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Many fine-grained soils have been documented to contain fractures. Fractures influence the balance of water, air, and nutrients in the subsurface providing a beneficial environment for ecosystems to flourish. In turn, these ecosystems can create and expand the network of fractures or change the biogeochemistry within a given fracture. The more permeable fractures allow preferential root penetration beyond what would be expected in unfractured parent materials. Earthworm burrowing can redistribute nutrients to the deeper subsurface, facilitating root growth at depth. In a series of laboratory studies on undisturbed soil blocks, it was found that water flow through the soil was dominated by earthworm burrows. These burrows can transmit water directly to shallow ground water, agricultural tile drains, or animal holes. Burrows contain the castings of fecal matter left behind by the worms which provide nutrients for plant growth. Likewise, the decaying organic material may be used by soil bacteria and fungi leading to calcite precipitates lining and/or filling of the fractures. These linings can have implications on the efficacy of soil bioremediation and soil-based wastewater treatment systems. This paper includes field observations of these phenomena and presents a conceptual model of the aerobic / anaerobic pathways for microbial calcification of fractures.