Why poisoning the soil contributes to failed “restorations”

We are members of an international team of people who are concerned about the destructive consequences of ecological “restorations.”  Trees, Truffles, and Beasts (1) was recommended to us by one of our collaborators in Australia because the book was written by several academic scientists in Australia and the Pacific Northwest of the United States.  The book compares and contrasts the forests of these disparate locations and finds that below the ground, they have much in common.

Much more is known about the important ecological functions performed by forests above ground than below ground.  However, there are many equally important things happening below ground that are essential to the health of forests:

  • The soil is inhabited by millions of microbes that decompose organic matter, making it available to plants as nutrients. These microbes recycle dead plants and wood back into usable material for living plants.
  • Nitrogen is essential to plant growth. Microbes and fungi in the soil convert nitrogen in the atmosphere into forms needed for plant growth.  Specific plant species (e.g., legumes, such as acacia and lupine), called nitrogen “fixers,” are mediators in this process.
  • Fungi in the soil deliver water and nutrients from the soil to the roots of trees in exchange for carbohydrates provided by the trees. This symbiotic relationship is essential for the health of trees and in the absence of fungi, tree growth and development are severely retarded.
  • Most carbon is stored in the soil, and soil fungi play a role in converting atmospheric carbon dioxide into carbon that is stored in the soil. “Recent research has shown that mycorrhizal fungi hold 50 to 70 percent of the total carbon stored in leaf litter and soil on forested islands in Sweden.” (2)

Relationships between animals and forests

The animals that live in the forests contribute to forest health and forests also benefit the animals.

Mature Parasol mushrooms - note hand for size comparison
Mature Parasol mushrooms – note hand for size comparison

Fungi in the soil produce “fruiting bodies” that are their means of reproducing.  Fruiting bodies above ground are called mushrooms.  Fruiting bodies below ground are called truffles.  In both cases, they are important sources of food for animals.  The animals in Australia are different from those living in the Pacific Northwest, but they have in common that the fruiting bodies of fungi are equally important sources of food for them.

In the case of mushrooms above ground, dispersal of their spores is accomplished primarily by wind.  But in the case of truffles, dispersal of their spores is dependent upon the animals that eat them and “deposit” them elsewhere.  So, animals are crucial to the reproductive cycle of fungi that fruit below ground.

Long-footed potoroo is an Australian marsupial that eats primarily mushrooms and truffles.
Long-footed potoroo is a rare Australian marsupial that eats primarily mushrooms and truffles.

In their search for truffles, the animals also till the forest floor, which contributes to the decomposition of leaf litter and the dispersal of nutrients into the soil.  As the animals defecate in the forest, they are also making contributions to forest health and there are species of microbes and insects that specialize in the use of animal feces.

Golden mantled ground squirrel, Western North America. Prefers to eat mushrooms and truffles.
Golden mantled ground squirrel, Western North America. Prefers to eat mushrooms and truffles. Creative Commons

What happens to the forest ecosystem when it is clear cut?

The forest is a complex and delicate ecosystem.  When the forest is destroyed, we should not be surprised to learn that this ecosystem is destroyed.  Here are a few of the consequences of clear-cutting a forest:

The Bay Area is often blanketed in fog. Courtesy Save Mount Sutro Forest.
The Bay Area is often blanketed in fog. Courtesy Save Mount Sutro Forest.
  • The forest precipitates fog and the shade provided by the canopy retains that moisture on the forest floor. When we destroy the forest, we lose that source of moisture.  The ground dries out in the sunshine.  The fruiting bodies of fungi—mushrooms and truffles—require moisture to bloom and they die quickly in the absence of moisture.
  • The herbicide (Garlon) used to prevent the trees from resprouting is known to damage the mycorrhizal fungi that are essential to forest health. The herbicide that is applied to the tree stump immediately after the tree is destroyed, travels though the cambium layer of the tree down through the roots of the tree.  The tree is killed by killing its roots.  Mycorrhizal fungi are essentially extensions of the root system.  When roots are killed, so are the mycorrhizal fungi.  In the absence of mycorrhizal fungi, the survival of “replacement” plants is compromised.
  • The loss of fruiting bodies as food for animals reduces animal populations and the contributions they make to forest health.
  • Glyphosate is the herbicide most commonly used to foliar spray non-native vegetation that colonizes the unshaded ground after a clear cut. Glyphosate was originally developed as an anti-bacterial agent.  Glyphosate kills bacteria in the soil (and in the mammalian gut, 4) that are playing a role in recycling nutrients to plants (and in digesting our food). (3)

