Fungi in your soil: a reason to celebrate

By Lauren Lewis

The weeks following our late winter rains, when the soil is as soaked as it’s ever going to be in SF, is when we’re most likely to find mushrooms in our gardens. If you do, it’s a reason to rejoice, because a mushroom is the above-ground evidence of fungi in the soil, and it’s hard to overstate just how important fungi are for healthy soil and healthy plants. We mostly don’t even notice its presence, but our plants depend on fungi for their growth.

Around 90% of all plants form a mycorrhiza with fungi, a symbiotic relationship whereby the hyphae of the fungus (a fungus’s massive underground network of microscopic filaments) connect to the plants’ roots and nutrients are passed between plant and fungus. Fungi receive carbon that was photosynthesized by the plant, and the plant receives…so much assistance. Nutrients: mycchorizae supply roots with necessary nutrients like phosphorus that are hard for the plant to absorb independently. The fungi exude acids that break down rock and solidified soil, which turns existing nutrients into a form that’s absorbable by plant roots. Water: the network of hyphae in effect expands a plant’s surface area in the soil, letting the plant reach more available water. Mycorrhizal soil also tends to have greater water retention capacity, so there’s more water for the roots and hyphae to reach. Communication: this underground network also creates a means of communication between plants– a plant enduring a pest attack sends out chemical signals to neighboring plants, and the mycchorizal network allows the warning signal to reach farther. The list of benefits received between fungus and plant goes on.

From a gardening perspective, we can celebrate fungi for their ability to support perennial plant growth over annual (i.e. weedy) growth. Research has shown that fungal soils can deter growth of weeds, while supporting other plants in the ways described above. Over time, myccorhizae create a soil environment that’s hostile to more short-lived plant species and welcoming to long-lived plants, mimicking mature “wild” plant communities.

Fungi support our gardening ambitions, and they can also help fix the messes we humans have made. In urban settings, where soils are often contaminated with oils and petrochemicals, fungi offer a grassroots solution via mycoremediation. Most fungi get their energy by breaking down large carbon-based molecules, like those in wood, which means they’re also good at breaking down petroleum and related carbon-based chemicals. Communities are starting to employ controlled use of fungi to clean up soils, and there is data to support the practice. It’s a method that can be done piecemeal, by leaving discovered garden mushrooms to do their thing and avoiding fungicides, or on a community level to solve more serious contamination. (To sate all your fungal curiosity, check out the indispensable book Mycelium Running: How Mushrooms Can Help Save the World, by Paul Stamets.)


Small but meaningful action through wildlife corridors

By Lauren Lewis

As the title of this blog implies, our primary focus is: how does an individual garden in the city fit into the bigger picture? And the answer is: there are so many different ways that it’s exhilarating to think about (if you’re nerdy like us!). Arguably the most approachable example of how a garden connects to the world around it is the movement of wildlife in and out of a garden. The vast majority of urban animal species, both invertebrate and vertebrates, are not particularly restricted by fences between gardens, but their viability is hindered by limited green space and limited appropriate vegetation. So that’s where our gardening choices become important. They help determine the presence or absence of wildlife corridors.

Urban wildlife corridors exist at the intersection of urban ecology and movement ecology, which is a very new branch of study in ecology. On a larger physical scale, movement ecology has enjoyed a recent uptick in attention because of executive branch efforts to open up previously-protected US land to natural resource extraction, which creates more barriers to animal movement. The New York Times just highlighted new research showing the extent to which human activity restricts animal movement globally, and also the surprisingly bipartisan efforts to protect migratory paths in the American West. In an urban context the animals are smaller and less attention-grabbing, but gardening in a way that promotes urban wildlife movement can be a small but meaningful action.

img_5431.jpgA perfect example is CalAcademy biologist Tim Wong (@timtast1c), who learned about the struggling Pipevine Swallowtail butterfly population in SF and took action that has substantially improved the species’ population. The Pipevine Swallowtail caterpillar feeds only on California pipevine, which has become rare in SF, so Tim found the plant and began growing it in his butterfly-friendly garden at home. As the butterflies have thrived there he has brought both the plant and the caterpillars to the California Native garden at the SF Botanical Garden, and the population is growing.

