Newswise — June 15, 2021 – Did you know that microbes breathe rust? They do. In this Soils Matter blog, Caitlyn Hodges, from Pennsylvania State University explains this process:

Most living creatures extract the energy in food through a process called respiration. During respiration, organisms take in oxygen and organic carbon (food) and breathe out water and carbon dioxide.

Humans (and most creatures) require oxygen for respiration and therefore survival. But many microorganisms in soils do not need oxygen to survive! Unlike humans, soil bacteria have the capacity to respire molecules and elements other than oxygen.

This capacity comes in handy for soil microbes because rainfall and groundwater often limit oxygen availability in soils. When soils are very wet, oxygen cannot make its way into the soil subsurface. Under such conditions, rather than drown or suffocate (as humans would), microbes simply find a suitable alternate for respiration. There are many molecules and elements these microbes use as oxygen substitutes. Some of the most common oxygen alternates are nitrate, manganese, iron, and sulfur.

This blog focuses on microbial respiration with iron as an oxygen substitute.

Iron is one of the most abundant elements in soils. Soils inherit their striking red, orange, and yellow colors from the abundance of different forms of iron minerals. These colorful iron minerals are very similar to the rust that forms on old steel and iron left outdoors for too long. For this reason, I often call microbial respiration using iron as an oxygen substitute “microbes breathing in rust.”

When microbes use iron in respiration, the rusty iron minerals dissolve in soil water. Over time, this dissolution of iron may remove the reddish-orange pigmentation from part or all an area of soil.

This loss of pigmentation is one method scientists use to identify wetlands and how well a soil drains water. Wetland soils are often gray and dull because the iron minerals have been removed by microbes that used the rusty iron minerals as an alternative to oxygen for respiration.

In soils that are drier than wetlands but still do not drain water quickly, gray patches may form where the microbes have used the iron minerals for respiration.

Iron minerals are important for other reasons than identification of soil drainage and wetlands. Iron minerals also play an important role in nutrient availability and water quality. Nutrients, like phosphorus, stick to the rust-like minerals in soils. When microbes use iron for respiration, the phosphorus “un-sticks” and becomes mobile. This un-stuck phosphorus could be an important source of nutrients for plants. However, if not taken up by plants, the phosphorus could also become a pollutant in streams and larger bodies of water. This type of phosphorus pollution is partly responsible for the poor water quality of places like the Chesapeake Bay.

Obviously, microbes “breathing in rust” plays an important role in soils. Since it is so important, scientists are interested in where and when microbes “breathe in rust.” We use many methods to track microbes using iron for respiration. Some scientists insert rust-like iron minerals into the soil and track the removal of the rust by microbes over time. Others measure oxygen concentration in soils and infer that when oxygen concentrations are below a threshold, microbes may be using iron or other oxygen substitutes for respiration.

I take a different approach to measure when microbes use iron as a substitute for oxygen in respiration. I trick soil microorganisms into believing that a piece of graphite is an iron mineral! I bury the graphite in soil and then connect the graphite to a special machine. The machine – called a potentiostat – makes the microbes interact with the piece of graphite as if it were an iron mineral.

The potentiostat then tracks when microbes in the soil attempt to use the graphite electrode as they would when “breathing rust.” From these measurements I calculate how much iron microbes dissolve when using iron as an oxygen substitute. Don’t worry, these electrodes and potentiostats do not hurt the microbes. In fact, over time microbes that prefer to use iron for respiration start to grow on the graphite!

The next time you see some soil – while driving by a roadcut, passing a construction site, or gardening – look for the rusty-red iron minerals and think about the amazing microbes that use those minerals to live and grow in the soil!

For more information about soils, follow SSSA on Facebook at, Twitter at SSSA_Soils. SSSA has soils information on, for teachers at, and for students through 12th grade,

The Soil Science Society of America (SSSA) is a progressive international scientific society that fosters the transfer of knowledge and practices to sustain global soils. Based in Madison, WI, and founded in 1936, SSSA is the professional home for 6,000+ members and 1,000+ certified professionals dedicated to advancing the field of soil science. The Society provides information about soils in relation to crop production, environmental quality, ecosystem sustainability, bioremediation, waste management, recycling, and wise land use.

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