Prescribed burning is another land management method used to eradicate “invasive” plants.  In addition to polluting the air, releasing carbon into the atmosphere, and increasing the risk of wildfire, prescribed burns also damage the soil:  “Prescribed burning in California pine forest decreased the ectomycorrhizal biomass by almost 90 percent in the upper organic layers of the soil as compared to unburned sites.  A decrease of that magnitude in the mycorrhizal energy source of the fungi would affect not only fungal fruiting but also fungal populations.”  (1)

In the absence of fungi and bacteria, the soil is essentially sterile and is no longer capable of contributing to the health of a new generation of plants and animals to replace the forest.

Eucalyptus forest in California and Australia

Trees, Truffles, and Beasts was written by academic foresters who are primarily concerned about the destructive consequences of destroying native forests and replacing them with timber plantations, often of another, faster growing species.  Ironically, in the case of old growth eucalyptus forests in Australia, the choice of replacement species is often Monterey pines.  Since some of the species of mycorrhizal fungi are specific to certain species or types of trees, this change of species is not successful without the inoculation of appropriate species of fungi.  For example, some of the mycorrhizal fungi that grow on the roots of conifers are not found on eucalyptus species.

Before writing this article, we corresponded with the authors of Trees, Truffles, and Beasts to confirm that fungi are found in the eucalyptus forests of California.  Since eucalyptus was brought to California as seeds, rather than potted plants, we needed confirmation that our eucalyptus forests are also enjoying the benefits of mycorrhizal fungi.  We are grateful that the authors replied.  They report that eucalyptus forests in California are populated with fungi, including some species that are native to Australia, which implies that some eucalyptus were imported from Australia with native soil.  Therefore, we can assure our readers that our description of how the forest functions applies to the eucalyptus forest in California, as well as in Australia.

Predicting the consequences of destroying our urban forest

Plans to destroy non-native forests on 2,000 acres of public land in the East Bay will result in a dry, barren landscape populated primarily by non-native annual grasses.  Fantasies that the forest will be magically replaced by a landscape of native plants and trees are just that…fantasies.  Every reputable source of information about the planned project predicts this outcome, from the US Forest Service to the Audubon Society and the California Native Plant Society.  There are many reasons why this outcome is predictable:

  • UC Berkeley's "Vegetation Management"
    UC Berkeley’s “Vegetation Management”

    The ground will be covered by as much as 24 inches of wood mulch, which will retard the germination of any plant. The plants most likely to penetrate this physical barrier are those that are most competitive, such as broom and other non-native weeds considered “invasive.”

  • The moisture available to plants will be reduced by the loss of fog drip and shade provided by the tree canopy. Fog drip in eucalyptus and Monterey pine forests in the East Bay has been measured at 10 inches per year. (5) Young plants and trees require more water than established plants, so the water deficit will retard the growth of a new landscape.
  • The climate of the San Francisco Bay Area has changed in the 250 years since the arrival of Europeans. Plants that were native at that time are no longer competitive in the warmer, drier climate and an atmosphere higher in nitrates and carbon dioxide.  The rapidly changing climate is making the concept of “native” increasingly irrelevant.

And now we know that the damage that will be done to the soil and the forest floor by the destruction of our urban forest will further handicap the successful establishment of a new landscape.  Aside from the physical damage done by removing hundreds of thousands of trees with heavy equipment, the herbicides used to kill trees and plants considered undesirable by the perpetrators of this devastating project will sterilize the soil.  The resulting weed-dominated moonscape will probably recover in hundreds of years, although the eventual outcome is impossible to predict in our rapidly changing environment.  Neither the supporters of this project nor its critics will live to see the recovery.

