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Biotic activities are involved in almost all sedimentation processes throughout the evolutionary history of life on our planet. However, deep-time organism-induced sedimentation and biosedimentary records remain unclear in terms of lithologic types, strata stacking patterns and possible controlling factors. We document biosedimentary features of major transitions from microbe-dominated switching to metazoan-dominated biosedimentary systems based on the global distributions of both microbial and metazoan carbonates through Precambrian to Phanerozoic times, with emphasis on sedimentary records from China. The compilation of 150 and 180 well-documented metazoan and microbial reefs, respectively, from China, reveals that metazoan reefs proliferated during the Middle Ordovician, Middle Devonian and Middle Permian, whereas microbial reefs were well developed during the Cambrian, Late Devonian and Early-Middle Triassic, plus a moderate development during the early Silurian. These stratigraphic abundances of metazoan and microbial carbonates of China generally match the global patterns. The updated variation trends of microbial and metazoan carbonates throughout the late Precambrian and Phanerozoic reveal that there were five major microbe metazoan transitions (MMTs): the late Ediacaran, the Cambrian, and the aftermaths of the mass extinctions of the end-Ordovician, Late Devonian, and end-Permian. The late Ediacaran MMT began with microbe-dominated oceans with occasional occurrences of metazoans. The presence of Cloudina-dominated reefs in the latest Ediacaran marks the completion of the switching of this microbe-dominated depositional system into a metazoan-dominated system. The Cambrian saw the expansion of skeletal microbes (i.e., Epiphyton, Renalcis) in the oceans; and the stratigraphic successions yield the most diverse biosedimentary deposits and/or structures of the entire Phanerozoic. The Cambrian MMT was the longest microbial-metazoan alternation period and is marked by two metazoan occurrence peaks marked by dominance of abundant archaeocyath buildups during its Epoch 2 and by maceriate and lithistid sponge reefs during the late Furongian Epoch. The early Silurian in China saw the deposition of a thick suite of organic-rich black shales followed by alternations of microbe-rich sediments (oil shales) and metazoan-bearing deposits, which are replaced by microbial and metazoan reefs during the late early Silurian. The Late Devonian MMT started during the late Frasnian and persisted into the early Mississippian, and thus extended slightly longer than the aftermath of the Frasnian Famennian extinction interval. Alternating occurrences of microbial and metazoan reefs characterize this Late Devonian MMT. Almost all microbe-mediated sediments/structures observed in the Cambrian MMT reoccurred in the aftermath of the end-Permian mass extinction during the Early Middle Triassic MMT, suggesting high similarities between those two MMTs. Cambrian and Early Middle Triassic MMTs also share comparable carbon and sulfur isotopic perturbations, warming regimes, and generally oxygen-deficient seawaters. Some of these environmental and climatic extremes may also occur during other MMTs, but they usually did not occur synchronously.

Most MMTs seem to have undergone four developmental stages. They initiated as microbe-dominated successions (Stage A), and then were characterized by alternations of microbe-dominated and of metazoan-bearing or bioturbated successions (Stage B). Both microbial and metazoan reefs co-occurred during Stage C; and a dominance of metazoan reefs marks the development of Stage D. Ediacaran and Cambrian MMTs seem to have undergone the first three development stages, whereas the three post-extinction MMTs experienced the full set of Stages A D, corresponding to metazoan survival, initial recovery and full recovery.

The majority of volatile-rich Large Igneous Provinces (LIPs), coupled with intensive acidification events, anoxia and global warming regimes, took place during the Mesozoic Cenozoic. However, microbe-dominated sediments were only widely deposited during the Early Triassic, and greatly declined after that time. Therefore, it seems that microbial abundance in MMTs may not be directly related to these extreme LIP events. This is probably because a primary source of food for the metazoans might have shifted to phytoplankton (e.g., coccoliths, dinoflagellates, and radiolarians) in the marine waters since the Triassic. Certainly, the pre-Mesozoic oceans were not dominated by phytoplankton. Perturbations in the carbon isotope record characterize all MMTs, and thus may be reliable proxies indicating MMT biosedimentary systems.