The "Cambrian substrate revolution," also called the "Agronomic revolution," is shown by trace fossils and marks a sudden increase in the variety of animals that burrowed during the early Cambrian period.

Before this change in behavior, animals living on the ocean floor mainly ate the microbial mats that covered the surface of the sediment. These animals moved along the surface, like freshwater snails do today, or dug only slightly below the mats. The microbial mats formed a barrier between the water and the sediment below, which was not as wet as modern ocean floors and had very little oxygen. This environment was home to sulfate-reducing bacteria, which released hydrogen sulfide gas, making the area toxic for most other life.

At the start of the Cambrian period, animals began digging deep into the sediment, creating many different types of burrows that became fossils. These burrowing animals weakened the microbial mats, allowing water and oxygen to reach deeper into the sediment. This limited the sulfate-reducing bacteria and their hydrogen sulfide gas to deeper layers, making the upper layers of the ocean floor suitable for more life. The upper layer became wetter and softer because burrowing animals constantly moved the sediment.

Burrowing before the Cambrian

Fossils showing the movement of organisms on and under microbial mats that covered the Ediacaran seafloor from about 565 million years ago have been preserved. The only burrows found from the Ediacaran period are horizontal, on or just below the surface, and were made by animals that fed above the surface but burrowed to avoid predators. If these burrows were made by living things, they suggest the existence of moving organisms with heads, likely bilaterians (animals with symmetrical body plans). Some possible "burrows" dating to 1,100 million years ago might have been made by animals that fed on the undersides of microbial mats, which could have protected them from a chemically harsh ocean. However, these burrows have uneven widths and tapering ends, making it hard to confirm they were made by living organisms. The original author proposed that the marks might instead have been caused by the menisci of broken bubbles. Ediacaran burrows found so far suggest simple behaviors, while the complex, efficient feeding traces common in the Cambrian period are not present. Some simple horizontal traces from before the Cambrian period may have been made by large single-celled organisms, similar to how protists create similar traces today.

The early Cambrian diversification of burrow forms

During the Cambrian period, which began about 538.8 million years ago, many new types of traces first appeared in the fossil record. These include famous vertical burrows, such as Diplocraterion and Skolithos, and traces typically linked to arthropods, like Cruziana and Rusophycus. The presence of vertical burrows suggests that worm-like animals developed new behaviors and possibly new physical abilities. Some Cambrian trace fossils show that the animals that made them had hard exoskeletons, even if those exoskeletons were not always made of minerals.

It is important to understand the difference between two types of burrowing. Bioirrigation is the process of adding oxygen to sediment, while biomixing involves moving sediment grains without adding oxygen. Biomixing can reduce oxygen levels in sediment by bringing organic material to deeper layers, where it is used without oxygen. In terms of the variety of trace fossils (ichnodiversity), the same proportions of these two types of burrowing (mostly biomixing) are found on both sides of the Ediacaran-Cambrian boundary. However, bioirrigation becomes more common in the Terreneuvian stage of the Cambrian period.

Advantages of burrowing

Many organisms dig into the ground to find food, such as other burrowing creatures or organic material. The remains of planktonic organisms sink to the sea floor, offering a food source. If these materials mix into the sediment, they can be eaten by other organisms. However, before the Cambrian period, plankton may have been too small to sink, which meant no organic carbon reached the sea floor. However, organisms did not eat the sediment directly until after the Cambrian period.

A benefit of living within the substrate is protection from being carried away by water currents.

Organisms also burrow to escape predators. Predatory behavior first appeared over 1 billion years ago. However, predation on large organisms became important just before the Cambrian period began. Precambrian burrows helped protect the animals that made them, as these animals lived above the surface. These burrows appeared at the same time as other organisms started developing mineralized skeletons.

Enabling burrowing

Microbial mats formed a blanket over the sediments. This blanket separated the sediments from the ocean water above. This made the sediments without oxygen, and hydrogen sulfide (H₂S) was present in large amounts. The movement of pore water between the sediments and the oxygen-rich ocean water was necessary for the sediments to support life. Tiny animals, called meiofauna, were too small to dig their own burrows. Instead, they lived in the spaces between sand grains in the microbial mats. Their movement stirred the sediment, moving sand grains and breaking up the tough microbial mats. This allowed water and chemicals from above and below the mats to mix.

