Healthy soil is key to sustaining life on this planet. Yet human-created drivers and extreme natural events, such as wildfires, are upsetting the thriving sub-surface ecosystems that are responsible for maintaining soil health, leading to a feedback cycle that is accelerating carbon turnover and release from soils. How can researchers gain a better understanding of the role of soil-based communities in our natural world? What are these communities telling us about pathways to recovery and resilience? And what can be done to help these communities thrive in a world impacted by climate change?
We convened a group of experts on the AskScience subreddit to answer your questions about soil microbes.
- Dawson Fairbanks, Ph.D. – Bioinformatician, Funga
- Janet K. Jansson, Ph.D. – Chief Scientist/Laboratory Fellow (Retired) at Pacific Northwest National Laboratory
- Elliot Weiss, Ph.D. – Postdoctoral Fellow, University of California, Berkeley, and Lab to Land
- Zoey Werbin, Ph.D. – Ecological Data Scientist, Funga
Q&A Highlights
Dawson Fairbanks –
Some of the most impactful things we can do are surprisingly simple: reduce soil disturbance (like no-till or low-dig gardening), avoiding synthetic fertilizers and pesticides and add organic matter like compost or mulch. Planting native species and increasing plant diversity also helps support microbial diversity too, especially fungi and nitrogen fixers. Incorporating thoughtful landscaping properties is also important for water storage and helps water move more efficiently through the soil, which also helps soil carbon and microbial diversity, and lessens your water bill!
Elliot Weiss –
There tends to be an obsession with removing leaf litter from our yards, and I’m often guilty of this myself. However, we’d be better off supporting the detrital food web by letting that organic matter decompose and return to the soil.
As you maintain your yard, try to avoid compacting the soil, especially when it’s wet, since compaction reduces the pore space that microbes and plant roots rely on for oxygen and water.
Finally, consider rewilding even a small, “unkempt” corner of your yard or allowing native plants to establish there. It doesn’t have to be large. Even a little wild patch can help support both microbial and macro-organism diversity, from fungi and beetles to pollinators and birds.
Dawson Fairbanks –
At the societal level I often advocate for a shift in how we value soil. This means investing in regenerative agriculture and restoration practices, supporting policies that protect soil biodiversity, and reducing overreliance on chemical inputs and improving access to data and tools for land stewards. Healthy soils underpin everything from food security to carbon storage, and microbes are the hidden engines making it all possible.
Zoey Werbin –
Standard turf lawns have pretty simplified microbial communities compared to natural grasslands. They’re dominated by bacteria rather than fungi, partly because of frequent mowing, compaction from foot traffic, and often fertilizer use. The root systems are also relatively shallow, so there’s less of the deep soil microbial activity you would see in native prairie grasses.
Zoey Werbin –
Watering definitely affects the microbes! Frequent shallow watering tends to favor fast-growing bacteria over slower fungi, and it can actually make lawns more dependent on inputs. Deep, infrequent watering generally supports healthier microbial communities and stronger root systems.
Zoey Werbin –
Avoid establishing lawns that are monocultures of non-native grasses treated with herbicides and pesticides. Otherwise, maintaining some sort of lawn can have ecological benefits like providing shade to soil and small animals, preventing mechanical erosion, and making it easier to spot invasive species early. Whenever possible, I’d convert lawn to native species, which tend to root more deeply (requiring less water) and support much more diverse microbial communities and wildlife.
Native alternatives develop beneficial fungal networks that store more carbon and cycle nutrients more efficiently. There are lots of region-specific programs testing lawn alternatives:
- Cornell Botanic Gardens
- University of Texas at Austin Lady Bird Johnson Wildflower Center
- Native Plant Trust Yard Futures Project
Even partial conversion, like replacing some lawn with native groundcovers or creating “messy” edges, can make a big difference for soil health!
Read more:
Janet Jansson –
It depends on the type of lawn. If you use a prairie lawn with deep rooted grasses, that could be beneficial. Lawns use a lot of water, so it also depends on where you live. Not recommended for arid regions. Then you can xeriscape.
Elliot Weiss –
Mulch type can have a huge effect on soil health and microbial community structure.
At a high level, organic mulches (like wood chips, straw, or crushed leaves) and inorganic mulches (like rubber chips or gravel) have drastically different effects. Organic mulch adds organic matter as it decomposes, enriching the soil and feeding microbial life. This process ultimately improves soil structure, water-holding capacity, and nutrient cycling.
In contrast, inorganic mulch doesn’t decompose. While both types can help suppress weeds and retain soil moisture, inorganic mulch doesn’t contribute to the biological activity of the soil as it lacks the inputs that support microbial and invertebrate communities.
Within the realm of organic mulch, wood-based materials break down more slowly, favoring fungal communities and supporting long-term soil building. Finer substrates, like straw or leaf matter, decompose more quickly, releasing nutrients faster and promoting higher microbial turnover.
Zoey Werbin – Another downside of inorganic mulch (i.e. plastic sheeting used as a weed barrier): it can also break down to form microplastics in the soil. These microplastics persist in ecosystems and can be taken up into plant tissues, disrupting microbial and plant ecosystems (in addition to human health risks). We’re only recently recognizing how widespread the problem is with plastic mulch and microplastic contamination!
Janet Jansson – Here are a few resources to learn more:
Zoey Werbin –
Many soil microbes rely heavily on each other through something called cross-feeding – one microbe’s waste becomes another’s food. When you isolate them in lab dishes, they lose those essential partnerships and can’t survive on their own.