  1. Chris Maser, Andrew W. Claridge, James M. Trappe, Trees, Truffles, and Beasts, Rutgers University Press, 2008
  2. https://en.wikipedia.org/wiki/Mycorrhizal_fungi_and_soil_carbon_storage
  3. http://www.nytimes.com/2013/09/20/business/misgivings-about-how-a-weed-killer-affects-the-soil.html?ref=todayspaper&_r=1
  4. http://www.fooddemocracynow.org/blog/2015/apr/13
  5. Harold Gilliam, Weather of the San Francisco Bay Region, UC Press, 2002


The importance of soil microbes for forest health

Yale Environment 360, the on-line science blog, published an interesting article last week about new discoveries in forest ecology regarding the importance of microbes in the soil for forest health.  These root fungi—called mycorrhizal fungi— form a symbiotic relationship with many plants and trees, both native and non-native.  They provide water and mineral nutrients in exchange for plant carbohydrates.  Scientists have known of the existence of these microorganisms for some time, but recent advances in DNA analysis has enabled scientists to identify thousands of different species of mycorrhizae and their association with certain tree species.

Scientists at Yunnan University in China had been trying for some time to save a critically endangered tree that had dwindled to only 200 individuals.  They had been transplanting seedlings into protected areas, with little success.  Finally, they discovered that inoculating the seedlings with mycorrhizae increased survival rates from 46% to 80%

Certified arborists evaluating the Sutro Forest called it "mycorrhizal heaven."  Courtesy Save Sutro
Certified arborists evaluating the Sutro Forest called it “mycorrhizal heaven.” Courtesy Save Sutro

Root fungi and our urban forest in the Bay Area

We learned of the importance of these root fungi to our urban forest from Colin Tudge’s book, The Tree, nearly ten years ago:  “Most forest trees and many other plants too, make use of mycorrhizae; some, like oaks and pines, seem particularly reliant on them.”  And eucalypts are also dependent upon mycorrhizae:  “Many trees have mycorrhizae, but pines and eucalypts seem particularly adept.” (1)

Volume of pesticide use by San Francisco's Natural Areas Program,  Courtesy Save Sutro
Volume of pesticide use by San Francisco’s Natural Areas Program, Courtesy Save Sutro

And in 2010, we learned from the Marin Municipal Water District’s “Herbicide Risk Assessment,” that one of the most frequently used herbicides sprayed on the stumps of eucalypts when they are cut down is known to be harmful to mycorrhizal fungi in the soil.  This herbicide is also foliar sprayed on non-native vegetation such as broom, Himalayan blackberry, ivy, etc.  The active ingredient in Garlon 3A and Garlon 4 Ultra—triclopyr–is known to be toxic to microrganisms such as mycorrhizae:

 “Mycorrhizal fungi are symbionts with plants that provide water and mineral nutrients in exchange for plant carbohydrates. Cenococcum geophilum, the slowest growing fungus, was least sensitive to the effects of triclopyr, exhibiting decreased growth at 742 ppm a.e. A similar study found that triclopyr (formulation not reported) could inhibit growth in five mycorrhizal species: Hebeloma crustuliniforme, Laccaria laccata, Thelophora americana, Thelophora terrestris, and Suillus tomentosus.94Fungi were kept in liquid culture for 30 days and the reduction of biomass with increasing triclopyr concentrations was measured. A 90% reduction in biomass was observed for all species at concentrations of 720 ppm; greater than 50% reduction biomass was observed in four of the five species at 36 ppm. The most sensitive species, Thelophora americana, exhibited a 6% decrease in growth rates relative to controls at triclopyr concentrations of 0.072 ppm (this result was statistically significant). In other species, statistically significant decreases in growth were reported between 0.72 ppm and 7.2 ppm.” (2)

These studies tested this herbicide on only six species of mycorrhizal fungi.  We should probably assume that other species would also be harmed and it is likely that other herbicides would also be harmful, though no tests have apparently been conducted.  Testing of pesticides is woefully inadequate because legal requirements for testing are minimal and most testing is funded by manufacturers with little motivation for learning more bad news.

