Biodiversity Soil and Fertilizer

Life in the Ground ~ Soil Biota

Over the next few posts, I’ll be trying to catch up on the many articles I’ve collected about soil.

Samples were harvested at two time points in July and October 2019 at two long-term warming experiments, SWaN and PH, at the Harvard Forest long-term ecological research station, which had been established for 13 and 28 years, respectively. Credit: Global Change Biology (2022).

How are soil microbes affected by climate change?

The largest terrestrial carbon sink on Earth is the planet’s soil. One of the big fears is that a warming planet will liberate significant portions of the soil’s carbon, turning it into carbon dioxide (CO2) gas, and so further accelerate the pace of planetary warming. A key player in this story is the microbe, the predominant form of life on Earth, and which can either turn organic carbon—the fallen leaves, rotting tree stumps, dead roots and other organic matter—into soil, or release it into the atmosphere as CO2. Now, an international team of researchers led by the University of Massachusetts Amherst has helped to untangle one of the knottiest questions involving soil microbes and climate change: what effect does a warming planet have on the microbes’ carbon cycling? The answer is surprising: increased temperature decreases the rate at which soil microbes respire CO2—but only in the summer. During the rest of the year, microbial activity remains largely historically consistent.

But there’s a catch to this seemingly happy story. Soil microbes are releasing less CO2 in the summer because they’re starving. And they’re starving because long-term warming is threatening the viability of deciduous trees, on whose dead leaves the microbes depend. “One of the major outcomes of our study,” says Kristen DeAngelis, professor of microbiology at the University of Massachusetts Amherst and senior author of the study, published in the journal Global Change Biology, “is that all those autumn leaves mitigate the negative effects of global warming on soil microbes.” For now. But fewer dead leaves means less food for the microbes and seems to be leading to a reduction in microbial biomass during the summer.

Modelling bacterial diversity of soils

Credit: Pixabay/CC0 Public Domain

A new set of quantitative models that incorporates pH into the metabolic theory of ecology (MTE) has been developed by an international team that includes Penn State assistant professor of plant science Francisco Dini-Andreote. The work is included in a paper published by the Proceedings of the National Academy of Sciences. In general terms, the metabolic theory of ecology links rates of organism diversification (i.e., the metabolic rate of an organism) with the organisms’ body size and body temperature. “Soils are the most complex and biodiverse ecosystems on Earth,” said Dini-Andreote, a member of Penn State’s Microbiome Center. “In soils, microbial diversity plays indispensable roles in the anabolic and catabolic cycles of carbon, nitrogen and sulfur, without which the diversity of life forms—including plants, animals and other microbes—that evolved on our planet would not have been possible. In addition, advancing our ability to predict patterns of soil biodiversity is critical to better understanding how climate change will affect soil functioning and how soil microbes will respond to shifts in temperature and precipitation regimes.”

It isn’t the picky eaters that drive soil microbial metabolism

Soil sample from the Washington State University field site in Prosser, Washington. Credit: Andrea Starr, Pacific Northwest National Laboratory

Interactions among microorganisms in soil lead to the release of nutrients derived from complex organic matter in that soil. This community metabolism creates food for both microbes and plants. However, scientists don’t fully understand the specific nature of many of these interactions. For example, scientists want to know why some microbes are more successful than others and what roles individual members play in their communities. To find out, researchers from Pacific Northwest National Laboratory, Iowa State University, University of Nebraska–Lincoln, and Argonne National Laboratory studied a model microbial community fed with a complex source of carbon and nitrogen commonly found in soils—chitin.

Their findings, published in the journal mSystems, show that certain microbes drive specific steps of the chitin breakdown process, but the most abundant microbes are not necessarily the most important. The model microbial community used in this study included eight soil bacteria—some chitin degraders and some non-degraders. The researchers observed that the species organized into distinct roles when it was time to break down the chitin. Intriguingly, the most abundant members of the model community were not those that were able to break down chitin itself, but rather those that were able to take full advantage of interactions with other community members to grow using chitin breakdown products. The study answers important questions about how complex carbon and nutrient sources are metabolized by interacting microorganisms to support plant and microbial growth in soil ecosystems.

Microbes could be used by farmers as natural fertilizer for poor soil

A hammer and chisel were required to collect samples from the terrain where Barbacenia macranta lives, in this case, exposed rock. Credit: Rafael Soares Correa de Souza/GCCRC

A study published in The ISME Journal identified 522 genomes of archaea and bacteria associated with the roots and soil of two plant species native to the Brazilian montane savanna ecoregion known as campos rupestres (“rocky meadows”). Hundreds of microorganisms hitherto unknown to science were identified, showing that the ecoregion is a biodiversity hotspot and that many new organisms have yet to be described and classified in Brazil.

The discovery could potentially be a basis for the development of biological substitutes for the chemical fertilizers used by farmers, especially those containing phosphorus. “Phosphorus is normally present in the soil, but not always in a form that plants can use. Most of the microorganisms we found make phosphorus soluble so that plants can absorb it,” said Antônio Camargo, first author of the article.

Fungi and bacteria are binging on burned soil

Signs of microbial life in the Holy Fire burn scar. Credit: Sydney Glassman/UCR

UC Riverside researchers have identified tiny organisms that not only survive but thrive during the first year after a wildfire. The findings could help bring land back to life after fires that are increasing in both size and severity. The Holy Fire burned more than 23,000 acres across Orange and Riverside counties in 2018. Wanting to understand how the blaze affected bacteria and fungi over time, UCR mycologist Sydney Glassman led a team of researchers into the burn scar. “When we first came into fire territory, there was ash up to my shins. It was a very severe fire,” Glassman said.

The researchers visited the scar nine times over the course of the next year, comparing the charred earth with samples from nearby, unburned soil. Their findings, now published in the journal Molecular Ecology, show that the overall mass of microbes dropped between 50 and 80% after the fire, and did not recover during that first year. However, some things lived. 

UCR researcher sampling soil in the Holy Fire burn scar. Credit: Sydney Glassman/UCR.

It wasn’t just one type of bacteria or fungi that survived. Rather, it was a parade of microbes that took turns dominating the burned soil in that first post-fire year. “There were interesting, distinct shifts in the microbes over time. As one species went down, another came up,” Glassman said.

Certain microbes called methanotrophs regulate the breakdown of methane, a greenhouse gas. Fabiola Pulido-Chavez, UCR plant pathology Ph.D. candidate and first author of the study, noticed that genes involved in methane metabolism doubled in post-fire microbes. “This exciting finding suggests post-fire microbes can “eat” methane to gain carbon and energy, and can potentially help us reduce greenhouses gases,” Pulido-Chavez said.

What the researchers saw in the soil bears some resemblance to the human body’s response to a major stress. What is now being learned about post-fire microbe behavior could change older theories about plant behavior, since microbes were not factored into them. “To me, this is exciting, as microbes have long been overlooked, yet they are essential for ecosystem health,” Pulido-Chavez said.

One open question that remains is whether adaptations that plants and microbes have developed in response to wildfires will adapt again to megafires or recurrent fires. Whereas there might have been a period of several decades before a plot of land burned more than once, it is increasingly common for the same soil to burn again in fewer than 10 years.

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