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Soil Microbes Sacrifice Ribosomes in Response to High Temperature

The researchers used high-throughput shotgun sequencing of total RNA to understand how bacterial communities respond to warming from a functional standpoint.

Shivam Dwivedi
Observing Soil Microbes
Observing Soil Microbes

Sustained increases in soil temperature cause microbes to reduce protein synthesis over time, potentially on a weekly basis. Warming microbial populations increase their carbon dioxide production and growth rate, according to a study published on March 25 in Science Advances, indicating that bacteria can adapt to changing environments by maintaining a high rate of cell division in the face of warmer conditions.

Findings of Research:

According to Kristen DeAngelis, a microbiologist at the University of Massachusetts, Amherst, who was not involved in this study, "warming of any duration appears to lead to reduced need to invest in protein machinery, because the kinetic energy of warming accelerates enzymatic and metabolic rates in a compensatory way." "This is a really exciting observation, and it appears to be generalizable across systems, not just soils."

The study authors used the longest-running experiment exploring soil warming in situ, called ForHot, in which researchers have monitored a grassland in Iceland's subarctic region that has experienced geothermal soil warming for more than 50 years to measure how microbial activity changes over time. Furthermore, to investigate how soil microbes respond to warming on shorter timescales, the researchers studied microbes at a nearby site where an earthquake in 2008 relocated one of the geothermal channels.

In addition to the historical site, this provided an opportunity to study a newly formed heat gradient. "It could be a glimpse into how future global warming will affect soils," says Alexander Tveit, a microbiologist at The Arctic University of Norway who led the study.

The researchers used high-throughput shotgun sequencing of total RNA to understand how bacterial communities respond to warming from a functional standpoint. They were able to study a wide variety of organisms found in the soil microbiome at the same time using this metatranscriptomics approach, comparing which genes were expressed differently when the soil was warmer than usual.

The researchers collected soil samples from both ends of the decades-old temperature gradient and the gradient formed after the 2008 earthquake: four samples from one end of each gradient, where the soil was at ambient temperature, and four samples from the other end, where soil had been heated to more than 6 °C above ambient temperature via geothermal warming.

The researchers discovered that "the amount of RNA in the soil is lower in the warm [soil], Tveit says, indicating reduced protein synthesis," when they examined the total RNA extracted from each of the 16 samples. "Even if the microbial biomass does not change- or changes only slightly- the RNA content is decreasing," Tveit adds.

Sequencing revealed that the protein biosynthesis machinery, specifically ribosomal proteins, was downregulated in warm soil bacterial communities. "The main finding of this study is that genes involved in protein synthesis were down-regulated under warmer conditions," writes Sylvain Monteux, a microbial ecologist at Stockholm University who was not involved in the study, in an email to The Scientist. "Most importantly, they were able to demonstrate that this was not due to a change in microbial community structure, indicating that while the same microbes are present, it is their activity that is changing."

These findings suggest that ribosomal content is lower in bacteria in warmer soils than in bacteria in cooler soils, according to the authors. Normally, this would be detrimental to the bacteria's survival, but Tveit found that bacterial communities in warming soils had higher biochemical reaction rates at higher temperatures. "When it gets warmer, the organisms and all their enzymes will work faster," Tveit claims, allowing microbes to sacrifice ribosomes while still maintaining high metabolic and cell division rates, even as they deplete soil carbon faster than usual.”

"They can maintain a high rate of growth and decomposition in warm soil because they are removing parts of themselves—sort of like losing weight—even when the soil contains fewer nutrients." These changes take months and years to manifest, but preliminary evidence presented in the paper indicates that downregulation occurs after only one week of warming.

Tveit believes that drawing conclusions about how this phenomenon affects the rates of carbon dioxide released from warming soils and how this contributes to climate change is "a step too far" at the moment. "It is likely that it will allow the organisms to deplete more carbon from the soil than they would have been able to do without ribosome regulation." They can continue at a faster rate for a longer period of time than they would otherwise [be able to]."

"While these findings need to be confirmed in other soils to see if they can be generalized," Monteux writes, "they represent a decisive step toward a better mechanistic understanding of microbial responses to warming." "The fate of soil organic matter, as well as the greenhouse gas emissions that may result from its decomposition in a warmer world, has global implications." Understanding microbial responses to warming is also required for accurate inclusion in biogeochemical models."

Coauthor Andrea Sollinger, a microbial ecologist at The Arctic University of Norway, is now looking into whether such warming-induced ribosome regulation occurs on a smaller timescale, such as within weeks or days.

According to Tveit, preliminary experiments show that a similar reduction in ribosomes occurs in other types of soils, such as forest soils. "They adjust the central protein biosynthesis machinery in response to the removal of their own resources."

(Source: The Scientist)

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