For the rest of us in SF, there’s a wonderful resource for learning and garden planning- the Green Connections Ecology Guides. The city’s Green Connections program will create a bunch of long “paths” through the city over the next decade that are specifically designed to be safe and pleasant for travel by foot or bike. The idea of the program’s Ecology Guides is that if humans can travel along those routes, then appropriate plantings can make them pleasant routes for animals we want to support too. Check if there’s a route near your garden that can help guide some of your planting choices, but even if not, some plant-focused routes, like the Coyote Bush route along Kirkham out to the beach, are very informative about the ecosystems our city was built upon.

Using weedy plants to fight weeds

By Lauren Lewis

A weed is a weed almost always because it grows fast. It sprouts quickly and grows quickly, and can therefore take up more water, sunlight, and nutrients than its neighbor plants. At Small Spot Gardens, our primary strategy for weed control is finding ways to help our desired plants outcompete the weeds that are always trying to get a foothold. In a brand new garden, this often means planting some larger plants that take up space and sunlight, which makes the environment a little more challenging for little weeds. It also means choosing plants with the same speedy growth as weeds. If our chosen plants can grow as quickly or quicker than their weedy competitors, weeds will be less of an issue over time. These plants are some of our favorite fast growers.


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Centranthus ruber, often known as Jupiter’s Beard: Once you learn about this plant, you’ll start to notice it everywhere. Its bright red or pink flowers produce seeds with little fluffy wings like dandelions, so it really does grow everywhere, and therefore is sometimes considered an aggressive weed. In South Africa, where the climate is Mediterranean like ours and many native plants are endemic, Centranthus is treated as an invasive and banned from use. Here in California it’s not viewed as invasive by the California Invasive Plant Council, but it is counted among those plants that could become invasive. In our gardens it provides vibrant color and pollinator food, and its reseeding capabilities make it overall low maintenance. If you want to keep the reseeding to a minimum, trim off dying flowers and put trimmings in the green bin to isolate seeds.



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Fragaria chiloensis, beach strawberries: Beach strawberry is native to our region, and while Native Californians did collect and eat the fruit, it was a small treat rather than a staple of the diet because the fruit are tiny and relatively sparse. What’s great in our gardens is that this plant reproduces by sending out runners, and quickly forms a lovely thick mat that covers the soil surface. This kind of growth is ideal for crowding out weeds, and also for protecting the soil surface from erosion during rain and from drying out at all other times. The cute white flowers and occasional fruit are aesthetic bonuses.



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Oxalis, wood sorrels: You probably think of oxalis, with its highlighter-yellow flowers and clover-like leaves that take over, as your garden’s biggest springtime nuisance, but that is specifically bermuda buttercup (oxalis pes-caprae), which we would never intentionally plant. However, the oxalis family has hundreds of varieties, and many of the others are beautiful and hearty, but not nearly as invasive. Our choices, like oxalis vulcanicola, create gently-floating groundcover, and they can be dispersed around the garden purposefully by simply cutting stems and sticking them in the ground.

Follow us on Instagram for more wonderfully weedy species this month!

Seed Power

By Lauren Lewis

One of the defining characteristics of plants is unfortunately a limitation: their inability to move around. They have to reach out from where they are to find water and mates, or let those resources come to them, and they’re certainly disadvantaged when it comes to escaping danger (although many have evolved ingenious compensating strategies). Because of this limitation, the seed, the small but mobile plant part, holds great power. The seed has arguably the greatest power over a plant’s survival: it determines where the plant will forever live and grow by “choosing” when to germinate. Recent groundbreaking research has illustrated the almost decision-making power seeds possess for this purpose.

IMG_5067As a general rule, seeds move through space in a dormant state, waiting until conditions are right for germination. The timing of germination is crucial- the environment might be too cold if germination is too early, but too late and the plant will likely be outcompeted by surrounding plants who are already bigger. Seeds respond to environmental cues by producing the hormones abscisic acid (ABA) and gibberellin (GA), which promote dormancy and germination, respectively.

