As a general rule, pelagic sediment is totally bioturbated, and primary sedimentary structures are rarely preserved. The fabric and internal structure of the sediment are modified post-depositionally by the burrowing activities of the infaunal benthos. However, various aspects of the original depositional environment, such as water depth, sediment type, and substrate stability, may be reflected in the ichnofacies. The ichnotaxa apparently differ in their environmental requirements and tolerances; thus, ichnofacies transitions exist even within the pelagic depositional regime.

Today fine-grained, calcitic nannofossil ooze is deposited beyond the reach of terrigenous sources in water depths of about 2,000 and 4,500 m (6,562 to 14,764 ft). At certain times in the past, however, such as during the Late Cretaceous in northern Europe, fine-grained calcareous ooze was deposited in much shallower depths as well, perhaps as little as a few hundred meters.

Trace fossils aid our understanding of the paleobathymetry and substrate conditions in ancient chalky sea bottoms. Deep-sea chalks differ from their shallow-water counterparts in northwest Europe in their typical lack of abundant shelled megafossils and flint horizons. The European chalks commonly contain a Thalassinoides-dominated ichnofacies, which very directly influenced such early diagenetic processes as hardground formation and silica reprecipitation. A deeper water ichnofacies in the European chalks, dominated by Zoophycos, is less commonly associated with hardgrounds and flint horizons. In truly deep-sea chalks, Thalassinoides, bored hardgrounds, and well-developed burrow flints are very rare; a Zoophycos-Chondrites-Planolites association is characteristic.

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