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Beneath Our Feet

Soil modeling for everyone: From concept to simulations

By Katherine Todd-Brown, USA @KatheMathBio

Computational and mathematical modeling are increasingly in demand as society tries to apply current scientific understanding to future soil management practices. The flux of carbon from the soil to atmosphere in particular is a major uncertainty of future climate projections. Soil carbon is also a critical component of soil health. In addition, many funding agencies are interested in coupling experimental and modeling approaches to better target scientific inquiry and extrapolate into murky futures.

Computational and mathematical models are generally thought of as tools for projecting into the future, but they can also help design and run experiments that might otherwise be costly or even impossible to carry out in the lab/field. You can turn off gravity in a model. While I say this with a bit of tongue in check, imagine directly exploring the effects of capillary action vs gravitational forces in soil wetting. Something that is completely impractical in the real world can become almost trivial in the computer.

Models are frequently seen as this magic box that, if you can just figure out how to plug your data in, will tell the rest of the world how critically important your research is. As a modeler, I’ve found that my colleagues who work primarily in the field and/or on the bench are frequently at a bit of a loss how to wave this magic wand. Fully characterizing a site to run an off-the-shelf model like DayCent can be overwhelming or just plain intractable depending on the location. Plus experimental treatments or particular measurements will often not have direct representation in these off-the-shelf models, precisely because their effects are novel or uncertain and thus of interest.

 

So where does that leave us?

Fortunately, if you design experiments and interoperate their results, you are most of the way there; even if you are a field or laboratory scientist who hasn’t written mathematical equation since your college math class. Numerical models are formalizations of conceptual frameworks that every scientists use on a daily basis. We tell stories of how we think the world works in our grant proposals and manuscripts. Those stories are models in their most basic forms; English, Mandarin, mathematics, and computer code are just a different languages that can be used to convey some scientific understanding to the broader world. By telling stories of how we think the world works, scientists are creating models.

The main difference between conceptual models and numerical models is precision. Human language is generally very fuzzy leaving quite a bit of room for interpretation to the listener. Mathematics, on the other hand, is extremely precise. It’s one thing to say that the change in soil carbon is the difference between the inputs and outputs, and another to state: . This mathematical formulation has several embedded assumptions in it like: soil carbon does not change with space, and inputs change over time but that the decay rate doesn’t. Mathematics does not allow you to sweep anything under the rug, instead you must explicitly state what your assumptions are and under what conditions those hold true. While you can be as precise with an English description of your conceptual framework, it can be challenging to attain the level of detail you get from a mathematical formalization. But underpinning all this is still your original conceptual understanding of the research system.

 

On a practical level how do you move from this conceptual framework to a precise mathematical formulation?

One way to do this is to collaborate with a mathematician or computer scientists. Be aware however that this will frequently require several conversations since you are likely talking with someone who has no soils training. The nutrient, parent material, and biological differences between a tropical oxisol and temperate molisol might be obvious to you but not to someone trained to locate bifurcation points in dynamical systems. Often times the different soil conditions will tie directly to different mathematical assumptions in ways that are not obvious at first glance. Lobbing your data over the discipline dividing wall won’t cut it. Instead, these collaborations require a lively and ongoing exchange.

Alternatively you can develop your own model. Frequently if you have a strong hypothesis driven experimental design, you can frame this hypothesis as a numerical model and probably already do on some level. Many statistical tests like linear regressions are, themselves, numerical models. A common problem with these statistical tests is that they assume normally distributed data and linear relationships, frequently not the case in soil systems. Diagramming the mass or energy path you are interested in will often lead to a set of differential equations. Once you have this mathematical formalization you can apply model-data integration techniques to fit descriptive parameters to your data.

By using numerical models informed by your scientific understanding you can dramatically increase the power of your statistical tests, compete different hypothesis, explore the relative importance of entwined mechanisms, and extrapolate findings into management scenarios. Models allow you to convey your scientific understanding, supported by your experimental data, with a precision that is difficult to achieve in a standard scientific narrative. While the end goal is scientific understanding not mathematical poetry, models are playing an increasingly important role in biogeochemistry.

 

Mathematics is the language of size, shape and order […] ~ Lancelot Hogben (1936)

 

Kathe Todd-Brown is a computational biogeochemist at the Pacific Northwest National Laboratory in Richland, Washington. She initially trained as a mathematician but it was a bit too clean. She transitioned to soil carbon cycling and couldn’t be happier to work in one of the most interesting systems on the planet.

 

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An Experience with Interntaional Soil Reserach Networks



Collaborators discuss grassland soil carbon research
near Hulanbuir, China. Photo credit Jiqiong Zhou

By Adam Cobb, Postdotoral Researcher, Oklahoma State Univeristy, USA

 

There is nothing quite like touching new soil. The soils of China are ancient, but this is my first chance to grab a handful. After leaving our hotel in Beijing at 4am, flying for three hours, and driving on a bombed-out road for another hour, we are in the steppe grasslands of Inner Mongolia in Northwest China.

We are here – with chestnut-colored soil in our hands – because of Jiqiong Zhou (soon to be Dr. Zhou) and her advisor, Dr. Yingjun Zhang. Sixteen months previously, Jiqiong (who also goes by Jolie) emailed Dr. Gail Wilson and asked if she could spend nine months with us at Oklahoma State University. Jiqiong’s research links above- and belowground influences on grasslands with particular emphasis on plant-microbial relationships, such as rhizobia/meliloti and arbuscular mycorrhizal symbioses, which is precisely Gail’s area of expertise.

This PhD student exchange and research collaboration has been amazing. While Jolie was with us, she had the chance to visit the Konza Prairie Biological Research Station (NSF-LTER site) near Manhattan, Kansas, USA. We went up to establish grassland restoration plots, but took time to show her around the station, and particularly to see the bison. Later, she told us how lucky she thinks we are to research in such productive grasslands.

Back in China, her research grasslands are not as productive. With typically 300-400mm annual precipitation, they are a contrast to our tallgrass prairie systems. However, these semi-arid grasslands are critically important, not just for local sheepherders, but for soil ecologists. Climate models predict many mesic grasslands will become more arid during the 21st Century. It is crucial that we untangle the belowground drivers influencing aboveground productivity, plant species diversity, and ecosystem functions in semi-arid grasslands, if we are to manage our global grazing resources in a warmer and drier world.




Cattle grazing in the meadow steppe grasslands
of Inner Mongolia, China. Photo credit Jiqiong Zhou



Bison on Konza Prairie Biological Research Station
near Manhattan, Kansas, USA. Photo credit Adam Cobb


This is where Jolie, and her colleagues in Dr. Zhang’s lab, conduct their valuable soil research. We walk across her plots, and see the yellow-flowered alfalfa (Medicago falcata) she established to rehabilitate these overgrazed areas. Belowground, she assessed how these reseeded legumes influence nutrient cycling, soil microbial communities, and soil metabolites. Today is a hot and sunny one, and we remark at how much data she has collected in these plots, often working by herself.

Jolie’s research is the combination of mechanistic assessments (e.g., microbial genomics) and applied questions. As part of the China Agricultural University’s College of Animal Science and Technology, she is keenly aware that these grasslands are provisioning ecosystems. Grazing treatments (real or simulated) are always part of the research design. Jolie is passionate about reseeded alfalfa because it can regenerate the landscape, increase incomes, and improve soil health.

Gail and I had an amazing experience with Jolie, Dr. Zhang, and their associates. We learned more about their culture, and we touched China’s soil. We are currently planning paired experiments assessing grassland plant and soil dynamics in both China and the USA. These collaborative research networks are key as we strive to conserve and restore global soils.

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Building mud castles: A perspective from brick laying termites



Termite mound construction using bricks.
Image by N. Zachariah

By Nikita Zachariah, Graduate Student, Centre for Ecological Science, Indian Institute of Science, Bengaluru, India

 

Walking in the wild or even in a metro city like Bengaluru you are sure to find animal homes in all their grandeur — bower bird nests, bee hives, spider webs and termite mounds. These aesthetically designed structures have always fascinated architects, naturalists and laypersons alike, yet we barely know how they are built — what are the basic building blocks or bricks in these constructions and how materials are chosen for these constructions.