In a 2017 study of Arabidopsis, a fast-growing cress common in plant research, researchers mapped the 3-4000 cells in a seed and found that different cells produced these two antagonistic hormones, and that these cells were clustered in a dormancy group (ABA) and a germination group (GA) separated but near each other, and in the root tip of the seed. This layout is somewhat analogous to a “brain,” where differentated cells can send signals between each other, and the space between them is meaningful. The production and transport of more dormancy hormone (ABA) in this “brain” center of the seed maintains dormancy, and greater germination hormone (GA) stimulates germination. The researchers found that the physical separation of the cells is key because it allows the plant to more precisely respond to variations in temperature, which is an environmental signal of changing season.

Discoveries like this “brainy” cell layout in seeds are finally helping us appreciate agency that plants are capable of. In a managed setting like a garden, plants have us to determine their fates through propagation techniques. A plant off on its own appears to have a comparative disadvantage, but happily, recent science is giving us a better understanding of a plant’s own active role in its rebirth and survival.

Gardens for the protection of the SF Bay

By Lauren Lewis

The winter rainy season is a happy time for our gardens, and a less happy time for the San Francisco Bay. That’s because heavy rains, which typically happen a handful of times each winter, bring more water than Bay Area cities’ sewer systems can handle, and the result is more minimally-treated wastewater making its way into the Bay.

Most of San Francisco has a combined sewer system, which means that sewage and stormwater travel through the same pipes. Under normal circumstances, all that combined wastewater goes through primary treatment (basins for removing settled heavy junk and floating light junk) and secondary treatment (use of microbes to consume organic matter) before being discharged into the bay. When there’s a storm, there’s more rain in the system than can be treated in the secondary treatment plants, so the discharged water retains all its organic matter, like bacteria, and people who come in contact with the water are more likely to get sick from it. In the 90% of the city with a combined sewer system, the key mitigating factor is how much water we can prevent from entering the storm drains.

In the other 10% of the city, stormwater and sewage travel through different pipes, and stormwater flows directly to the bay, untreated. In these areas, the key to protecting the bay is improving the cleanliness of the water going down storm drains.

In both cases, there’s a variety of practices that the city and its residents can use to keep some stormwater from getting into the bay. The most basic way is plant-covered ground. Even bare soil allows for more water infiltration than cement or asphalt, but a well vegetated piece of land can do so much more than soil alone. The plants hold the soil in IMG_4694place, so the water doesn’t wash it away. Plant roots, dead plant matter, and all the soil organisms plants support make soil more porous, so more rainwater can soak in.

“Rain gardens” situated where rainwater gathers and flows are an inexpensive way for the city to prevent some stormwater from reaching drains, and if you look carefully you’ll notice more and more of these popping up around the city. Bits of sidewalk torn out and replaced with gardens can have a similar effect (in addition to the obvious side-benefit of beautification!). The city of San Francisco partners with Friends of the Urban Forest to do this, and you can spearhead a sidewalk garden with FUF’s help.

If you’ve read any of our previous blog posts, you’ve probably noticed some repetitive themes for how we garden and how we want others to garden, and this post is no different. Our advocacy is for dense and diverse plantings, hidden organic matter, and location-appropriate plant choices- practices that improve the water-infiltration capacity of soil, and also apply to all the various topics of our previous posts. What a wonderful thing. When you copy nature’s patterns in the controlled environment of a garden, your garden and the much bigger world it’s connected to all benefit.

Planting for soil health

By Lauren Lewis

With the arrival of the (hopefully) rainy season, our thoughts go directly to what the rain can do for our gardens. Besides the obvious benefit of free, un-transported, apolitical water to nourish the plants, the rain also benefits the soil, by catalyzing the decomposition of dead plant material that’s lying around. So much of the soil in a city is compacted beneath buildings and pavement, but the health of our remaining exposed urban soils has a real impact on how our city responds to the winter rains. So with soil health in mind, my next thought is how can our gardening behavior most benefit the soil?