Our standard lab growth media is another part of the problem: most were developed for medical research using microbes like E. coli that grow easily. Soil microbes have evolved in much more complex chemical environments and often need specific nutrients we don’t typically include in basic media.
There are other practical issues. Many soil microbes grow extremely slowly – some take weeks or months to form visible colonies when lab scientists expect results overnight. Others need very specific conditions like particular pH levels, oxygen concentrations, or need to attach to surfaces rather than grow in liquid. Some microbes are obligate partners with plants or fungi and literally cannot survive without those relationships (see Dawson’s other answers on this topic!). Some microbes produce compounds that become toxic to themselves at higher concentrations, so they kill themselves off in dense lab cultures.
We’re making progress though! There are new computational tools (Barnum et al. 2024) can predict growth requirements from genome sequences, and some researchers are experimenting with “co-culturing” multiple species together to recreate some of those natural partnerships.
This study elegantly illustrating how common cross-feeding is among soil microbes: the researchers removed the food source and the microbes survived just through the waste products of other microbes: Goldford et al. 2018. “Emergent Simplicity in Microbial Community Assembly”
And the paper on predicting culture conditions from DNA: Barnum, et al. 2024. “Predicting microbial growth conditions from amino acid composition.” bioRxiv 2024.03.22.586313
Elliot Weiss –
Sure! In general, laboratories use standardized media to grow microbes, but soil microbes are incredibly diverse and often require very specific conditions that standard media can’t provide. Some microbes need particular nutrients, in precise ratios, that may be missing from typical lab setups. Others are not able to grow on their own and depend on symbiotic relationships with other microbes. In nature, these organisms thrive alongside partners that help supply essential compounds or signals, but in the lab they are often isolated and expected to grow independently. Some microbes also require highly specific environmental conditions, such as a certain temperature, pH, or oxygen level, which may not be replicated in the lab. Even when conditions are somewhat suitable, some microbes grow very slowly and might be missed if not enough incubation time is allowed.
The good news is that more organisms are becoming culturable as techniques improve. Approaches like co-culturing, microfluidics, and genome-informed media design are helping to recreate the conditions that these microbes need to grow successfully.
Janet Jansson – Also, some soil microbes grow better on solid media than liquid media. There have been several advances in solid state fermentation techniques for growing bacteria like STreptomyces (common soil microbes).
Dawson Fairbanks –
We often think about plants depending on microbes but the relationship can be mutual. For example, arbuscular mycorrhizae form symbiotic relationships with most land plants and exchange nutrients for carbon. Many species can’t complete their life cycle without a living host root and may rely entirely on plant-derived sugars to grow and reproduce. There are also ectomycorrhizal fungi that specialize in certain tree species, like pines or oaks, requiring the simple sugars provided by trees to obtain carbon, where other forms of carbon in the soil are often locked away in complex compounds that are more difficult to break down. In addition, some nitrogen-fixers are tightly coupled to legume roots. So yes, many microbes are deeply dependent on plant partners to survive and function and this mutualism has been around since the evolution of land plants.
Elliot Weiss – There are some types of fungi that are dependent on certain plants! An example would be Arbuscular Mycorrhizal Fungi. These fungi depend on plant hosts for their survival. They need chemical signals from plant roots to germinate, and they rely on the plant for essential nutrients such as sugars. Without a host, they can’t grow or reproduce, so the plant is required for them to complete their life cycle.
Janet Jansson – Yes, there are some fungi that form specific associations with plants. These are called mycorrhizal fungi. They depend on the plants for photosynthetically derived sugars and in return they extend the root zone into the soil and help the plant to get minerals and other nutrients. It is a symbiotic relationship, both organisms benefit.
Janet Jansson –
We do know that monoculture crops of genetically modified Roundup Ready soy and corn, with it’s associated Round Up herbicide, have been devastating to pollinators and soil health in general. But some GMOs can be useful, for example to improve plant drought tolerance and to enhance beneficial interactions with soil microorganisms. It really should be considered on a case-by-case basis with respect to risks versus benefits. Here is an article with some information.
Janet Jansson – I think that the most important action that should be taken with respect to the soil is to eat less meat. Much of our fertile soil is being used for soy and corn that is used for biofuel and feed for cattle in feedlots – both of which are bad environmental choices and that aggravate climate change by greenhouse gas emissions. Instead to encourage planting of perennial grasses (e.g. native prairie) that enrich soil fertility and microbial diversity. Individuals can grow native plants that naturally recruit beneficial microorganisms in their soil.
Links related to experts’ work:
An Evaluation of Biotechnology Approaches to Wildfire Resilience from Lab to Land
Soil Microbiomes Under Climate Change and Implications for Carbon Cycling
Funga Public Benefit Corporation’s approach to restoring forest soil
Additional links related to the topic:
Unearthing the Soil Microbiome, Climate Change, Carbon Storage Nexus from American Society for Microbiology
The shocking decline of Earth’s microbiome – and how to save it article from NewScientist
Soil Health resources from Farmers.gov
Alternatives to genetically altering organisms for improving soil health:
Available now
- Cover crops
- Biodiversity
- No-till practices
- Increasing ‘native’ microbe populations without genetic alteration
- Mulching
- Crop rotation
In development
- Silica rock amendments
The non-living part of soil is made from rocks that wear down over long stretches of time in a process called rock weathering.
Soil is a silo for the majority of carbon found in land ecosystems (nearly 80%)