In consultation with my PhD advisors Prof. Renee M. Borges and Prof. Tejas G. Murthy I decided to explore the physical, chemical and behavioural aspects of one such construction — the termite mound. Though made up of soil, termite mounds can stand in sun and rain for decades together without dissolving thanks to termite secretions that are mixed with soil during construction imparting ten fold increase to its strength. Termite mounds can house more than a million termite individuals and can reach a height of 10 metres. At a human scale this would correspond to a building 10 kilometres tall… taller than Mount Everest!! Termites construct these mounds without an architect, without a masterplan, in fact without even seeing the structure they are building. Yes, these termites are blind. Not only do termites engineer their mounds, they also engineer entire ecosystems making them drought resistant. Yet, little do we know about the basic building blocks of these mounds and what makes a geographic region conducive for mound construction.

I studied Odontotermes obesus species of termites in Bengaluru, India. It is widely distributed in the Indian subcontinent and makes mounds that are upto 2.5 meters tall. It aggregates moist soil particles into tiny balls which act as bricks during mound construction. The different castes of termites (such as major and minor termites) make different sizes of bricks which they jointly pack like golf balls in a jar with marbles filling the space between the balls thereby achieving tight packing and consequently high strength. Moreover, in the lab they were even able to use materials like glass beads for making bricks. Since termites used a totally unfamiliar material, glass beads, I was curious to know what else can they handle? In order to understand this I gave them every material I could get my hands on — metal powders, jellies, even tissue paper and paraffin wax!! To my surprise they used all the materials as long as they were able to walk and chew on them. But they do had their personal favourites, e.g. they loved granular materials over others and were equally willing to use non-familiar materials like glass beads as the familiar ones (soil). Other properties that determined the ease of handling were hydrophilic, osmotically inactive and nonhygroscopic nature, surface roughness, rigidity and presence of organic matter. These material properties along with the availability of moisture and favourable climatic conditions will determine the global geographic distribution of termites, a matter of considerable importance given their roles as ecosystem engineers. This study also takes us towards understanding how tiny termites make mounds that any engineer would envy.



Bricks made by different castes of termites.
Photo credit: N. Zachariah



Packing of large and small bricks during construction.
Photo credit: N. Zachariah

 

The study was published in the journal Scientific Reports (https://www.nature.com/articles/s41598-017-04295-3) and was featured in Science magazine (http://www.sciencemag.org/news/2017/07/thesetermites-can-use-glass-beads-build-mounds).

Lab webpage: Prof. Renee M. Borges (http://ces.iisc.ernet.in/renee/), Prof. Tejas G. Murthy (http://civil.iisc.ac.in/~tejas/)

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Biodiversity in a warmer world: lessons from soil nematodes



Predatory female nematode Clarkus sp.
Image by M. Ciobanu

By Madhav Thakur, postdoctoral researcher, German Centre for Integrative Biodiversity Research (iDIV)

 

John Haldane, the famous evolutionary biologist, popularized the immense diversity of beetles by writing: “The creator, if he exists, has an inordinate fondness for beetles”.  I wonder if Haldane was aware of nematodes. Nematodes are incredibly diverse and abundant tiny worms living almost everywhere on planet Earth. Some estimates point that we may have a million of nematode species on Earth. I remember Tom Bongers, a world-known nematode taxonomist, in his lectures saying every time one samples a forest soil, s/he is likely to find a new species of nematodes.

At the beginning of my PhD in 2013, I got interested in how on-going climate warming affects biodiversity. At this point, I already was familiar with the free-living nematodes in the soil, and in particular, impressed by their omnipresence in any environment.  After the consultations with my PhD supervisor, Prof. Nico Eisenhauer, I decided to investigate whether warmer soil harbours less or more diversity of nematodes. Fortunately, I was offered to investigate nematode diversity in a long-term climate warming experiment in the meadows of Cedar Creek in Minnesota, USA. This climate warming experiment was unique for two reasons: 1) Climate warming was experimentally crossed with plant diversity and, 2) Plant diversity treatments in this experiment were the part of the BigBio experiment, which is one of the oldest biodiversity experiments in the world. Further, I was very excited to work with Prof. David Tilman, who is the principal investigator of this experiment, and well-known for his contributions for our understanding of the causes and consequences of biodiversity.



Areal view of Biodiversity & Climate experiment
Image by J. Miller

Once I was able to collect nematodes and identify them with the help of colleagues (Dr. Marcel Ciobanu in particular), I started getting back at the warming and biodiversity question. Since we understand biodiversity in many different ways, I calculated many different metrics of biodiversity and see whether I could find any consistent pattern. The most striking and consistent pattern was that warming both increased and decreased nematode diversity. The key was whether the nematodes were from plant monoculture soils or from the soil of diverse plant communities. Warmer plant monocultures were lower in nematode diversity, whereas warmer diverse plant communities were higher in nematode diversity. Although these results were exciting, I did want to explore further. With the help of Dr. Oliver Purschke, I investigated whether warming also structures nematode communities in a given way. Indeed, the results revealed that nematodes were taxonomically more similar than expected in warmer soils independent of plant diversity. So even if warming increased nematode diversity in diverse plant communities, nematode communities become increasingly similar. We published these results recently in Science Advances.

 

The climate warming and biodiversity question will stay with ecologists for a longer time. Our results do provide some clues by using one of the most diverse and abundant organisms. At this stage, I am even more curious by the question how general are our results. Whether Haldane’s beetles, or our nematodes, biodiversity in a warmer world is very likely to be different than the past and present biodiversity.

 

Reference

M. P. Thakur, D. Tilman, O. Purschke, M. Ciobanu, J. Cowles, F. Isbell, P. D. Wragg, N. Eisenhauer (2017), Climate warming promotes species diversity, but with greater taxonomic redundancy, in complex environments. Science Advances 3, e1700866. Doi: 10.1126/sciadv.1700866.

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Earthworm invasions in northern forests



Lumbricus terrestris
Image by E. Cameron

By Erin Cameron, Postdoctoral Researcher, Helsinki University, Finland

 

 

Finishing my paper route always took longer on rainy days when I was a kid – I had to walk slowly to avoid stepping on earthworms and occasionally I stopped to move them off the sidewalk. I would never have believed that earthworms were invasive in much of Canada and the northern United States! In those previously glaciated areas, there are no native earthworms, but instead only European earthworms that were introduced to North America with the arrival of European settlers.

Earthworm populations can only expand about 5 to 15 meters per year on their own, and consequently people play a key role in their spread. For my master’s thesis with Dr. Erin Bayne at the University of Alberta, I tried to determine how earthworms were spreading in Alberta’s boreal forest. I was sold on the research question once I realized that I’d need to canoe or kayak across lakes to test whether earthworms were most common near boat launches where anglers might dump their earthworm bait. After a couple near misses but only one capsizing incident, we found that earthworms were present at approximately 70% of the boat launches and roads sampled, but only 35% of far shores and less than 15% of forest interiors. They were also more likely to occur at older roads than more recently built roads, suggesting that earthworms were introduced by vehicle traffic (their eggs can become stuck in tire treads) not during construction of the roads.

After examining how earthworms were being introduced, we started to investigate their effects in the boreal forest. Surprisingly to most people, earthworms do not always improve soil health or benefit other organisms. When exotic earthworms invade forests where there are no native earthworms, they consume leaf litter layers, mix organic and mineral soil horizons, and affect nutrient cycling. These impacts on soil structure and ecosystem functioning can then lead to cascading effects on other organisms. In northern Alberta, we found that earthworms decreased the thickness of the leaf litter layer, reduced the abundance and diversity of microarthropods, and decreased plant biomass, depending on the species. Not all species were negatively affected though – one of the key predators of earthworms, the American robin, was more likely to occur in areas where earthworms were present.



Sampling for earthworms in the boreal forest
Image by R. Rocha

Earthworm invasions are at an earlier stage in northern boreal forests than temperate hardwood forests, where the deep burrowing and mineral soil dwelling species that cause the largest changes are more widespread. At our study sites, the most common species is a litter dwelling species called Dendrobaena octaedra. But because most people are not aware that earthworms are invasive, they continue to introduce earthworms by dumping their bait, moving soil, or not cleaning their tires when travelling to remote areas. We started a citizen science project to collect data on earthworm distributions across Alberta, which at the same time serves to increase public awareness about earthworm invasions: http://worms.educ.ualberta.ca

 

However, earthworm invasions are occurring globally, rather than only in North America. We also lack data on distributions of native and exotic species of earthworms at broad scales, making it difficult to determine the key factors driving their distributions. To address this issue, we started a working group (sWORM; https://www.idiv.de/?id=429) at the German Centre for Integrative Biodiversity Research (iDiv) to synthesize data on earthworm distributions. Let us know if you have earthworm data and want to participate!