Effects of the revolution

The Cambrian substrate revolution was a long and uneven process that happened at different speeds in different areas during the Cambrian period.

After the agronomic revolution, the microbial mats that covered the Ediacaran seafloor became limited to certain environments:

• Very harsh environments, such as extremely salty lagoons or slightly salty estuaries, where burrowing organisms could not survive.
• Rocky areas that burrowers could not dig into.
• The deep parts of the ocean, where burrowing activity today is similar to what it was in shallow coastal seas before the revolution.

The first burrowers likely fed on microbial mats while digging underneath them for protection. This burrowing activity caused the mats they depended on to decline.

Before the revolution, bottom-dwelling organisms were divided into four groups:

• "Mat encrusters," which were permanently attached to the mats.
• "Mat scratchers," which grazed the mats’ surfaces without destroying them.
• "Mat stickers," which were suspension feeders partially embedded in the mats.
• "Undermat miners," which burrowed beneath the mats and fed on decaying material.

"Undermat miners" likely disappeared by the middle of the Cambrian period. "Mat encrusters" and "Mat stickers" either died out or developed stronger anchors suited for soft or hard surfaces. "Mat scratchers" were limited to rocky areas and the ocean depths, where both they and the mats could survive.

Early sessile echinoderms were mostly "mat stickers." Helicoplacoids could not adapt to the new conditions and died out. Edrioasteroids and eocrinoids survived by developing holdfasts to attach to hard surfaces and stalks that lifted their feeding parts above debris stirred up by burrowers. Mobile echinoderms (stylophorans, homosteleans, homoiosteleans, and ctenocystoids) were not significantly affected by the substrate revolution.

Early mollusks likely grazed on microbial mats, so it is reasonable to think that grazing mollusks were limited to areas where mats could survive. The earliest known fossils of monoplacophoran ("single-plated") mollusks date to the Early Cambrian, where they grazed on microbial mats. Most modern monoplacophorans live on soft substrates in deep ocean areas, though one genus lives on hard substrates near the edges of continental shelves. The oldest known fossils of polyplacophorans (mollusks with multiple shell plates) are from the Late Cambrian, when the substrate revolution had significantly changed marine environments. Since these fossils are found with stromatolites (stubby pillars built by some microbial mat colonies), it is believed that polyplacophorans grazed on microbial mats. Modern polyplacophorans mainly graze on mats in rocky coastal areas, though some live in the deep sea. No fossils of aplacophorans (shell-less mollusks) have been found. These mollusks are considered the most primitive living group. Some burrow into deep-sea floors, feeding on microorganisms and detritus, while others live on reefs and eat coral polyps.

The revolution ended the conditions that allowed exceptionally preserved fossil beds, such as the Burgess Shale, to form. Direct consumption of carcasses had little effect on fossilization compared to changes in sediment chemistry, porosity, and microbiology, which made it hard for the chemical gradients needed for soft-tissue mineralization to develop. Like microbial mats, environments capable of this type of fossilization became limited to harsher and deeper areas where burrowers could not live. Over time, burrowing became widespread enough to make this type of preservation impossible. Post-Cambrian fossil beds of this kind are usually found in unusual environments.

The rise in burrowing is significant because burrows provide clear evidence of complex organisms. They are also more easily preserved than body fossils, leading scientists to use the absence of trace fossils to suggest that large, mobile bottom-dwelling organisms were not present. This helps paleontologists understand the Early Cambrian and shows that the Cambrian explosion was a real diversification, not just a result of fossil preservation conditions, even if it did not directly coincide with the agronomic revolution.

The rise of burrowing marks a major change in ecosystems, and the appearance of the complex burrow Treptichnus pedum is used to define the start of the Cambrian period.

Increased bioturbation meant that sulfur, supplied to the ocean from volcanoes and rivers, was more easily oxidized. Instead of being buried in its reduced form (sulfide), burrowing organisms exposed sulfur to oxygen, allowing it to become sulfate. This activity is linked to a sudden increase in sulfate levels near the base of the Cambrian, which can be recorded using δS isotopic tracers and by measuring the abundance of the sulfate mineral gypsum.