The four elements of soil are minerals, organic matter, water and air. Those last two are counterintuitive because they really have to do more with the spaces in between the minerals and organic matter than can be filled with water or air. The spaces are created mostly by the movements of soil-dwelling insects, worms, microbial species, etc. Those animals move through the soil in search of food, so the presence of organic matter (their food) encourages their presence and facilitates their movements, which in turn creates space in the soil. The spaces created, and also the sponginess of the organic matter itself, makes that soil much more able to soak up rain and prevent it from running off into the streets and drains and into the bay.

Happily, our gardening practices have a big impact on soil health. To increase the amount of organic matter (dead plant and animal parts) in the soil we can choose to leave dried leaves and chopped up plant cuttings hidden around the garden rather than moving them to the green bin. When the rain comes, the moisture helps that organic matter soften and become easily accessible food for the soil animals.


Research has shown that the diversity of our landscape plant choices can also affect soil health. In a study of prairie species, researchers created plots planted with between one and 16 species, and tracked various measures of soil health over many years. The study found that more diverse plots had greater overall plant production, meaning the diverse mix of plants facilitated each other’s growth, and as a result, the soil had greater microbial biomass and fungal presence. The researchers point out that this relationship is likely only relevant in a soil that’s lacking in organic matter to support the soil dwellers, which suggests that when a soil is low on organic matter, diverse plantings can help remedy the problem.

Diverse plantings and hidden piles of organic matter are two of the Small Spot Gardens calling cards. Soil health has always been our guiding goal, since healthy soil grows better plants and makes a small but real impact on our Bay Area environment. It works out so nicely that the soil-supportive practice of diverse plant choices also lets us design gardens with the dense, varied aesthetic we love.

In our Mediterranean climate, the seasons reverse

By Lauren Lewis

The tree losing its leaves is arguably the most recognizable image of autumn. In temperate areas of the world, like North America, the most common reason that trees lose their leaves, a process called abscission, is to protect themselves from cold damage. The plant senses a decrease in daylight hours, and responds by withdrawing nutrients from leaves for storage (the withdrawal of green chlorophyll results in a yellow leaf), creating a layer of barrier cells between stem and leaf, and then letting the leaf detach. Here in SF you’ll see plenty of this going on pretty soon in the gingkos, stone fruits, London planes, etc.


This buckeye was in full bloom in early June in preparation for July leaf-drop.

But in plants native to Mediterranean climates like we have here in coastal California, the reason for leaf abscission isn’t cold, it’s dryness. Mediterranean climates occur in parts of Australia, central Chile, coastal California, South Africa, and of course the land around the Mediterranean Sea. These places have relatively mild temperatures year-round, dry summers, and wet winters. With mild temperatures, plants don’t have to prepare for cold by dropping leaves. Instead, the dangerous time for the plant is the dry summer, and one adaptation to this challenge is to lose leaves and go dormant during the driest months of the year. A great example is the buckeye (Aesculus californica), a staple of California’s native landscapes, whose leaves brown and drop in July. Purple sage (Salvia leucophylla) drops its large, springtime leaves during summer and replaces them with smaller, whiter leaves that reflect light and withstand heat.

This very regional pattern is made even more nuanced in San Francisco and other especially coastal parts of the Bay Area, where summers are characterized by fog and an even smaller temperature range. Plants here get some summer moisture from the fog, so they’re under less pressure to go dormant, and their dormancy can be shorter or less extreme. The first winter rain, which is possible in October, jolts dormant plants back into growth mode.

Climate change is producing changes in dormancy patterns by way of hotter summers and drier winters. A recent study of California perennial grasses noted that non-native annual grasses have recently been out-competing the once-dominant perennial species in California landscapes. The study showed that perennial species with more pronounced summer dormancy characteristics, like earlier reproduction and shallow roots, are similar to annual grasses in those characteristics, and therefore might be more competitive as droughts worsen and dormancy is made more advantageous than before. In other words, recent success of annual grasses suggests that perennial grasses that “mimic” annuals by going dormant in summer are likely to have higher survival as the climate changes. Landscape restoration efforts would therefore do well to promote summer dormant plants.