 

Further reading:

Cameron EK, Bayne EM, Clapperton MJ. 2007. Human-facilitated invasion of exotic earthworms into northern boreal forests. Ecoscience 14: 482-490.

Cameron EK, Bayne EM. 2012. Invasion by a non-native ecosystem engineer alters distribution of a native predator. Diversity and Distributions 18: 1190-1198.

Craven D et al. 2016. The unseen invaders: introduced earthworms as drivers of change in plant communities in North American forests (a meta-analysis). Global Change Biology 23: 1065-1074.

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The Mysterious Case of the Microbe in the Soil



Microbial biosensors sense and environmental signal and,
in response, produce a measurable reporter such as a gas.
Image by E. Fulk

By Emm Fulk, graduate student, Rice University, Houston, TX, USA

 

Flagella? Check. Cell wall? Check. Cheesy music? Yes, that's right. What's a microbial detective without a melodramatic theme song?

Studies of soil microbiology have traditionally - and necessarily - been conducted from the outside in. Net fluxes of nutrients and gases from the soil environment can be chemically measured. High-throughput sequencing techniques can give metagenomic data, which provides a snapshot of the general composition of a soil microbiome. This is, essentially, a stakeout - we can get a general sense of a soil  community by observing the surrounding environment and may be able to infer some activities by measuring who and what comes in and out. These strategies give us an overall picture of soil communities and their net interactions within the ecosystem but lack the spatial, temporal and chemical sensitivity to fully understand the internal  dynamics of soil microbiomes.

We need a microbe on the inside.

The idea of using living microbes as biosensors is not especially new. To survive and adapt to new environmental stresses, such as nutrient or water deprivation, microbes have evolved networks to sense these changes and adapt their metabolism accordingly. Tying these naturally-evolved systems to a measurable reporter (for example, a fluorescent protein) is a logical step for understanding how microbes interact with their environment. Think of a light bulb and a light switch. The light switch senses whether it is on or off. The light bulb reports on the ON/OFF state of the light switch. Even if you can't see the switch, you can infer whether it is on or off by looking at the light bulb. Likewise, we can detect when a particular environmental condition elicits a microbial response by monitoring the production of the reporter.

I know just the microbe for the job… he's sensitive, discreet and reports only to me.

For microbial biosensors to be useful in soil, their sensors and reporters must both be suitable for monitoring interesting  
environmental conditions - for example, drought conditions, concentrations of nitrogen or carbon species, or cell-cell  
communication signals. Sensors for -osmotic stress, nitrate, quorum sensing molecules and various heavy metals have been or are being  
developed. These systems must also be sensitive to an environmentally relevant level of the signal. If too sensitive or not sensitive  
enough, reporter production is not triggered at the right times to give useful information. Ideally, reporters need to be measurable in  
situ. Traditional fluorescent or pigmented reports can't be used because, well, you can't see them in soil. Expanding our toolbox of  
reporters would allow us to monitor cell growth as well as environmental response and to measure multiple signals.

The name's coli. Escherichia coli.

Even after engineering a useful biosensor, it remains to find suitable host microbe. Most synthetic biology is initially done in E. coli, because it is relatively well understood and easy to engineer. E. coli can also a good first organism to test biosensor function. Expanding our ability to engineer other microorganisms is a key challenge both for biosensors in soil ecology and for synthetic biology as a whole. Numerous other organisms - for example, several soil-dwelling Pseudomonas species - have successfully been engineered as biosensors. However expanding our repertoire of bacterial hosts will enable biosensors to be used in more microbial communities.

Where were the suspects on the night of the…high nitrate concentration?

Recent developments in synthetic biology have greatly expanded our ability to manipulate microbes and perform increasingly difficult computations. For example, microbes can now be programmed to produce a reporter only if both signal 1 AND signal 2 are present. Other logic functions (1 OR 2, 1 AND NOT 2, etc.) could allow for studying specific combinations of environmental conditions, such as in hot spots or during hot moments.




In standard biosensors without memory, microbes produce a reporter directly
in proportion to the level of signal. In biosensors with memory,
the reporter is induced by the first instance of the environmental cue and remains on thereafter.
The top cartoon shows how these two scenarios compare at the level of individual microbes.
The bottom graph illustrates how reporter production differs at the whole-sample level.
Image by E. Fulk


Additionally, microbes can now be programmed to "remember" certain events. By using a class of enzymes called DNA recombinases, permanent changes can be made in the DNA of a microbial biosensor in response to the environmental signal. This change catalyzed by the DNA recombinase - specifically, a reversal of a short section of DNA - can be induced by the environmental signal and results in permanent, stable, and heritable expression of the reporter. Thus, the microbes have memory of the signal. Think again about the light switch - once the light switch is turned on for the first time, the light bulb is permanently on whether the switch turns off again. This could be useful for studying long-term behavior of microbes where consistent measuring of the signal is not always possible, or for situations where suitable reporters are limited (since the recombinase-mediated reversal of the DNA sequence is a sort of reporter in itself).

It was the Rhizobia! Case closed.

Well, not quite. This is just a small slice of the synthetic biology tools that may be of interest, and there are still engineering challenges to be addressed. Most crucially, however, we need to find the right soil ecology mystery to solve.

 

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Urban Expansion, Land Cover, and Soil Ecosystem Services

By Ciro Gardi, Scientific Officer, Animal & Plant Health Unit, European Food Safety Authority, Parma, Italy

 

We are aware, especially the readers of this blog, of the immeasurable value of soil and of its unique and essential role. The focus of the Global Soil Biodiversity Initiative is the variety of living forms that soil can host, and it is clear that in order to have soil biodiversity we need to have soil. In other words, we will not be able to protect soil biodiversity if we are not protecting the soil as whole. Unfortunately, there are several processes leading to soil degradation and the intensity and combination of them vary across the globe.

One of the most irreversible process, often overlooked, is represented by soil sealing, consequent the expansion of urban and industrial areas or the construction of transport infrastructures. The intensity of this process can be extremely high, especially in the countries with fast economic and/or demographic growth, and often it occurs at the expenses of the most valuable and fertile soils. After the soil is sealed, due to the construction of buildings, roads, etc., all the soil ecosystem services are lost or severely compromised. Not only to the capacity of soil to be used for agriculture, but also its capability to infiltrate water, to store carbon, etc.

A newly published book, Urban Expansion, Land Cover and Soil Ecosystem Services, is an accurate overview of the impact of urban expansion processes on the provision of soil ecosystem services. From the analysis of the magnitude and intensity of these processes at global scale, to the assessment of the impact of soil sealing and land take on the capability of soil to produce food and biomass. The role of soil in agricultural production is probably the most obvious: according to FAO, 95% of our food derive directly or indirectly from soil, and by to 2050 we will need to increase the food production by 70%. There are however other soil ecosystem services essential for human wellbeing, and more in general for the protection of life on the Earth. The regulation of water cycle and most terrestrial biogeochemical cycles rely on soil. The existences of the majority of terrestrial ecosystems also depend on soil.

It is essential then to have a more responsible use and planning of this strategic and pivotal non-renewable resource, sharing our knowledge of its values and role, with policy makers, land use and urban planners, but also citizens. In Europe, a public campaign has been recently launched (People4Soil - https://www.people4soil.eu/en ) to request the declaration of a soil protection Directive at the EU level. This is an example of the efforts of awareness raising that made possible to spread among citizens the comprehension of the role of soil, as essential element of the natural capital.



Often new residential, commercial
or industrial buildings are realised
only for speculative reasons and remain
unused for ever. Photo credit: Ciro Gardi



Soil sealing prevents, or strongly
compromise all soil ecosystem functions.
This is an example of an exception:
the vigour of this plant is able to break
the asphalt coverage sealing the soil.
Photo credit: Ciro Gardi



An example of a construction site.
Soil is subject to several types of
degradation processes: compaction,
contamination and finally sealing.
Photo credit: Ciro Gardi

 

 

Learn more about the book here:

https://www.routledge.com/Urban-Expansion-Land-Cover-and-Soil-Ecosystem-Services/Gardi/p/book/9781138885097

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Cast in clay

By Max Helmberger, graduate student, New York State Agricultural Experiment Station, Geneva, New York, USA

 

Growing up an only child on a dirt road in the Northern Minnesota woods, I spent a lot of time outside, overturning the many thousands of glacier-strewn rocks around my house (at least the ones small enough to move) and gazing in awe at the centipedes, isopods, and invasive European earthworms underneath (which were promptly relocated to our compost bin). My first interest in soil in an academic context came the year after I graduated from high school, when I took a soil science course at my local community college. That class instilled in me a firm conviction that soil is humankind's most important natural resource, and clued me in to the fact that, in soil, there's far more than meets the eye.

