and ecosystems as a holistic approach to help communities world-wide build sustainable futures.


The Drylands Advantage: Protecting the environment, empowering people is a report from the UN International Fund for Agricultural Development (IFAD) highlighting the importance of arid, semi-arid, and dry sub-humid areas in supporting biodiversity and livelihoods and cultural identity of many people.  Soils are central to the ecosystem services drylands provide.  Soil biodiversity is part of the overall diversity drylands provide.  Drylands also house 27% of the worlds soil organic carbon reserves!  Drylands are particularly vulnerable to impacts from human use and climate change.  The increased rate of degradation in arid areas in recent years in negatively impacting people and their economic livelihoods around the world.  The report includes five case studies from China, Jordan, Nicaragua, Senegal, and Swaziland.  In each case study, stabilization and revitalization of soil played a central role in meeting the sustainable development goals for individuals, communities, and ecosystems.  A holistic focus on restoration of environment and communities lead to progress on multiple Sustainable Development Goals.  Download and read the full report (44 pgs) here:


The dryland area north and south of the Sahara Desert is home to approximately 500 million people, and these communities rely on the land for food, water, and livelihoods.  The Great Green Wall for the Sahara and Sahel Initiative is a project from the African Union focused on reducing soil erosion and improving ecosystem service capacity to support communities.  Building Africa’s Great Green Wall: Restoring degraded drylands for stronger and more resilient communities presents a mapping effort, executed by the FAO and partners, to pinpoint areas with high restoration needs and opportunities.  It is estimated 21% of the 780 million hectares in this area is in need of restoration to prevent further land degradation and build a foundation for a sustainable future.  Soil stabilization is critical to achieving this goal along Africa’s Great Green Wall.  Soil biodiversity is at the heart of stabilizing and restoring soils in these vulnerable areas.  The recommended restoration interventions include promoting natural regeneration and planting of native plant species.  Re-establishment of plants stabilizes soil directly through root growth and rebuilds soil food webs, supporting organisms such as mycorrhizal fungi, earthworms, and termites, which also stabilize soil.  You can download and read the full report here (7 pgs):


In Latin America and the Caribbean, numerous communities also rely on land for food, water, and economic livelihoods.  There are 300 million hectares of degraded land and 350 million hectares of deforested lands in this region, spurring the World Resources Institute report The Economic Case for Landscape Restoration in Latin America.  This is a first attempt to quantify the potential economic benefits to local populations from restoring approximated 20 million hectares of degraded land across the biomes of Latin America and the Caribbean by the year 2020.  The report estimates an average net gain of $1,140 per restored hectare, or a total of $23 billion over 50 years.   Soil is again central to the benefits included in this estimate.  The estimate includes forest products (wood and non-wood), agricultural products (from adopting conservation farming practices), ecotourism income, and carbon sequestered in vegetation and soil.  Restoration of these ecosystem products and services rely of rebuilding soil biodiversity and re-establishing strong connections between these organisms.  The minutia of these estimates depends on many factors including future refinement of estimates of services provided by these lands, the likelihood these ambitious goals will be met, and the realized values of the products considered.  However, it is clear that restoration of only 6-7% of total degraded land in Latin America and the Caribbean can have major positive impacts on efforts to achieve local, regional, and global sustainability goals, including direct positive economic impacts on local populations.  You can download and read the Executive Summary (6 pg) and full report (68 pg) here:


African Soil Microbiology Project

written by Elizabeth Bach, Executive Director, Global Soil Biodiversity Initiative


Of all the continents, Africa faces the largest challenges concerning soil conservation and food security, in the face of increasing populations and environmental change.

Scientists from several sub-Saharan African countries including South Africa, Namibia, Mozambique, Kenya, Botswana and Zambia met recently at the University of Pretoria to launch the African Soil Microbiology Project (AfSM), funded by USAID.

Over 3-years, soil samples will be collected methodically across the continent of Africa.  Using the Earth Microbiome standard methodology, soil samples will be analyzed in the laboratories of the collaborating scientists to extract DNA, amplify and sequence the 16S rDNA gene, and analyze matches to known bacterial and archaeal taxa.  This unique multi-national project is the first such study to ever be undertaken in Africa at this scale.

“AfSM is a consortium of soil microbiology researchers from across sub-Saharan Africa, representing about 15% of the total land area of the region.  The core project will involve a coordinated assessment program of collecting 1000 soil samples across each of the partner nations for microbial community fingerprinting,” said Dr. Diana Wall, an International Advisor to the project.