Here is one of the comments posted on the Yale Environment 360 article by an academic at University of Philippines, about presumed damage to agricultural soils by pesticide and fertilizer use:

“The article on microbes by Conniff follows what I pointed out earlier to Yale e360, that there is a group in the Philippines, of which one is a geneticist trained in the U.S. and two are foresters trained in the Philippines, who believe in fertilizer- and pesticide-free agriculture methods that do not kill off microorganisms in the soil that are much needed by the plants. They (the three happen to be brothers) applied this principle to rice and other crops and are harvesting more with less input. They have a growing following among farmers as well as a flourishing broadcasting business. They fight an uphill battle against fertilizer and pesticide multinationals and their local partners. They are slowly winning their battles and will later win the war for food security. Advances in tropical forestry will broaden horizons. Thank you Yale e360!”

Posted by Bienvenido R. Rola, PhD on 10 Oct 2013

 Implications for ecological “restorations” in the Bay Area

It seems likely that the huge amounts of herbicide that are used by local projects to eradicate non-native vegetation are damaging the microbes in the soil that are essential to forest health.  This is probably one of many explanations for the lack of success of these projects.  Here is a recap of the many reasons why these projects are rarely successful unless they are intensively planted and gardened:

  • Higher levels of CO₂ and associated climate change are promoting the growth of non-native plants. 
  • The growth of non-native annual grasses is encouraged by higher levels of nitrogen in the soil found in urban environments as a result of the burning of fossil fuels. 
  • Hundreds of species of California native plants require fire to germinate their seeds and most of the population will die within 5 years of the fire.  Prescribed burns are prohibited in San Francisco and are severely limited in most urban areas because of air quality standards and safety concerns.
  • Herbicides are damaging the soil.


(1)     Colin Tudge, The Tree, Three Rivers Press, 2005

(2)    Chapter 4, Marin Municipal Water District, “Herbicide Risk Assessment,” 2010

Why are native plant installations often failures?

We have been watching attempts to eradicate non-native plants and replace them with native plants on public lands in the San Francisco Bay Area for over 15 years.  Few of these efforts have been successful.  Non-native plants are repeatedly eradicated, then natives are planted.  Within months the natives are dead and non-natives have returned. 

The few projects that are successful are usually fenced, irrigated, and intensively planted and weeded.  Few managers of public lands have the resources to achieve success.  We have identified here on the Million Trees blog many reasons why attempts to return native plants to places in the Bay Area where they have not existed for over 100 years are often failures.  Many of those reasons are related to the changes in the environment:

  • Higher levels of CO2 and associated climate change are promoting the growth of non-native plants.  A USDA weed ecologist (1) studied the effects of higher temperatures and CO2 on the growth of non-natives (AKA weeds) by growing identical sets of seeds in a rural setting and an urban setting with higher temperatures and CO2 levels.  Seeds grown in the urban setting produced substantially larger plants with much more pollen and therefore greater reproductive capability.
  • The growth of non-native annual grasses is encouraged by higher levels of nitrogen in the soil found in urban environments as a result of the burning of fossil fuels. (2)

 The methods used by the projects undermine success

With the exception of the project on Mount Sutro in San Francisco, all of the projects use herbicides to eradicate the non-native plants and trees.  Most of the non-native trees will resprout if their stumps are not sprayed immediately with herbicide and this must be done repeatedly to kill the roots of the trees.  Many of these herbicides persist in the ground for years and probably suppress subsequent plant growth.

This problem is illustrated by a USDA study of the effects of a one-time aerial spraying of herbicides on grassland after 16 years.  Although the herbicide is assumed to “dissipate” within a few years, the negative effect on the natives persisted 16 years later:  “…the invasive leafy spurge may have ultimately increased due to spraying.  Conversely, several desirable native herbs were still suffering the effects of the spraying,,,” 

Anyone who is familiar with native plant restorations in the Bay Area knows that most are covered in a thick layer of mulch.  When tree removals are required for a project, the mulch is usually composed of the chips of the trees that have been cut down.  The projects of UC Berkeley for which UC is applying for FEMA funding (based on its claim that the clear-cutting of all non-native trees will reduce fire hazards) say specifically that the clear-cut areas will be covered with 24 inches of mulch composed of the chips of the destroyed trees. 

The UC Berkeley projects also claim that native vegetation will return to these clear-cut areas without being planted based on an assumption that the seeds of native plants are dormant in the soil.  One wonders how these seeds would be able to germinate when covered with 24 inches of mulch, or how the sprouts could penetrate it.  Their proposal contains the fanciful suggestion that squirrels will plant the acorns of oaks in the mulch, which may be true of the oaks, but is an unlikely scenario for the many other native plants and trees which UC claims will populate their “restorations” without being planted. 