After transferring to the University of Minnesota in Duluth to major in Biology, I took an entomology class and worked as a research assistant in an aboveground plant-insect ecology lab. I had always loved insects, arthropods, and invertebrates in general, and I greatly enjoyed the coursework and research experience, but wanted to connect it with my love of soil. I started searching Google Scholar for “soil arthropods”, and a few dozen soil ecology articles later, I was hooked, and I eventually sought and out and accepted a M.S. position in the lab of Dr. Kyle Wickings at the New York State Agricultural Experiment Station, a satellite campus of Cornell University located in Geneva, New York. What I didn't know as I was reading all those papers, was that I would end up reporting all the knowledge I gained from them in a most unusual way.

Clay animation, for those unaware, is a form of stop-motion animation in which clay models are photographed, moved slightly, photographed again, and so on. The pictures are strung together and played in rapid succession to give the appearance of movement. Wallace and Gromit is arguably the most famous example of the medium. When I was 7 years old, my grandmother took me to an hour-long class in clay animation. I made a video of an anthropomorphic flower dancing to some sort of classical music riff. The VHS tape is certainly hiding somewhere in my house. Fast forward to my undergraduate entomology class, and I drew on those old memories for the course's final project to make a clay animation video on the life cycle of the gallmaking fly Eurosta solidaginis, the main study organism of my research advisors’ laboratory. The video was crude by my current standards, but got me a good grade in the class nevertheless.

At Cornell, where I'm currently working on my M.S. in Entomology, I’ve had the opportunity to draw from a unique funding source called the Extension/Outreach assistantship. Instead of working off a grant or being a teaching assistant (something difficult to do when based at a satellite research campus rather than the main university campus), I earned my stipend via progress on a variety of extension and outreach projects of my advisor's and my own devising. When applying for the assistantship and listing my project objectives, my advisor and some of the faculty members on the Extension/Outreach assistantship committee were skeptical until they saw the E. solidaginis video as a proof-of-concept, and in Spring semester of 2017, I was off to the races. To avoid some of the mistakes I made with my previous clay animation, I was very careful with how I went about planning and "filming" the videos. I wrote out all of my narration in advance as well a clear script of what specific actions I would portray. Then, I timed myself reciting the narration for each scene, and so could know in advance how many frames of animation I needed. This, combined with a nice DSLR camera as a Hanukkah present from my parents, would allow for much more cohesive and polished videos than my tale of the gallmaking fly. In the end, I produced three videos, Life Cycle of Entomopathogenic Nematodes, The Soil Food Web, and Ecosystem Services in Agriculture (though the latter includes some functions performed by aboveground organisms). My funding next semester will be from the same Extension/Outreach assistantship, so I plan to produce at least one more video in addition to my other projects, possibly two. From start to finish (writing the script, creating the models, creating the set, taking the photographs, editing the video, and recording the narration), each video took me between 15 and 20 hours to make. Each video consists of 350-400 individual images, with some being repeated here and there. They’ve been received well in the department, and the entomopathogenic nematode video has even been incorporated into several extension talks. The rest of the videos have ben showcased in a few classroom settings, and I am hoping to further expand their reach. I plan to make at least two additional videos in the fall, as I will again be funded through an Extension/Outreach assistantship.

My ultimate goal is that these videos provide an accessible way of communicating soil ecology and biodiversity to lay audiences, especially young ones. Despite being the prototypical "science nerd" growing up, and being an avid consumer of books, documentaries, and Web resources about the natural world, many of the soil animals I read about during my first forays into the primary literature were completely unknown to me. I had no idea there were mites beyond dust mites and the various parasitic taxa, and certainly didn't know there were any mites as cute as a galumnid oribatid. I had never even heard of diplurans, symphylans, pauropods, and some of the other more obscure soil organisms. I knew what a pseudoscorpion was, but didn’t know I could find them in the peat bog less than a mile from my house. And that rubbed me the wrong way. It's hard for young people to learn about the marvels of soil biodiversity, especially on their own. I know that 7 year-old Max would have gotten much more out of these videos than from one about a dancing flower, and he would have started playing around with Tullgren funnels much earlier than junior year of college. As such, if you enjoy my videos, I encourage you to share them however and wherever you like. They are available online as a YouTube playlist.

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Digging deeper in urban ecology: the urban ecosystem convergence hypothesis

By Dietrich Epp Schmidt, Graduate Reserach Assistant, University of Maryland

“Even the mightiest of us return to dust, they say. Nothing remains but these shattered fragments of their kingdom… But that's not really the point, is it? These shattered fragments remain- that's the point. We look upon the magnificent temples and stelae and ball courts of Caracol in awe. There's no despair here. The Maya built something astounding and permanent. Look on our works, ye mighty, and revere. The ancient Maya speak to the twenty-first century through those temples and say: We did something amazing here.

What will our descendants think when they come upon Chalillo [dam]? When they scrape away the deep layer of dirt covering its stepping-stone facade, what will they make of the dogleg design, the Chinese gauges, the long-stopped turbines? What will they make of the skeletons and fossils of birds long gone? Will they connect the two?"

 

-Bruce Barcott, The last flight of the Scarlet Macaw

 

For a very long time, humans have experienced the world as having two fundamental domains: that which we understand as being under human control, and that which is not. Canonically, we call the latter “natural” and the former “unnatural;” and while the broader society may perceive there to be a distinction between the two, we know that our existence has an impact on ecological process, and vice versa. Our social processes, which are as basic to us as defining our identity and competing for status within our community, are intricately linked to our individual and global consumption of resources. Our economic trade is itself an ecological process that transports resources and organisms across the globe [see telecoupling]; our civilization alters community composition and function wherever we can make a living, all the while affecting global biogeochemical cycles. Our framework for understanding the role of social process on ecosystem function is just in its infancy, and there is no vernacular language for describing the built environment as an ecosystem. This is not how our society understands the environments we inhabit. One goal of the Global Urban Soil Ecology and Education Network (GLUSEEN) is to increase the exposure of urban citizens to the important role that soils play in maintaining ecosystem health.

Within the discipline of ecology, there exist frameworks to describe the outcomes of human behavior in terms of ecosystem process. For instance, biotic homogenization (BH) describes a process of convergence among biotic communities; generally communities become more similar (converge) when endemic specialist species are extirpated and generalist species come to dominate. Convergence is a process that is often applied to understanding the effect of both urbanization and agriculture, where the implied (or assumed) mechanisms are generally anthropogenic disturbance and/or facilitated dispersal. In this instance, BH describes how land-use conversion (habitat loss) drives local extinctions, while the cultivation of exotic species facilitates the dispersal of a common set of organisms. In this context, BH helps to explain the paradox of high urban and peri-urban biodiversity concomitant with significant global biodiversity loss. Endemic species go extinct, while opportunists thrive in the human-disturbed landscape (see, for example, this). To bring the mechanisms into focus, BH has been reformulated somewhat as the Urban Ecosystem Convergence Hypothesis, which relates structural changes in the built environment to changes in community process. It predicts that if urban landscapes are constructed and maintained in a similar manner (causing a convergence of habitat characteristics across biomes), then their biotic community and ecosystem processes should converge as well. For example, in their paper entitled “Ecological homogenization of urban USA,” Groffman et al. show that the practice of maintaining irrigated lawns causes a convergence of biophysical conditions across biomes within urban areas in the United States; in temperate forest systems, land-use conversion to lawns increased surface temperatures by reducing shade and evaporative cooling that normally occurs in the canopy. Whereas irrigating arid land for lawns increased evaporative cooling at the ground level, causing the two environments to converge with respect to temperature as well as humidity.



Image recreated from Pouyat et al., 2017
Journal of Urban Ecology.

