Soil microbiome, Earth’s ‘living skin’ under threat from climate change
Novel approach to measuring microbe activity in wetted soil leads to better understanding of vulnerability, researchers report
Peer-Reviewed PublicationIMAGE: PENN STATE GRADUATE STUDENT RYAN TREXLER COLLECTS CORES OF BIOCRUST FROM THE FIELD BEFORE BRINGING THEM BACK TO THE LAB TO STUDY. view more
CREDIT: PENN STATE
UNIVERSITY PARK, Pa. — Using a novel method to detect microbial activity in biological soil crusts, or biocrusts, after they are wetted, a Penn State-led research team in a new study uncovered clues that will lead to a better understanding of the role microbes play in forming a living skin over many semi-arid ecosystems around the world. The tiny organisms — and the microbiomes they create — are threatened by climate change.
The researchers published their findings in Frontiers of Microbiology.
“Biocrusts currently cover approximately 12% of Earth’s terrestrial surface, and we expect them to decrease by about 25% to 40% within 65 years due to climate change and land-use intensification,” said team leader Estelle Couradeau, Penn State assistant professor of soils and environmental microbiology. “We hope this work can pave the way to understanding the microbial functions supporting biocrust resilience to the rapidly changing climate patterns and more frequent droughts.”
Biological soil crusts are assemblages of organisms that form a perennial, well-organized surface layer in soils. They are widespread, occurring on all of the continents wherever a shortage of water limits the growth of common plants, allowing light to reach bare soil. But there is still sufficient water to support the growth of microorganisms that perform valuable ecosystem services such as taking carbon and nitrogen from the air and fixing them in the soil, recycling nutrients and holding soil particles together, which helps prevent dust.
That soil-stabilizing function — which reduces erosion by providing the means for soil to clump and not break down into dust — is extremely important, according to Couradeau. Her research group, now in Penn State’s College of Agricultural Sciences, has been intensively studying biocrusts for a decade.
“Most dust is generated in drylands, and studies suggest that the presence of biocrusts in drylands greatly reduce the amount of dust that would otherwise make its way into the atmosphere,” she said. “We think losing biocrusts would cause a 5% to 15% increase in global dust emission and deposition — which would affect the climate, environment and human health.”
In the semi-arid regions where biocrusts exist, the organisms — tiny mosses, lichens, green algae, cyanobacteria, other bacteria and fungi — may experience just a few rain or snow events a year, explained Ryan Trexler, a doctoral degree candidate in the Intercollege Graduate Degree Program in ecology and in biogeochemistry, who spearheaded the research.
“When the soil is dry, for the most part, the microbes in the soil are dormant, not doing much,” he said. “But as soon as they sense water, they're resuscitated very quickly, within seconds to minutes. And they are actively making chlorophyll and fixing carbon and nitrogen until the soil is dry again — and then the microbes go dormant again. They go through cycles of activity every time it rains.”
To study biocrusts, the researchers took samples from three plots of undisturbed, cyanobacteria-dominated biocrusts located on the Colorado Plateau near Moab, Utah. Biocrust samples were taken in fall following rain that wetted the soil sufficiently to activate the microbes. The samples were subsequently dried and stored in the dark and then rewetted much later in the research.
“We sampled what we call ‘a cold desert,’ because it’s very arid, but in the winter, it sometimes snows,” Trexler said. “So, it's not as hot as many other arid places, but still plants cannot thrive there because there's not enough water. And so, the only community that we find in soils at the site are microbial.”
To determine which microorganisms are active within soil communities, the researchers coupled bioorthogonal non-canonical amino acid tagging — known as BONCAT — with fluorescence-activated cell sorting. BONCAT is a powerful tool for tracking protein synthesis on the level of single cells within communities and whole organisms, while fluorescence-activated cell sorting sorts cells based on whether they are producing new proteins.
The researchers combined these processes with shotgun metagenomic sequencing, which allowed them to comprehensively sample all genes in all organisms present in biocrust samples. They applied this method to profile the diversity and potential functional capabilities of both active and inactive microorganisms in a biocrust community after being resuscitated by a simulated rain event. The researchers found that their novel approach can discern active and inactive microorganisms in wetted biocrusts.
The active and inactive components of the biocrust community differed in species richness and composition at both four hours and 21 hours after the wetting event, the researchers reported.
Contributing to the research were Marc Van Goethem, Lawrence Berkeley National Laboratory, and King Abdullah University of Science and Technology, Jeddah, Saudi Arabia; Danielle Goudeau, Nandita Nath, Trent Northen and Rex Malmstrom, Lawrence Berkeley National Laboratory, U.S. Department of Energy Joint Genome Institute.
