Dr. Mallory Choudoir, microbial ecologist and evolutionary biologist at the University of Massachusetts Amherst shares how she leverages microbial culture collections to infer ecological and evolutionary responses to warming soil temperatures. She discusses complexities of the soil microbiome and microbial dispersal dynamics, and introduces fundamental concepts about the intersection between microbes and social equity.
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Ashley's Biggest TakeawaysMicrobial culture collections are fundamental resources, serving as libraries where diverse species of microbes are identified, characterized and preserved in pure, viable form. Culture collections ensure conservation of species diversity and sustainable use of the collected microbes.
For soil microbiologists, like Mallory Choudoir, culture collections provide the opportunity to connect patterns of genomic variation and microbial physiology to the conditions under which a particular microbe was isolated.
Soil is a complex environment from the perspective of a microbe. In order to coexist in such a biologically diverse environment, which consists of spatial heterogeneity, as well as heterogeneity in access to moisture and nutrients, microbes must evolve different strategies to survive as part of a stable community.
Choudoir’s field site is based in the Harvard Forest Long Term Ecological Research Program's field site, where coils are buried and have been heating the forest soil to 5 degrees above ambient temperatures for nearly 30 years. The study allows Choudoir and colleagues to observe and evaluate long-term responses to chronic soil warming stress.
This research is important because microbes function as resources to the health and well-being of ourselves and our planet. Understanding how microbes adapt to biotic and abiotic stresses can help inform future conservation strategies, biotechnological approaches and applications and equitable allocation of microbial resources.
“The great thing about culture collections is you have this organism, this individual, that represents existence under very specific environmental conditions where you isolated it from. So the environmental stress, the temperature, the nutrient conditions, it’s fellow microbial neighbors and community—and also this snapshot of earth time and evolutionary history—all of these pieces of metadata are informed and informed by the specific genomic patterns of variation and also different microbial physiology traits.”
“Culture collections are really a labor of love for me, and creating media recipes is more like baking an old family cookie recipe.”
“Unsurprisingly in the heated plots, there is less soil carbon, and the quality of that carbon is also decreased, so a lot of the labile, easy to digest carbon is gone and there is more complex plant carbon substrates left in these heated plots.”
“We also see a shift in microbial community structure and composition.”
“Microbes are so fundamentally tied to the health of humans, plants and animals, and also our environmental ecosystems, that I think sometimes we perhaps don’t recognize the indirect resources that microbes provide to our personal physical and mental well-being and also our food systems, our food, fiber, fuel systems and also how microbes contribute to global nutrient cycles and clean air and water.”
“We hope that microbes can become more centered in climate change initiatives. The American Academy of Microbiology Climate Change taskforce, hopes to bring together interdisciplinary scientists working towards these goals and to support this scientific roadmap across the next few years.”
Links for This Episode
- Choudoir et al. A framework for integrating microbial dispersal modes into soil ecosystem ecology. iScience. 2022
- Ishaq et al. Introducing the Microbes and Social Equity Working Group: Considering the Microbial Components of Social, Environmental, and Health Justice. mSystems. 2021
- Choudoir et al. Phylogenetic conservatism of thermal traits explains dispersal limitation and genomic differentiation of Streptomyces sister-taxa. ISME J. 2018
- Decadal Shifts in Microbial Ecology: James Tiedje Discusses
History of Microbiology
Mallory’s research specifically looks at the ecological and evolutionary responses of soil microbes under warming conditions, and seeks to understand ways in which various microbial seed treatments can increase crop yield, to ultimately improve food production.
Plant beneficial microbes, or PBMs, such as rhizobia, arbuscular mycorrhizal fungi, and Trichoderma, can promote plant growth and increase tolerance to biotic and abiotic stresses, thus reducing the need for chemical pesticides and synthetic fertilizers in agriculture. Seed coating, a process that consists of covering seeds with low amounts of PBMs, effectively inoculates beneficial microbes directly into the soil, where they can colonize seedling roots, facilitate protection against soil-borne diseases and promote plant growth. However, this technique is not without technical and manufacturing challenges. Namely, formulations must ensure survival of both the seed and microbes during storage and must be deliverable at commercial scale.