The Global Urban Soil Ecology and Education Network (GLUSEEN) applied the Urban Ecosystem Convergence Hypothesis to urban soils. We sampled from soils that occurred within four different land-uses, which were categorized to represent land-use histories that are typical of urbanized landscapes (published here). These four categories were reference, remnant, turf and ruderal. Reference sites served as our control; they were sites located outside of the urban matrix, which are representative of the historic state of the ecosystem and are being managed to mitigate human impact. Many reference sites were areas set aside for habitat conservation. Remnant sites are similar to reference sites in community structure but occur within the urban matrix, and thus exposed to urban environmental factors. Turf sites were defined as sites under management to maintain a turf-grass system, which include municipal, residential, or park lawns. Ruderal sites were defined as sites that have experienced recent and substantial disruption of the soil profile, and typically were areas with a history of demolition or construction activity. Using these land-use and cover categorizations, we asked whether specific types of land-use and cover (both largely an outcome of cultural processes) caused physicochemical properties and microbial communities of soils to converge; and whether these changes result in a convergence of function among these soils.



Within-group variance of edaphic factors, among land-use;
2a shows the convergence of soil pH, OC, and N
under turf and ruderal land-use relative to the reference;
2b shows the divergence of P and K under turf
and ruderal land-use relative to the reference.
Recreated from: Pouyat et al., 2015.

As an assessment of the soil habitat characteristics, and to test the first question, we measured edaphic features such as phosphorus (P), nitrogen (N), and potassium (K) availability, as well as other characteristics such as organic carbon (OC) and pH. To quantify and identify the archaeal, bacterial, and fungal community, and to test the second question, we used quantitative PCR and amplicon sequencing. And finally, as a test of soil function, we conducted a decomposition experiment using tea bags in each of the study sites (see here). First, we found that in fact some physicochemical properties of soils converged under turf and ruderal land-use and cover types. Soil pH, OC, and N in particular converged. However, not all characteristics converged as K and P actually diverged under urban land-use (Figure 1).  We believe that it’s likely that cultural differences in how fertilizers are formulated (N vs N:P vs N:P:K fertilizers) and the variability in their rates of application may explain the increased variability among P and K nutrients; while N is also enriched systematically by fossil fuel combustion that leads to consistent atmospheric deposition of N in urban areas (and thus convergence). The convergence of soil pH is likely related to the widespread use of concrete, and the resulting concrete dust in urban areas; the calcium oxides and carbonates found in concrete effectively act as a liming agent as they dissolve, buffering soil pH towards a more alkaline condition. And finally, while specific land-use and cover types might have differing effects on the soil OC concentration, the effects within each land-use are consistent; disturbances often result in lower OC, while irrigation and fertilization in the absence of disturbance may actually increase carbon storage in soils. Thus, cultural factors may drive convergence of some habitat characteristics while causing other habitat characteristics to diverge.



Within-group variance of the fungal, bacterial, and archaeal
communities; the fungi converge in ruderal sites
relative to reference,the bacteria do not converge,
and the archaea converge in the turf and ruderal sites.
Recreated from Epp Schmidt et al., 2017.

Our next question was whether communities of organisms living in the soil converge under similar land-use and cover. We found that of the three phylogenetic domains making up the soil microbial community, the archaea and fungi exhibited a marked convergence, while bacteria did not (published here). We also showed that this convergence may be driven by different ecological factors. For example, we found that convergence in the fungal community was largely due to the loss of ectomycorrhizal fungi (ECM), while the convergence of archaeal communities was due to the increased abundance of ammonia oxidizing archaea. ECM function as symbionts with woody plants, and thus are highly reliant on the abundance of their host species. When land is converted from forest to any non-forested urban land-use, it appears that there is no longer viable habitat for most of these species. Archaea, on the other hand, actually increased in overall abundance under lawn use, and their community became dominated by organisms that derive energy from the oxidation of reduced nitrogen species. This means that, unlike for fungi, the N enrichment of urban environments is favorable to these members of the archaeal community. Moreover, since absolute abundance increased and richness also increased, it appears to be the case that the metabolic differentiation among archaea allowed convergence to occur without competitive exclusion. Therefore our dataset demonstrates the two mechanisms by which convergence might happen; a loss of unique species, or an increased dominance of just a few species that can be found in all sites. It is of course possible that both mechanisms operate in tandem to cause convergence.

The urban landscape represents the zenith of human development; it is the cultural hub of our civilization and the control center for our social process. It is also the area with the highest land-use intensity, and therefore is the most significantly disrupted ecosystem. With our dataset, we are able to show some effects that human culture has on ecosystems; the cultural process that drives the globalization of our economy and the homogenization of our global culture also has global impacts on ecosystem process via the local decisions that land managers make. Our data demonstrates that human culture may cause either a convergence (soil pH, N and OC) or divergence (P and K) of soil habitat characteristics, and that microbial communities may (fungi, and archaeal) or may not (bacteria) converge as a result. We were also able to determine multiple mechanisms that drive convergence. The fungi likely converged due to our impacts on cover (reducing the abundance of host species), while the archaeal likely converged because of our N enrichment of the urban landscape (enhancing the fitness of organisms that rely on certain forms of N metabolism). Thus there are specific interactions between human alteration of the landscape and biotic community response. The impacts of urbanization on the function and makeup of the biotic community may be long lasting, and indeed, might even outlive civilization itself. In 2008, when he published his book The last flight of the scarlet macaw, Bruce Barcott could scarcely have known that within a decade scientists studying the Mesoamerican landscape would be using the color of tree leaves (by reflecting laser light off of them from high altitudes) to discover the location of lost ancient Mayan structures. It is remarkable that urban centers, constructed and abandoned nearly a millennium ago, can still be discovered using their legacy impact on the biotic community.

 

Read the full manuscript here:

Epp Schmidt, D. et al. 2017. Urbanization erodes ectomycorrhizal fungal diversity and may cause microbial communities to converge. Nature Ecology & Evolution doi:10.1038/s41559-017-0123

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Soil ecologists define research priorities

By Nico Eisenhauer, Professor for Experimental Interaction Ecology, German Centre for Integrative Biodiversity Research

Many, if not most, of the ecosystems on Earth are dependent on, or substantially influenced by, interactions and processes occurring within and among the planet’s soils. The remarkable biodiversity harbored in soil provides essential ecosystem services, and the sustainable management of soils has attracted ever-increasing scientific attention. Although soil ecology emerged as an independent field of research many decades ago, and we have gained important insights into the functioning of soils, there still are fundamental aspects that need to be better understood to ensure that the ecosystem services that soils provide are not lost and that soils can be used in a sustainable way. In a recent Opinion Paper (Eisenhauer et al. 2017; https://doi.org/10.1016/j.pedobi.2017.05.003), we highlight some of the major knowledge gaps that should be prioritized in soil ecological research. These research priorities were compiled based on an online survey of 32 editors of Pedobiologia – Journal of Soil Ecology. The questions were categorized into four themes:

(1) soil biodiversity and biogeography;

(2) interactions and the functioning of ecosystems;

(3) global change and soil management;

(4) new directions.

While some of the identified barriers to progress were technological in nature, many respondents cited a need for substantial leadership and goodwill among members of the soil ecology research community, including the need for multi-institutional partnerships, and had substantial concerns regarding the loss of taxonomic expertise. Global efforts such as the Global Soil Biodiversity Initiative suggest that meaningful collaborative endeavors among researchers could be possible and may represent a starting point from which to build this concerted effort to address the questions presented in our Opinion Paper.




Interaction in the soil caught in the act: a predatory mite from the family Bdellidae
feeding on the springtail Sminthurinus elegans. Image by Andy Murray.


Reference:

Eisenhauer N, Antunes PM, Bennett AE, Birkhofer K, Bissett A, Bowker MA, Caruso T, Chen B, Coleman DC, de Boer W, de Ruiter P, DeLuca TH, Frati F, Griffiths BS, Hart MM, Hättenschwiler S, Haimi J, Heethoff M, Kaneko N, Kelly LC, Leinaas HP, Lindo Z, Macdonald C, Rillig MC, Ruess L, Scheu S, Schmidt O, Seastedt TR, van Straalen NM, Tiunov AV, Zimmer M, Powell JR (2017) Priorities for research in soil ecology. Pedobiologia 63: 1-7.

http://www.sciencedirect.com/science/article/pii/S0031405617301063

 

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Ploughshares are swords… if you are an earthworm

By Olaf Schmidt (University College Dublin, Ireland) and Maria J. I. Briones (University of Vigo, Spain)

 

Let us beat our swords into ploughshares” is an evocative slogan used by peace builders around the world. However, when it comes to earthworms, ploughs are swords that can kill you and destroy your homes.