Results from the project will shed new light on the bacterial biodiversity of African soils.  It will provide new insights into the presence of beneficial and pathogenic bacteria.  Knowing the distribution of key groups of bacteria, such as nitrogen-fixing Rhizobium and Azotobacter, may provide new information for land use and crop management decision-making.  Uncovering the ecology of these soil communities may provide new ideas for managing pathogens of crop plants, livestock, wildlife, and humans.  The data and collaborations will serve as foundations for future explorations of microbial soil biodiversity in Africa.

For more information, contact the project director, Prof Don Cowan (

The African Soil Microbiology project team, in the Centre of Microbial
Ecology and Genomics laboratories at the University of Pretoria, South Africa.


Belowground visions of life: Soil makes Art

Art communicates the importance of soil life
Original artwork by Ed Reynolds

Dr Tancredi Caruso, School of Biological Sciences and Institute for Global Food Security, Queen’s University of Belfast


The relationship between soil and humans is deteriorating: soil biodiversity is threatened by global change dynamics, pollution and intense agriculture while fewer and fewer people appreciate that we need to save soil biodiversity to grow food, have clean water and sustainably recycle waste. A big challenge soil biologists face in their battle to save soil is that the public is often just unaware of the critical role soil plays in our society. How can soil biodiversity scientists share their knowledge with the public? Art is the answer given by “Belowground visions of life: Soil makes Art”, a project funded by the Leverhulme Trust in the UK. This project supports an artist in residence, Ed Reynolds, working with Dr Tancredi Caruso, soil ecologist at the School of Biological Sciences, Queen’s University Belfast.

The idea was born after the 1st Global Soil Biodiversity Conference held in Dijon (France) in 2014. A key, recurrent theme of that conference revolved around the question of how scientists can make the public aware of the crucial role of soil biodiversity in our life.  We were particularly inspired by the observation that worldwide and across cultures, people from rural environments often show an almost religious appreciation of the key role soil plays in supporting our life cycle while in modern, urban environments many think that soil is populated by “awful germs” thriving in dirt. In our project, we want to overturn that view and show the beauty and importance of the kaleidoscopic biological universe that soil is. The arts can make people aware of the beauty and importance of soil biodiversity in our life, and help us rebuild the deteriorating relationship between humans and soil.


Artist Ed Reynolds at work
Photo credit: T. Caruso

Soil organisms are important.
Original artwork by Ed Reynolds

Predatory mites are a critical part
of the soil food web.
Original artwork by Ed Reynolds

Protozoa play important roles transferring
energy and nutrients in soil.
Original artwork by Ed Reynolds

The project will deliver a critical mass of graphical and pictorial pieces of art in the form of sketches, paintings and digital images. These artworks will be displayed in an exhibition and serve as the basis for a children’s book. Finally, Ed will deliver a mural in Belfast with soil biodiversity as the main theme. Soil life will for the first time be back to our urban lives to tell us its astonishing and forgotten story.

Read more about the project at Ed Reynolds' blog:



The Future of Farming is in the Soil

Adam Cobb tills soil to establish an experiment.

Adam B. Cobb, PhD  Oklahoma State University, USA


Humanity is exerting intense pressure on our planet, and many agricultural practices are degrading soil stability and fertility over time. Worldwide, we’re losing soil about thirty times faster than it’s being replaced.  As farms are depleted of topsoil and organic matter, increased fertilizer inputs are required to maintain crop yield, while mounting fertilizer costs are disproportionally affecting farmers in developing countries. I have witnessed these daunting issues in Africa and Central America, but there is hope.


Our research is part of the Brown Revolution, which seeks to harness the benefits of living soil to sustainability provide nutritious food. In one teacup of healthy soil there are enough arbuscular mycorrhizal (AM) fungi to stretch across 30 football fields.  Mycorrhizas partner with the majority of plants, including most agricultural crops, to enhance plant nutrient and water uptake.  These fungi also help ensure ecosystem health by limiting fertilizer runoff (eutrophication), reducing soil greenhouse gas emissions (climate change), and stabilizing soil structure (erosion). 


We assessed sorghum and cowpea genotypes for responsiveness to AM fungi in low fertility soil and how that symbiosis benefited seed (grain) nutritional contents, such as protein, zinc, and iron. The highly responsive crop genotypes produced around 200% more vegetative biomass and nearly 300% more grain compared to the less responsive genotypes. Furthermore, the average protein production of highly responsive genotypes increased more than 300% compared to the less responsive genotypes grown under the same conditions. Total grain zinc and iron content was also significantly correlated with AM fungal root colonization.