In this week’s History of Microbiology Tidbit, let’s take a look at the various treatments and cell carriers that have been explored for microbial inoculants over the years.
The first example of plant beneficial microbes being used as a commercial inoculant incorporated species of Rhizobium, nitrogen-fixing soil bacterium that naturally form endosymbiotic relationships with the roots of legumes and other flowering plants. Nitragin was patented and released in the U.S. in 1896. This product originally used gelatin, and later nutrient media, as the bacterial cell carrier, but unfortunately, and perhaps not surprisingly, high mortality rates were observed with such treatments. Peat, a unique nutrient-rich material, formed by the accumulation of partially decayed vegetation and organic matter, soon replaced these carriers as the new gold standard and remained the desirable option until the 1990s.
But variety of factors caused scientists to begin searching for alternative solutions in the late 1990s. For starters, peat is a valuable and limited natural resource. It is found in unique areas called peat bogs or mires, and destruction of these natural habitats causes significant environmental impact, including release of CO2 emissions. Furthermore, for countries where bogs are scarce, importation of peat can be costly. Liquid inoculants, consisting of microbial cultures suspended in nutrient-rich liquid medium and enhanced with various cell protectors, became the new target. The first liquid inoculant gained approval for commercial use in Brazil in 2000, and today, the vast majority of inoculants sold in Brazil come in liquid form.
In the last decade, research has centered around mixed inoculation, combining species or strains of microbes that act on different processes, including nitrogen-fixation, biological control and solubilization of phosphate, in order to reap the combined benefits of each player. Various species and combinations of Azospirillum, Pseudomonas and Bacillus, are being considered, in addition to Rhizobium.
Not only can soil microbes promote plant health and prevent disease, but they can also protect plants from abiotic stresses like pesticides.
To continue this week’s History of Microbiology Tidbit, I want to share another fascinating story about the impact of soil microbes that I learned during an engaging conversation with one of the most highly cited researchers in the world.
Last week, I had the pleasure of speaking with past ASM President and Lifetime Academy Fellow, Dr. James Tiedje, who, in Jim’s own words, “grew up with the field of Microbial Ecology.” Inspired by Rachel Carson’s, Silent Spring, and a summer as an undergraduate student spent mapping- none other than rhizobium serotypes of root nodules associated with soy beans across the state of Iowa, Tiedje entered a field of research that was in its infancy. He attended graduate school at Cornell University from 1964-68, when microbial ecology was just beginning to take shape. Silent Spring was published in 1962. This controversial book documented the adverse health and environmental effects of DDT, a powerful insecticide that was developed in 1939 and first gained traction when it was widely used to control populations of malaria-transmitting mosquitoes for U.S. troops inhabiting the South Pacific Islands during World War II. When DDT was released for public use in 1945, Carson pitched a story idea to Reader’s Digest hoping to share findings from tests that were being conducted on DDT at a site nearby her home. Her pitch was rejected. Thirteen years later, as a best-selling author, she tried again, after learning that massive bird kills in Cape Cod had been associated with DDT sprayings …Once more Carson was rejected by the magazine. So she decided to write a book that described how DDT targeted more than just insects. Silent Spring, explained how DDT remained toxic to the environment, even after rainfall, and how the pesticide entered the food chain, accumulated in the fatty tissues of humans and animals, and caused genetic abnormalities and cancer. Carson’s book led to a nationwide ban on DDT use in the U.S. in 1972.
When Tiedje began his assistant professorship at Michigan State in 1968, microbial ecology was just beginning to take shape, and his primary research foci centered around the biodegradation of pesticides. In other words, how microbes can be used to break down toxic chemicals. In the 1980’s Tiedje and colleagues discovered several soil microbes that biodegrade chlorinated pollutants, like DDT and PCB.
Tiedje is the Chair of the Steering Committee for the American Academy of Microbiology’s Colloquium Report on Climate Change, published at the end of April 2022, which you can find on our website at asm.org. He celebrates his 80th birthday this year, and we want to wish him a very Happy Birthday and thank him for the significant contributions he has made to the field of microbial ecology and the American Society for Microbiology.
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