ASU-led study finds bacteria tap unexpected carbon source

Most of us learn a simple story about carbon: Plants and other photosynthesizers pull carbon dioxide from the air to make their own organic carbon, while animals, fungi and many bacteria must consume organic carbon directly.

A new Arizona State University-led study suggests that bacteria may play a more complex role in carbon cycling than previously thought, challenging this familiar account of carbon flows from plants to animals and bacteria.

An interdisciplinary team of researchers found that two well-studied heterotrophic bacteria — one from soil and one from the sea — used inorganic carbon to build their cells under every laboratory condition tested. Heterotrophic bacteria are generally understood to get their carbon by consuming organic matter. The amount of inorganic carbon they used varied slightly with temperature, food availability and growth stage, highlighting how environmental conditions may influence the process and raising questions about its role in nature. The findings were recently published in Applied and Environmental Microbiology.

"We know that heterotrophic bacteria can use inorganic carbon, but we know less about why they do it, how much they use, or what controls this process. We wanted to take the bacteria into the lab and figure out why they do this," said lead author Emma Brown, graduate student in ASU’s School of Earth and Space Exploration. 

The process is called heterotrophic inorganic carbon fixation, or HICF. Unlike plants, these bacteria still rely on organic carbon for growth. But they can also use dissolved inorganic carbon, such as bicarbonate, to help build cellular material.

That matters because heterotrophic microorganisms are everywhere. They live in soils, oceans, sediments and subsurface environments, where they help transform, store and recycle carbon. If scientists overlook their ability to use inorganic carbon, they may miss part of how carbon moves through ecosystems.

The project grew out of earlier work by the Microbiology of the Deep (MOD) Lab at ASU, wherein researchers observed microbial communities taking up inorganic carbon in fluids from rocks beneath the Mid-Atlantic Ridge. The finding raised a question: Were organisms normally thought of as carbon consumers also helping pull inorganic carbon into biomass?

To test that idea under controlled conditions, the team grew two heterotrophic Gammaproteobacteria: Pseudomonas putida, a soil bacterium, and Pseudoalteromonas carrageenovora, a marine bacterium. The researchers varied two environmental factors that shape microbial life: temperature, and the amount of available organic carbon. Each treatment also received isotopically labeled bicarbonate, allowing the researchers to track whether inorganic carbon entered the cells.

The answer was yes. Both bacteria showed inorganic carbon uptake in all tested conditions.

"We often set up our experiments pitting organisms that make their organic carbon against those that need to take it up from their environment," said Elizabeth Trembath-Reichert, associate professor at ASU’s School of Earth and Space Exploration and the study's principal investigator. "This is yet another example of how biology is not as simple as we thought. We now appreciate that there is likely a spectrum of how bacteria use carbon rather than two separate camps of makers and takers."

The bacteria did not use inorganic carbon equally in every situation. In general, uptake was highest when cells were actively growing, kept at their preferred growth temperature, and had limited organic carbon available. This reveals a responsive metabolic strategy: The cells adjusted their carbon use in response to their current conditions.

The pattern suggests HICF may be especially relevant in environments where dissolved inorganic carbon and nitrogen are available, but easy-to-use organic carbon arrives in limited or intermittent pulses.

"These types of conditions exist in the rocks beneath the ocean," said Trembath-Reichert, "which nicely ties back to the original motivation for the work from studying microbes from the Mid-Atlantic Ridge. It is very satisfying when a theory from the environment can be tested in the lab and holds up."

To get a finer view, the researchers used NanoSIMS, a single-cell isotope imaging technique, on selected P. carrageenovora samples. The single-cell measurements showed that individual bacteria varied in how much labeled inorganic carbon they incorporated.

"Single-cell tools are especially powerful because they can reveal striking differences in activity among cells that would be completely obscured in a bulk measurement," said Carrie Harris, postdoctoral research scholar at ASU’s School of Earth and Space Exploration and co-author on the paper. 

The findings do not mean heterotrophic bacteria are replacing plants or other autotrophs as the major engines of carbon fixation. Instead, they show that a quieter pathway may be more widespread and more flexible than previously appreciated. 

The study also found that the bacteria changed size and shape under different conditions, a physical response that could help researchers model the effects of HICF in the future.

"With the support of the NASA Space Grant internship, I was able to assist in characterizing the physical changes bacteria undergo when confronted with environmental stressors like cold temperatures and limited food availability," said Kadin Pulliam, NASA Space Grant intern and undergraduate student at the School of Earth and Space Exploration. 

These findings may help scientists better understand life in resource-limited environments, including deep beneath Earth’s surface and in potential habitats beyond Earth. Microbes that can flexibly use small amounts of inorganic carbon may have more ways to persist when familiar food sources are scarce.

Understanding what drives that flexibility could also reshape how scientists search for life elsewhere, said Kate Weeks, a postdoctoral scholar at The University of Utah and co-author of the paper.

“By characterizing the drivers of this survival strategy, of this metabolic flexibility, we have the potential to challenge our preconceptions of what kinds of environments can support life, and even to identify biosignatures for detecting life on other planets.”

This research was supported by NASA through its Exobiology Grant Program, the NASA FINESST Award and the Arizona Space Grant Consortium. ASU's Metals, Environmental and Terrestrial Analytical Laboratory in Core Research Facilities also supported this research.