Cowpea flower
Photo credit A. Cobb

Root with mycorrhizal fungi
Photo credit A. Cobb













We then investigated the effects of alternative fertility inputs (compost & biochar) on the productivity and nutritional quality of highly mycorrhizal responsive sorghum and cowpea. Compared to plants grown with typical commercial fertilizer rates, plants grown with a blend of biochar, worm compost, and 50% less fertilizer produced similar plant biomass after 45 days of growth, with equal or greater tissue protein, iron, and zinc, significantly higher tissue phosphorous, and 30% more AM fungi in the host plant’s roots. These results indicate biochar and worm compost can boost belowground symbiosis with AM fungi, resulting in increased fertilizer use efficiency. These soil amendments can be produced at various scales, with potentially lower cost than commercial fertilizers, and can enhance soil carbon sequestration.


Nearly 30% of our population urgently needs more dietary protein, zinc, and iron; our results indicate that AM fungi improve both soil health and human health. Furthermore, farming costs and environmental fallout from nutrient pollution can be reduced by managing agroecosystems to encourage abundance and benefits of AM fungi. By encouraging these belowground and aboveground linkages, including the combination of crop genetics, alternative fertility amendments, and improved farm management may help regenerate our soils and nourish our growing population.

Adam Cobb mixes soil.


Nematology Meeting of the Americas, Conference Review

City of Montreal
Photo credit S. Xue

By Summer Xue, Bringham Young University Day 1

The 2016 Society of Nematologists/Organization of Nematologists of Tropical America conference was held in Montreal, Quebec, Canada.  I arrived in Montreal the morning before the meeting and had a free day to see the beautiful city.  There are some really cool architectures in Montreal, and one is located near the bus station.

Day 2

The conference began with registration and an opening reception.  All conference participants got a cool T-shirt and a small package. Honestly, the number of participants was more than I thought, and there were some brilliant scientists with a passion for nematodes I was really happy to meet!

Oral presentation at SoN/ONTA
Photo credit S. Xue

Day 3-4

I was so excited to be around fantastic scientists and couldn’t wait to find more idea about my own research from the speakers and posters! Society of Nematologists Dr. Byron Adams opened the meeting with words of welcome.  The plenary talks featured nematology VIPs such as Dr. Diana Wall, Dr. Graham Stirling, Dr. Sara Sánchez-Moreno, and Dr. Howard Ferris! There were many topics presented in the oral and poster sessions. This is a general conference, so you always can find topics related to your study and most of them were great! I was excited about a lecture about genetic variability and phylogenetic analysis of nematodes, particularly the methods or strategies they applied to their data.

I gave my poster presentation on Monday. To my surprise, there were many people interested in the Antarctica nematodes, and I got some really good comments on my genome study and experimental design. Some students shared their experiences about how to deal with the shorter sequence scaffolds in genomic work, which is super useful to me!




Day 4

This was a tour day, we went to different farms in Montreal and it was my first time to see bee hives this close. We saw little environmental chambers that integrated plant crop production with aquaculture.  They keep and feed fish in the bottom tank and use the fish by-products to grow crops on the top.

We ended the day with a river cruise was awesome because of perfect views and food!




The periodical millipede, Parafontaria laminata armigera

Toshio YOSHIDA, Professor emeritus, and Tadashi FUJIKAWA, Faculty of Agriculture, Shinshu University


Mating couple and eggs.

Every year in the autumn, I remember seeing swarms of many vivid colored creatures on the forest floor and their attractive “fragrance.” This “fragrance” is actually a disgusting smell for ordinary people, but it is a really impressive “fragrance” for me. This creature is relative large (c.a. 3 cm), orange with black stripe millipede (Parafontaria laminata armigera (Verhoeff), Diplopoda: Xystodesmidae) and is called “the train millipede.” Most millipedes produce a defense substance with a strong odor, so any creature (or person) who grasps a millipede once is sprayed with this chemical and remembers the annoying odor! The defense chemical of Parafontaria is a type of glycosphingolipid (Mori et al., 1994, 1995: Sugita et al., 1994), and has an almond-like smell.