Chips of destroyed trees, UC Berkeley project.  Photo courtesy Hills Conservation Network
Chips of destroyed trees, UC Berkeley project. Photo courtesy Hills Conservation Network

These heavy mulches prevent native bees from nesting in the ground, as most native bees do.  This reduces the population of pollinators which are essential to the germination of a new generation of the plants.  If long-term sustainability is the goal of these projects, an environment that is friendlier to pollinators would be helpful.

Lack of horticultural knowledge is also handicapping these projects

One of 5 native oaks that survive on Tank Hill 10 years after 25 oaks were planted.
One of 5 native oaks that survive on Tank Hill 10 years after 25 oaks were planted.

The managers of these projects often display a profound ignorance of basic horticultural knowledge.  For example, we have seen them plant natives that require full sun in the deep shade of trees where they will not survive.  We have seen them plant native trees that will not tolerate wind on the slopes of windy hills, only to watch the trees wither and die.

The managers of these projects are apparently unaware of the fact that hundreds of species of California native plants require fire to germinate their seeds and that most of the population will die within 5 years of the fire. (3) These are examples of such “pyroendemics” that sprout after a fire and are almost entirely gone within 5 years:

 Keeley - pyroendemics

UC Berkeley and East Bay Regional Park District do not plan to plant any natives after eradicating non-native plants and trees.  Their plans say that they expect seeds that are dormant in the ground to sprout when the ground is cleared of non-native plants.  Unless they set fire to that ground, many seeds will not germinate and most of the plants that are germinated by that fire will disappear within 5 years unless another fire germinates another generation of plants.  

UC Berkeley does not use prescribed burns on its property.  East Bay Regional Park District (EBRPD) conducts only a handful of small prescribed burns every year, which they claim are solely for the purpose of reducing fuel loads.  In an article about prescribed burns conducted by EBRPD, the District’s “Resource Analyst” is quoted as saying, “’This is not a restoration project.  Our primary goal is fuels reduction.’” (4) Ironically, both of these owners of public lands claim that their objective in the eradication of non-native plants is to reduce fire hazard, yet they are trying to reintroduce a landscape that is dependent upon fire for survival. 

The Natural Areas Program in San Francisco has never conducted a prescribed burn and the DRAFT Environmental Impact Report for their plan says they do not intend to do so in the future.

New and growing evidence that soil is altered by plants

 In addition to these issues which have contributed to the failed attempts to reintroduce an historical landscape to the San Francisco Bay Area, we are reporting today on a new issue.  Plants can change the microbial composition of the soil, including mycorrhizal fungi which have symbiotic relationships with plants. 

Researchers tested soil for changes in composition after just three growth cycles.  Several species of non-native annual grasses were grown in native soils.  They reported that the non-native species reduced the population and changed the composition of the mycorrhizal fungi, which reduced the ability of native species to establish and persist in modified soils. (5)

The Berkeley Meadow is a 72-acre native plant garden on a former garbage dump on landfill.
The Berkeley Meadow is a 72-acre native plant garden on a former garbage dump on landfill.

These changes in the soil were observed after only three growth cycles.  Our local projects are attempting to eradicate plants which occupied the soil for more than 100 years.  In some cases such as the former garbage dumps in the East Bay on landfill, the soil was never occupied by native plants.  Surely, the alteration of soil composition is a likely factor in the failure of attempts to turn these properties into native plant gardens. 

How many more decades and how much more taxpayers’ money must we spend on these projects before land managers acknowledge their failures? 


(1)    Lewis Ziska, USDA Scientist, Beltsville, MD

(2)    US Fish & Wildlife, Recovery Plan for Mission Blue butterfly

(3)    Jon Keeley, et. al., Fire in Mediterranean Ecosystems, Cambridge University Press, 2012

(4)    Wendy Tokuda, “Taming the Flames,” Bay Nature, July-September 2012

(5)    Nicholas Jordan, et. al., “Soil-Occupancy Effects of Invasive and Native Grassland Plant Species Composition and Diversity of Mycorrhizal Associations,” Invasive Plant Science and Management, October-December 2012