“Dust to dust” may not be God’s work so much as the enterprising efforts of soil microbes. But until now, little was known about how these tiny undertakers turn our bodies to dust. New research shows that, no matter where we’re buried, the same bacteria, fungi, and other small organisms in the soil ransack our bodies, as if they were just waiting for our corpses to arrive. The findings could have important implications for forensic science, including helping police better pinpoint time of death.
“I imagine that [the new] conclusions will end up featured in both ecosystem science textbooks and episodes of CSI,” says Brendan Bohannan, a microbial ecologist at the University of Oregon in Eugene, who was not involved with the work. “You can’t say that about most scientific articles!”
Compared with plants, decaying animals are an incredibly rich source of nutrients like nitrogen and carbon. Corpses represent a “gold mine” for microbes, says George Kowalchuk, a microbial ecologist at Utrecht University in the Netherlands, who was not involved with the study. He adds that although we’ve long known that scavengers such as buzzards, raccoons, and blowflies do some of the dirty work of breaking down dead bodies, we are only just learning how important microbial decomposers are.
To find out just what role they play, evolutionary biologist Jessica Metcalf of the University of Colorado, Boulder, set out to survey the microbes in, on, and around corpses. She started with mice, putting 126 bodies into individual containers with soil from three places: a short grass prairie and a subalpine lodgepole pine forest in Colorado, and a desert in Texas. Over the next year and a half, she sampled microbes on the decaying mouse skin, in the guts, and in the soil. With the help of colleagues from the Sam Houston State University Southeast Texas Applied Forensic Science Facility in Huntsville, she also tracked the decay of four human corpses donated to science, two placed outside in winter and two placed outside in spring.
Identifying the microbes was the real challenge because many cannot be grown, and thus studied, in the laboratory. To figure out which ones—including worms and fungi—were present, Metcalf and Rob Knight, a microbial ecologist at the University of California, San Diego, and their colleagues used metagenomics, a process of isolating and sequencing DNA from soil and corpse samples. To analyze the thousands of species they found, they developed sophisticated computer programs. “It’s a metagenomics tour de force … that gets complex microbial information into a useful form,” Kowalchuk says.
Their findings show that most of the microbes responsible for decomposition come from the soil, not from the gut as other researchers have suggested. What’s more, no matter the soil type, the weather, or the presence of other scavengers, the microbes are the same.
This suggests that soils may contain a "microbial seed bank,” a set of rare microbes that may be barely getting by until a nutrient-rich corpse arrives. That’s when their population explodes, says Greg Caporaso, a bioinformatician at Northern Arizona University in Flagstaff who was not involved with the work. That’s unexpected, notes Eva Cuypers, a forensic toxicologist at the University of Leuven in Belgium, who studies the “smell of death.” Cuypers, who was not involved with the work, says the most surprising insight is that the microbial decomposer community doesn’t depend on soil type. This could make it easier for her to answer whether there is a unique smell associated with death, she adds.
Moreover, the study shows that the microbial community changes through time in a predictable way. The decomposers were barely detectable at the beginning of these experiments, and the soil around each corpse supported seemingly quite different sets of organisms, the team reports online today in Science. But soon after the corpses ruptured—caused by the activity of gut microbes—their native microbial community was replaced by oxygen-loving microbes in the air and the soil. These once-rare decomposers then undergo a population boom, fueled by the decaying guts, which are rich in nitrogen from broken-down proteins. The array of microbes shifts through time, with nitrogen-recyclers starting out as dominant, and fungi and nematode worms getting a foothold in later stages of decomposition, the team reports.
After chronicling the different shifts of decomposers on the mice, and seeing the same shifts operating on the humans, the researchers built a computer model using the mouse data to see whether the microbial composition could be used to predict times of death, using the humans as a test case. “The mouse experiments in the laboratory predicted the time of death very well,” Metcalf says. “It was jaw-dropping.”
The findings could be a powerful new tool for crime-solving. Forensics experts sometimes use the presence of insects such as blowflies, whose young thrive on decaying flesh, to estimate time of death. But Bohannan says that microbial succession could prove to be a “more accurate source of forensic information than insect succession.”
To get to that point, however, more work needs to be done. With support from the National Institute of Justice, the research arm of the U.S. Department of Justice in Washington, D.C., Metcalf and Knight’s team will soon study corpses at facilities across the country, during all seasons, to see whether the microbes are the same and follow the same pattern of succession. Cuypers would like to see them test corpses on more soil types. And Bohannon wonders whether it might be possible to use the microbial makeup of soil to tell that a long-gone corpse was once there. No matter the outcome, bioinformatician Caporaso calls the paper an “early step” toward new forensic technologies based on advanced DNA sequencing.