Train millipedes are found in the central mountains in Japan. They mostly live in forests; however, most of those forests were probably long-term grasslands before about 70 years ago. The millipedes become adults in the autumn, 7 years after being laid as an egg. The adults live to reproduce and then die in mass the following year. Surprisingly, only individuals of the same age are found in one place. Because juveniles live completely in soil (endogeic), people only notice when the adult millipedes come up on litter, swarming in September and October (new adults) and the subsequent spring every 8 years. Swarming of big populations of millipedes has been observed worldwide. However, this species has been observed to swarm at exactly eight-year intervals since 1920 in the central mountains in Japan (Niijima, 1998). In this area, the millipede swarming is large enough to disrupt train service, so train operators keep precise records of the swarming. That’s why the millipede is called “the train millipede.”

The periodic specificity of Parafontaria millipedes make them good model organisms to study speciation (Sota and Tanabe, 2010; Tanabe et al., 2001), soil nutrient cycling (Kaneko 1999: Fujimaki et al., 2010; Hashimoto et al., 2004; Toyota et al., 2006), and effects of climate change (Makoto et al., 2014). The development of this millipede is fixed by the winter chill (Fujiyama, 1996), so any cohorts with different ages will not mate each other. For a long time, scientists could not find all the possible cohorts with different ages, but recently we found 8 different local populations, which reproduce in different years.

The largest local population of P. laminata becomes adults in 2016 in the southeast slope of Mt. Yatsugatake! Don’t you want to see the amazing swarming and try to hunt the “fragrance” this autumn? The best season will be from mid-September to mid-October.

The swarming population along a road side.

The train millipedes killed on a road.


Further Reading

Fujimaki, R., Sato, Y., Okai, N., Kaneko, N., 2010. The train millipede (Parafontaria laminata) mediates soil aggregation and N dynamics in a Japanese larch forest. Geoderma 159, 216-220.

Fujiyama, S., 1996. Annual thermoperiod regulating an eight-year life-cycle of a periodical diplopod, Parafontaria laminata armigera Verhoeff (Diplopoda). Pedobiologia 40, 541-547.

Hashimoto, M., Kaneko, N., Ito, M.T., Toyota, A., 2004. Exploitation of litter and soil by the train millipede Parafontaria laminata (Diplopoda: Xystodesmidae) in larch plantation forests in Japan. Pedobiologia 48, 71-81.

Kaneko, N., 1999. Effect of millipede Parafontaria tonominea Attems (Diplopoda: Xystodesmidae) adults on soil biological activities: A microcosm experiment. Ecological Research 14: 271-279.

Makoto, K., Arai, M., Kaneko, N., 2014. Change the menu? Species-dependent feeding responses of millipedes to climate warming and the consequences for plant–soil nitrogen dynamics. Soil Biology & Biochemistry 72, 19-25.

Mori, N., Kuwahara, Y., Yoshida, T., Nishida, N., 1994. Identification of benzaldehyde, phenol and mandelonitrile from Epanerchodus japonicus CARI (Polydesmida Polydesmidae) as possible defense substances. Appl. Entomol. Zool. 29, 517-522.

Mori, N., Kuwahara, Y., Yoshida, T., Nishida, N., 1995. Major defensive cyanogen from Parafontaria laminata armigera Verhoeff (Xystodesmidae : Polydesmida). Appl. Entomol.  Zool. 30, 197-202.

Niijima, K., 1998. Effects of outbreak of the train millipede Parafontaria laminata armigera Verhoeff (Diplopoda: Xystodesmidae) on litter decomposition in a natural beech forest in Central Japan. 1. Density and biomass of soil invertebrates. Ecological Research 13, 41-53.

Sota, T., Tanabe, T., 2010. Multiple speciation events in an arthropod with divergent evolution in sexual morphology. Proceedings of the Royal Society B-Biological Sciences 277, 689-696.

Sugita, M., Hayata, C., Yoshida, T., Suzuki, M., Suzuki, A., Takeda, T., Hori, T., Nakatani, F., 1994. A novel fucosylated glycosphingolipid from the millipede, I. Biochimica Et Biophysica Acta-Lipids and Lipid Metabolism 1215, 163-169.

Tanabe, T., Katakura, H., Mawatari, S.F., 2001. Morphological difference and reproductive isolation: morphometrics in the millipede Parafontaria tonominea and its allied forms. Biol. J. Linn. Soc. Lond. 72, 249-264.

Toyota, A., Kaneko, N., Ito, M.T., 2006. Soil ecosystem engineering by the train millipede Parafontaria laminata in a Japanese larch forest. Soil Biology and Biochemistry 38, 1840-1850.