We have known for a long time that tillage operations impact large soil macrofauna such as earthworms, directly by mechanical injury and indirectly by destroying their channels and burying surface plant residues. For example, a study from Ireland showed that very intensive soil cultivation for potato production (including grubbing, destoning and ridging) can virtually eliminate earthworm populations. Many such individual studies exist around the world. For the first time, scientists have assembled all available primary research results from individual field experiments from the five continents and analysed them together in a meta-analysis, a statistical tool that allows us to look for (and quantify) common effects or trends across many independent studies.

The scientists from the University of Vigo, Spain, and University College Dublin, Ireland, extracted data from 165 publications, from across 40 countries, published between 1950 and 2016. Each of the studies investigated earthworm populations under conventional tillage (inversion tillage such as mouldboard ploughing to 25 cm depth) and other forms of reduced tillage (such as soil loosening up to 25 cm depth and no tillage).

The findings published in the scientific journal Global Change Biology show a systematic decline in earthworm populations in soils that are ploughed every year. The deeper the soil is turned, the more harmful it is for the earthworms.

Results show convincingly that most forms of reduced tillage will increase earthworm numbers and biomass. Among the five forms of reduced tillage analysed separately, the most positive effects were seen in no-tillage (direct drilling) and also superficial tillage or soil loosening <15 cm (non-inversion tillage). Another form known internationally as Conservation Agriculture (which involves retention of at least 30% of organic residues or mulching) also prompted a significant increase in earthworm populations (see figure). These reduced tillage practices are increasingly being adopted world-wide due to their environmental benefits in terms of erosion control and soil protection. They are economically attractive because not having to plough brings savings in cost, labour and fuel.



The effect of the different forms of reduced tillage treatments on earthworm abundance (a) and biomass (b) as a percentage of the control (conventional ploughing). Treatments were No-tillage, Conservation Agriculture (CA), Shallow soil loosening (SSL), Deep soil loosening (DSL), and other forms of Reduced tillage (RT). Mean effect and 95% confidence intervals are shown. Sample sizes are shown on the right of each treatment (number of control–treatment pairs / number of studies). Reprinted with permission of John Wiley & Sons Ltd. from Briones MJI and Schmidt O: Conventional tillage decreases the abundance and biomass of earthworms and alters their community structure in a global meta-analysis. Global Change Biology DOI:10.1111/gcb.13744. Copyright © 2017 John Wiley & Sons Ltd.

The study also analysed ecological groups of earthworms (namely epigeics, anecics and endogeic) and the most common species separately. According to the findings, the earthworm species most vulnerable to tillage are the larger ‘anecic’ earthworms that create permanent vertical burrows and feed on soil surface residues. Of all species included in the study, the nightcrawler (Lumbricus terrestris) suffered most under conventional ploughing. The small ‘epigeic’ earthworms that live in the organic litter layers of soil and convert debris to topsoil were also found to be highly susceptible.

The study also analysed ecological groups of earthworms and the most common species separately. According to the findings, the earthworm speices most vulnerable to tillage are the larger ‘anecic’ earthworms that create permanent vertical burrows and feed on soil surface residues. Of all species included in the study, the Nightcrawler (Lumbricus terrestris) suffered most under conventional ploughing. The small ‘epigeic’ earthworms that live in the organic litter layers of soil and convert debris to topsoil were also found to be highly susceptible.



Lumbricus terrestris is an ‘anecic’ species,
seen here foraging at the soil surface at night.
Photo credit: Olaf Schmidt

These findings can be translated into advice for farmers in different parts of the world. Switching to reduced tillage practices is a win-win situation for farmers because they save costs and, in return, larger earthworm populations help in soil structure maintenance and nutrient cycling. The larger the populations of these beneficial soil organisms, the more of these beneficial functions a farmer will get – for free.  Earthworms are also good indicators of soil quality and soil health, it is easy to check for a farmer of his/her soil is in good status by just digging up a bit of soil and checking worm numbers (there are simple guides available that show how many worms you should expect in a spade-full of soil). We know of course that there is much more life in the soil (bacteria, fungi, mites, springtails, nematode worms etc), but to study them is difficult for non-specialists.  Earthworms are so useful because everybody can look for them easily.

Coming back to our opening slogan, when we speak about earthworm populations and soil protection, perhaps we should say “Let us beat our swords into ploughshares… but use them less often”. Reduced tillage practices will restore productive earthworm populations and help maintain soil structure, nutrient recycling and other biological soil functions.

 

Read the original manuscript here:

Briones MJI, Schmidt O (in press) Conventional tillage decreases the abundance and biomass of earthworms and alters their community structure in a global meta-analysis. Global Change Biology DOI:10.1111/gcb.13744

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Soil fauna responses to ecosystem disturbances



Soil fauna are central to soil ecology
Photo by R. Carrera-Martinez

By:  Dave Coyle, Southern Regional Extension Forestry and UGA – D.B. Warnell School of Forestry and Natural Resources.  Find Dave on Twitter @drdavecoyle, and check out his website: http://southernforesthealth.net/ Mac Callaham, USDA Forest Service – Southern Research Station.  See more about Mac at https://www.srs.fs.usda.gov/staff/447

 

Soil fauna are central to the field of soil ecology.  For a generation, scientific giants Drs. Dave Coleman, Dac Crossley, and Paul Hendrix at the University of Georgia - Odum School of Ecology taught a course on soil biology and ecology largely centered on fauna, training numerous ecologists and taxonomists.  After these three retired from UGA, however, the class went on a multi-year hiatus.  In 2013, Dr. Mac Callaham, a soil ecologist with the USDA Forest Service, and Dr. David Coyle, a forest health specialist with Southern Regional Extension Forestry and the University of Georgia, teamed up to bring the course back.  As part of the course, students from the Warnell School of Forestry and Natural Resources, Odum School of Ecology, and departments of Plant Sciences and Crop and Soil Sciences, conducted a literature review on the impacts of various land disturbance factors on soil biota and wrote term papers synthesizing their findings.  Student papers were combined and edited into the first-of-its-kind review on the impacts of disturbances on soil fauna, and was published in the journal Soil Biology and Biochemistry (http://www.sciencedirect.com/science/article/pii/S0038071717301530).



Publications on soil microbes have increased at a greater rate
than soil fauna. Modified from Coyle et al. 2017

Mac is well-known for his work with earthworms, and other macroinvertebrates, and in particular their responses to land-management activities.  Dave’s PhD research examined the impacts of a suite of non-native root-feeding weevils in the Upper Peninsula of Michigan.  Together, we have often lamented the fact that soil fauna – especially macrofauna – rarely get the attention they deserve (our opinion, obviously).  But, in researching this paper, we found that publishing trends confirm this notion (see right).  In recent years, there has been a disproportionate increase in papers dealing with soil microbes compared to soil fauna.  Anecdotally, with the exception of earthworms, ants, and a select few economically important taxa (think crop pests like corn rootworm, or citrus root weevil), soil fauna are somewhat ignored.  And for those of us who work on soil fauna, that isn’t cool.  Sure, we know that microbes are important actors in soil ecosystems, but they don’t act alone, and the soil ecology research community has amassed years of scholarship indicating that macrofauna can have big influences on the biomass, composition, and activity of soil microbes.

 

So, we acted like any good scientists and we wrote about it (and it was peer-reviewed, even!).  We synthesized what was known (and unknown) about the impacts of natural and anthropogenic disturbances on soil fauna.  For some taxa, there was very little information (published or otherwise) available.  For others, information was plentiful.  We know there are a LOT of complex interactions between organisms, disturbances, and their environments - especially when dealing with multiple scales (see below).  One of our challenges was capturing this heterogeneity and adequately conveying what it meant, in some cases, when information was only available from one scale.  Fortunately, there are some really good long-term studies in existence (e.g. Luquillo LTER: http://luq.lternet.edu/) that were great sources of information.  We examined natural disturbances like wind damage, flooding and water stress, drought, and fire; invasive plants and invasive invertebrates; and fire.  In each case we reviewed the impact of these factors on fauna in different parts of the soil (i.e. epigeic and endogeic/anecic).




Types and scale of ecosystem disturbances
Modified from Coyle et al. 2017


In what may hardly be considered groundbreaking to anyone who does research below the soil surface, the take home message was “it depends,” and it depends on a lot of different things.  A lot. The impacts of particular disturbances vary depending on the specific fauna in question.  It also matters at what scale – you may see fine-level impacts (e.g. in a plot) but at the watershed scale there is no discernable impact on fauna communities.  Short time duration versus long time duration also matters, as certain taxa are much better at “rebounding” after a disturbance than others.  Additionally, the issue of giving an accurate name to the organism under study (i.e. taxonomy) is important.  Most studies of soil fauna do not identify organisms to the species level, which makes interpretation of results incredibly difficult (not to mention complicating the comparison of data across studies).