The U.S. Department of Energy supported this research.
A cross-section of biocrust taken by confocal scanning laser microscopy. Soil particles are visible as various shades of gray, while the bundles of cyanobacterial filaments (fluorescent red) are situated between them.
A view of the Colorado Plateau near Moab, Utah, where biocrust samples were taken in fall following rain that wetted the soil sufficiently to activate the microbes.
CREDIT
Penn State
JOURNAL
Frontiers in Microbiology
METHOD OF RESEARCH
Observational study
SUBJECT OF RESEARCH
Not applicable
ARTICLE TITLE
BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event
Interdisciplinary team studies decomposition effects on soil
IMAGE: POSTDOCTORAL RESEARCHER STACY TAYLOR CONDUCTS RESEARCH ON SOIL SAMPLES COLLECTED FROM THE ANTHROPOLOGICAL RESEARCH FACILITY. view more
CREDIT: UT, KNOXVILLE
Forensic researchers at the University of Tennessee Knoxville’s famous Anthropological Research Facility, popularly known as the “Body Farm,” have made headlines for decades in their discoveries of what happens to human bodies after death. Now, a multidisciplinary team—engineers, soil scientists, and biologists—digs in with them for a deeper look at what happens to the soil underneath a decomposing body. Their study, “Soil Elemental Changes During Human Decomposition,” published in June 2023 by PLOS One, could benefit investigators searching for human remains in remote or hard-to access-vegetated areas.
“This study was part of a larger project where we were investing environmental changes in the vicinity of a decomposing body,” said Jennifer DeBruyn, co-author and professor in the Herbert College of Agriculture Department of Biosystems Engineering and Soil Science (BESS). “Our bodies are concentrated in nutrients and other elements compared to the surrounding environment. As they break down, these nutrients are released into the environment, resulting in changes to soil and vegetation nearby.”
A greater understanding of how and when soil and vegetation changes in the presence of decomposing human remains may offer clues to both locating bodies and estimating how long they have been there.
To test their ideas, this study asks: What elements are released from the human body during decomposition and how does it influence the local soil environment?
“We have previously looked at the major elements of the body, namely carbon and nitrogen,” said DeBruyn, “But we know there are lots more in our bodies.”
The next most abundant elements in the body are sulfur, phosphorus, sodium, and potassium. As the soft tissues in test bodies decomposed, the team observed an expected pulse of these elements in the soils as they were released into the environment.
“What we were surprised to see was that we also had higher concentrations of calcium and magnesium than what we would expect from the input of the body alone,” said Stacy Taylor, lead author on the study and a postdoctoral researcher in DeBruyn’s lab. “While we do have calcium (Ca) and magnesium (Mg) in our bodies, much of it is tied up in our bones, which would take years or decades break down. Soils have capacity to bind cations like Ca2+ and Mg2+, so our hypothesis is that the changing conditions resulted in the release of these elements from the soil itself.”
They were also surprised to see an increase in some trace metals a few months into the soil testing, after soft tissues were largely decomposed.
“Again, the concentrations in soil were higher than what we would expect based on just what would be coming from the body,” said Taylor. “Decomposition fluids result in a gradual acidification of the soil over time, so our hypothesis is that as the pH was dropping, these trace metals were slowly being solubilized from mineral complexes in the soil.”
The big-picture take-away from their study could lead to new approaches in finding missing persons or in determining how long remains have been in a location.
“This study was an important documentation of the types of elements released during human decomposition and how they changed over time,” said DeBruyn. “It contributes to our broader understanding of local environmental changes during human decomposition, which may ultimately help us understand the timing of decomposition in cases where human remains are found outdoors.”
DeBruyn and her students and postdocs have been conducting research at the Anthropological Research Facility for over a decade, investigating the microbiological and environmental changes during human decomposition.
Their team for the study included DeBruyn, Taylor, and Michael Essington from BESS; Scott Lenaghan and Neal Stewart from the Center for Agricultural Synthetic Biology within the UT Institute of Agriculture; Amy Mundorff and Dawnie Steadman of the Forensic Anthropology Center, and Adrian Gonzalez, manager of the Water Quality Core Facility (WQCF) in the Department of Civil and Environmental Engineering.
The WQCF analyzed hundreds of soil samples that originated from underneath deceased human donors—those whose decision to volunteer their remains offers ongoing contribution to the furthering of this investigative science.
JOURNAL
PLoS ONE
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