 

Our review reaffirmed some things we already knew: belowground ecology is hard, scale is important, and there isn’t enough taxonomy in the world.  It also highlighted some things we didn’t know: the pace of publishing work on soil microbes is much greater than that dealing with soil fauna.  As one would expect, there are some significant gaps in the knowledge.  But that’s why we’re all here working and reading this blog, in the hopes of filling those gaps.

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Soundtrack for Soil Biodiversity



Summer storm rolls across the Colorado Prairie
Image by E. Bach

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

 

Summer is arriving at the Global Soil Biodiversity Initiative secretariat headquarters in Colorado, USA. Like many of you all, we’re gearing up an active field season, some long hours in the lab, and maybe a road trip or two.  I always look forward to this shift in work as it usually allows me to jam out to some great music in the background. Inspired by a recent groundwater-themed playlist from the European Geosciences Union, I set out to put together a Soundtrack for Soil Biodiversity!

The playlist captures several musical styles.  Each of the songs on the list relates to soil or a soil organism, either literally or metaphorically.  Stream the full playlist in the link below this list.

Do you have a favorite song about soil biodiversity?  Share with me, and we’ll keep building the list!  I’d love to hear what everyone is listening to all around the world!

 

  1. Another one Bites the Dust by Queen: OK, I know they don’t mean “bite the dust” literally, as say an earthworm might, but this song has pushed me through some long days of sample processing.

  2. The Trees by Rush: Classic rock exploration of forest succession: oaks vs. maples competing for light! No musical exploration of research examining the differences in C and N cycling in arbuscular mycorrhizal fungi dependent maples in contrast to ectomycorrhizal fungi dependent oaks, but you can read up on that here: Phillips et al. 2013. New Phytologist
  3. Nematode by Charlemagne: Nematodes crawling through the soil, decomposition, erosion, this song is about the role soil organisms play in renewing life.
  4. Dirt by Florid Georgia Line: “You came from it, and some day you’ll return to it.” This country-western ballad captures a lifetime lived on the red ultisols (acrisols) of the southeast USA.
  5. I like Dirt by the Red Hot Chili Peppers:  The title speaks for itself.
  6. Termite Hop by the Beatnik Termites: Rock & Roll teenage love story song, “everybody’s got to do the termite hop.”  Curious about the role of eusocial insects including termites and ants in soil food webs? Check this recent review: King 2016, Soil Biology & Biochemistry
  7. Centipedes by Hot Box Machine: Become one with centipedes on the run, lost in all the fun. Connect with the centipedes and feel at one with the Earth.
  8. Centipede by Knife Party: Centipede vs. Tarantula, scientifically informative electronic dance music. Check out this video of a real centipede taking down a tarantula.
  9. Buggin’ Out by A Tribe Called Quest: A rapper wrestles with the pressures of fame “in between the girt and the dirt.”
  10. Wormship by Illiterate Light: Exploring one’s feelings through the experience of an earthworm in a rainstorm
  11. Earth by Sleeping at Last: Life reflects the processes of the Earth, digging into it tells many stories of disaster and hope.
  12. Cio da Terra (The Earth in heat) by Milton Nascimento: Brazilian ballad praises the "miracle" of soil generating life (in Portuguese).

 

 

Bonus tracks (not on Spotify)

All my Friends are Insects by Wheezer: Well, one of their friends is an earthworm, which is not an insect, but still a lot of fun!

 

Dichotomous Key by Billy Kelly & Molly Ledford: This focuses on trees, and it’s a great musical introduction to a dichotomous key:

Trees by Molly Ledford & Billy Kelly

 

If you’re working on some writing projects and want music to focus, check out the instrumental version of Aesop Rock’s Music for Earthworms.

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The Ground Beneath Us: From the Oldest Cities to the Last Wilderness, What Dirt Tells Us about Who We Are

By Paul Bogard, Assisstant Professor, James Madison University, Harrisonburg, Virginia USA

 

I came to soil from the stars. In my first book, The End of Night: Searching for Natural Darkness in an Age of Artificial Light, I did my best to call attention to the value of darkness and the many costs from light pollution. Most people in modern cities and suburbs—especially the younger among us—have no idea what a real starry sky looks like, and no idea of what they’re missing. The fact that life on earth evolved with bright days and dark nights, and needs both light and darkness for optimal health, is something most of us never think about. When I began to imagine the next book I would write, I quickly realized the same is true of soil.

            It’s hard to believe that so few people understand how important soil is for our survival. Hard to believe, perhaps, until you hear the estimate that we in the west spend on average 90-95% of our time inside, cut off from the natural world. My new book, The Ground Beneath Us: From the Oldest Cities to the Last Wilderness, What Dirt Tells Us about Who We Are, began when I heard this stunning number. It wasn’t long before I realized that when we do walk outside, we mostly walk on pavement or asphalt. We have gone from being intimately in touch with the natural ground at our feet to being almost completely separated from it. From there, I began to see how this literal separation was symbolic of our separation from the different grounds that give us our food, our water, our energy, and even our spirit. I decided to explore the many costs of this separation, and the value of knowing the life at our feet.

            I certainly could have written an entire book about the wonderful subject of soil. But I decided to place our relationship with soil within the larger subject of our relationship with the ground. I was fascinated by the notion that the oldest spiritual traditions and the newest sciences tell us the same thing about the ground—that it’s alive, and that we would be wise to treat it carefully. I was intrigued as well by the different kinds of “grounds” that give meaning to our lives, such as battlegrounds and burial grounds, hallowed ground and ground we deem sacred. I was—and continue to be—especially interested in the question, Why do we live so separated from and ignorant of that which sustains us?



Becoming grounded on the Alaska tundra
Image from P. Bogard

            From the paved ground of New York, London, and Mexico City, to the grounds that would inspire me to ponder the sacred—the Nazi death camp at Treblinka in Poland, the wild tundra of Alaska’s southwest—I went looking for answers. Between these bookends I placed the chapters in which I sought to share the amazing, mysterious, known-more-than-ever and yet still-barely-known world of soil. The similarities to the stars came back to me here. The numbers so large they bend our brains as we try to comprehend. The galaxies upon galaxies beyond anything we now know. And especially, the way that once you know what’s out there, you never look at the sky—or, in this case the ground—the same way again.

Everywhere I go now I find myself looking at the ground with wonder. This is the feeling that stays with me after writing this new book. Wonder that everything growing—even us, if we pause long enough to realize—is anchored in soil, dependent on its life for our life. If I had one wish for the new book, it would be that it help more people to realize this, and bring to soil the attention and respect it deserves. It would be that we would walk outside, look down, and know what we have been missing.

 

Learn more about Paul and his writing at http://www.paul-bogard.com/ Tags: 

30 Questions for Soil Protistology



Saccamoeba
Image from S. Geisen

By Stefan Geisen, Department of Terrestrial Ecology & Laboratory of Nematology, Netherlands Institute of Ecology, Wageningen, The Netherlands

 

 

With 47 authors of the soil protist initiative, a group closely linked to the GSBI, we have just compiled an important opinion paper to highlight 30 key open study questions dealing with soil protists. We show that protists are a highly-underrepresented group of soil organisms, especially compared with the other microbial bacteria and fungi. However, there are several reasons why protists are important and should be prioritized or at least be included in future soil biodiversity studies!

 

 

 

 

Protists are incredibly diverse!
  • Protists are taxonomically highly diverse; they represent the majority of the eukaryotic tree of life where fungi, plants and animals are small monophyletic groups.
  • We also highlight that protists are morphologically diverse, ranging from bacterial sized taxa of few micrometers to several centimeters.
  • Furthermore, protists span a huge functional diversity of organisms; in addition to the mainly considered bacterivorous taxa, many protists feed on fungi, nematodes, a huge diversity is parasitic to animals and pathogenic in plants.
  Protists are of key importance in soils!
  • Without protists, bacteria and fungi would have few enemies!
  • Protists are a key link in soil food webs- without them most soil animals had no food!
  • Without protists, plants would suffer from nutrient limitation!




Fig. 1. Common free-living soil protists as visualized by size (lengths), morphology and phylogenetic affiliation
Modified from Geisen et al. 2017


This is just a fraction of what we highlight in the paper. For more info, check out the paper published in Soil Biology and Biochemistry. More updates on the soil protist initiative can also be accessed directly at https://soilprotists.wordpress.com/ and https://www.researchgate.net/project/Soil-protist-initiative.

 

Don’t hesitate to get in touch with us and be connected- protists are a key part of future research!

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Six ways soil biodiversity sustains us!

By Elizabeth Bach, Executive Director, Global Soil Biodiversity Initiative & Sustainable Leadership Fellow at the School of Global Environmental Sustainability, Colorado State University This blog post first appeared in the HUMANnature blog from the School of Global Environmental Sustainability, Colorado State University  

As a 5-year-old, one of my favorite things to do was play in the dirt.  My cousins and I would make “soup,” a mixture of soil, leaves, twigs, and some unfortunate bugs, with just enough water to easily stir.  The “recipes” were endless; from which part of the yard we got the soil, the ratio of twigs to leaves, the addition of a stray earthworm or insect all contributed to different “soups.”  As a kid, this play occupied my imagination for hours at a time.  As an adult, the interactions of soil and organisms, dead and alive, continue to fascinate me.  Just like a hearty stew, soil provides nutrients and energy to all organisms living aboveground, including people, and sustains ecosystems and humanity now and into the future.  How, you ask?  Well, here are 6 ways soil biodiversity sustains us!

 


Clockwise from top left: nematode, psuedoscorpion, burrowing owl, tardigrade. Photo credit: D. Robson, A. Murray, M. Knoth, N. Carrera.

 

 

  1. It’s Alive! Soil is home to ~25% of all described species on Earth.  These range from microscopic nematodes and tardigrades to small psuedoscorpians and even larger animals like burrowing owls.  But wait, there’s more!  The majority of soil species likely have not even been described by scientists.  That means soil holds numerous biological mysteries and likely supports far more than 25% of all species on Earth.  Soil is a frontier for exploration and discovery, right beneath our feet.
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    Left: Legume Gliricidia growing with maize in Zambia, Right: mushrooms. Photo credit: ICRAF, D. Endico

     

     

  3. It grows our food! Some soil organisms people can eat directly, like mushrooms, truffles, and some insects.  Other soil organisms help fruits, vegetables, and grains grow by recycling nutrients from dead plant material.  All plants, including crops, need nutrients, such as nitrogen, phosphorous, and potassium, from soil.  Most soils have limited reservoirs of these nutrients.  But dead plants, perhaps from the previous year’s crop, retain many of these nutrients in their tissue.  Soil organisms like insects, earthworms, micro-invertebrates, fungi, and bacteria break down dead plant material, releasing nutrients for new plant growth.  Soil organisms are critical to recycling nutrients to grow food and support sustainable farming.
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    Left: a child receives medication, Right: bacteria colonies can vary in color, shape, and texture. Photo credit: hdptcar, P. Turconi/Fondazione Istituto Insubrico di Ricerca per La Vida

     

     

  5. It helps us live long and prosper! Soil organisms impact our health and lifestyles in both negative and positive ways.  For example, anthrax, tapeworms, histoplasmosis, and brain encephalitis are all caused by soil organisms, including bacteria, pictured above.  Valley Fever, or coccidioidomycosis, is a nasty and often deadly disease caused by the soil fungus Coccidioides immitis native in the southwest USA.

    Other soil organisms can cure many diseases.  In soil, all these organisms live together in a community.  Some organisms have evolved defenses, such as antibiotic compounds, that can minimize disease agents.  Antibiotics like penicillin, originate from soil organisms, and can combat many illnesses caused by bacteria or fungi, like pneumonia and strep throat.  Soils are also a promising frontier in the development of new pharmaceuticals, which may reduce antibiotic resistance.  People around the world, like the child receiving a shot in the photo above enjoy healthy lives thanks to soil organisms.

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    Reindeer grazing. Photo from pixabay.com

     

     

  7. It supports wildlife! Nutrient cycling from decomposition also supports food for wildlife that we enjoy viewing, hearing, and in some cases, hunting.  Without soil biodiversity, wildlife would not have plants, fruit, and nuts to eat.  Much like the effects on people, however, soil can also harbor disease organisms that can make wildlife sick, or even result in death.  For example, in July 2016, anthrax, a soil bacterium, released from thawing soil in Siberia killed >1500 reindeer. That’s right, Santa’s sleigh may be running slow this year because of a soil organism!
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    Soil organisms filter excess nutrients and pollutants from water, keeping it safe for wildlife and humans. Photo credit: R. Kayser, Dept. Foreign Affairs & Trade

     

     

  9. It filters water! As water moves through soil, soil organisms use the nutrients and minerals dissolved within it.  This effectively removes excess nutrients and some pollutants before water reaches ponds, streams, lakes, rivers, etc.  This is important not only for clean drinking water for animals and people (pictured above), but also for healthy fish and other aquatic organisms.  In many areas of the US, there is extra nitrogen and phosphorous in surface waters, in part due to run-off of fertilizers from crop fields and lawns.  When there is excess nitrogen and phosphorous in water, algae use it grow, consuming large amounts of dissolved oxygen.  Reduction in dissolved oxygen can cause fish and other large aquatic organisms to suffocate, generating a “dead zone,” also known as hypoxia.  The 2016 “dead zone” in the Gulf of Mexico was estimated to be about the size of Connecticut (5,898 square miles)!  Soil organisms can reduce this nutrient load, and the number of algae that grow, keeping our waters oxygenated and healthy.

    Soil biodiversity also helps store water in soil.  Earthworms, insects, and other animals create tunnels, which allows water to flow into the soil more easily during precipitation events.  In addition, soil organisms generate organic matter, made up of the byproducts of biological metabolism (think compost) that gives soils a dark color.  Because soil organic matter is charged, it holds water between organic molecules, allowing soil to store more water than clay, slit, and sand particles alone.

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    Cyanobacteria (top left, right) oxygenated Earth's atmosphere, Soil organisms cycle greenhouse gases like carbon dioxide (bottom). Photo credit: K. Siampouli, Futurilla, Art by MarkAC, EU Joint Research Center; Numbers calculated by US DOE, Biological & Environmental Research Information System.

     

     

  11. It recycles the air! Before plants covered our planet, cyanobacteria (pictured above) used simple carbon molecules and minerals from rocks as energy sources.  This released oxygen, which eventually built up in the atmosphere to levels that could support the evolution of more microbes, plants, fungi, and animals, like us.  We still rely on plants and soil organisms to maintain enough oxygen in the atmosphere for us to live. Soil organisms also cycle greenhouse gasses, which trap heat near the surface of Earth (pictured above, bottom panel). 

    Soil organisms can both pull greenhouse gases, like carbon dioxide, out of the atmosphere and respire carbon dioxide back into the atmosphere.  When soil organisms decompose dead material, they use carbon from the tissue as an energy source.  Some of that carbon is used for growth and reproduction.  That carbon can stick around in soil for weeks, years, decades, or even longer.  Some of the carbon is used for respiration, just like when we breath, soil organisms produce carbon dioxide.  This adds up to a lot of carbon!  As shown above, soils contain 2,300 gigatonnes of carbon.  By comparison, respiration by soil organisms contributes only 60 gigatonnes of carbon back to the atmosphere.  We can help soil organisms potentially reduce greenhouse gasses in the atmosphere through land management choices like ecosystem restoration, conservation farming practices, and increased urban green space.

 


Left, Mycen chlorophos, a bioluminescent fungus found in Asia, Top right, Fuligo septica is also known as “dog vomit slim mould,” Bottom right, scanning electron image of a tardigrade Photo credits: S. Axford, Stu’s Images, J. Méndez, and M.J.I. Briones

 

 

Soil organisms are truly the unsung heroes of sustainability.  We need them. Wildlife needs them.  Fish need them. Ecosystems need them.  Soil biodiversity not only sustains life on earth, it is intrinsically fascinating.  From bioluminescent fungi (pictured far left) to dog vomit slime mold (pictured top right) and adorable tardigrades (pictured bottom right) soil is home to some awesome living things.  It is organisms like these that captured my adult imagination long after my “soup” making days as a kid.  The best part is, it is not imaginary at all.  The real world beneath our feet is astounding and essential.  We all need living soil, so future generations can play and thrive in the dirt.

All images, except the reindeer, are from the Global Soil Biodiversity Atlas and available for free download (pdf) and use! 

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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.

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Illustrating Soil Life



Vorticella
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.




Rotifer
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.

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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.

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