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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.

We report two shallow marine, ichnofauna-bivalve-microbial mat biofacies from the Lower Triassic Xiahuancang Formation of the southern Qilian area, Qinghai Province, northwestern China, which was located at moderate-high paleolatitudes on the northern margin of the Paleotethys Ocean. Paleoenvironmental analyses show that Members I and II of the Xiahuancang Formation represent a shoreface and a lower shoreface to offshore transition setting, respectively. Biofacies 1, recognized from Member I, is characterized by a diverse ichnofauna (including deep-tiers of Rosselia and Diplocraterion), Claraia-dominated bivalves, and microbially induced sedimentary structures (MISSs). Biofacies 2, in succeeding Member II, is dominated by a diverse ichnofauna, epifaunal and shallow infaunal bivalves, and wrinkle structures. Primary co-occurrences, preservational features, and palimpsest or crosscutting relationships of all components within the biofacies indicate that microbial mats, bivalves, and trace-makers actively interacted with one another during deposition. They largely represent contemporaneous biotic associations. Microbial mats are interpreted to have grown under well-oxygenated conditions after storm deposition due to the association of deep-tiering infauna and diverse epifauna as well as well-developed cross-stratification, and the top layer of microbial mats could serve as an oasis for metazoans. Microbial mats not only proliferated in harsh environments, but also coexist with epifauna and deep-tiering infauna in well-oxygenated settings following the end-Permian crisis. Their occurrences in the Early Triassic are unrelated to environmental stresses, which are coincident with their sedimentologic record from other geological time intervals. Apparently, the southern Qilian ichnofauna-bivalve-microbial mat biofacies with juxtaposed epifauna, infauna and MISS- or wrinkle-related microbial mats represents a matground-adapted benthic metazoan ecosystem in the earliest Triassic, which provided sufficient oxygen, food, and other hydrodynamic conditions hospitable for metazoans and ecosystems to recover and reached a fairly high level (recovery stage 3) in a tough time when most biotas suffered biotic depletion and environmental stress. The biotic components in unique biofacies may represent a phase shift community in siliciclastic settings during the Early Triassic.

Microbially induced sedimentary structures (MISSs) are commonly present in siliciclastic shallow marine settings following the end-Permian mass extinction, but have been rarely reported in the post-extinction terrestrial ecosystems. Here, we present six types of well-preserved MISSs from the upper Sunjiagou Formation and lower Liujiagou Formation of Induan (Early Triassic) age in the Yiyang area, Henan Province, North China. These MISSs include: polygonal sand cracks, worm-like structures, wrinkle structures, sponge pore fabrics, gas domes, and leveled ripple marks. Microanalysis shows that these MISSs are characterized by thin clayey laminae and filamentous mica grains arranged parallel to bedding plane as well as oriented matrix supported quartz grains, which are indicative of biogenic origin. Facies analysis suggests that the MISS-hosting sediments were deposited in a fluvial sedimentary system during the Early Triassic, including lake delta, riverbeds/point bars, and flood plain paleoenvironments. Abundant MISSs from Yiyang indicate that microbes also proliferated in terrestrial ecosystems in the aftermath of the Permian–Triassic (P–Tr) biocrisis, like they behaved in marine ecosystems. Microbial blooms, together with dramatic loss of metazoans, may reflect environmental stress and degradation of terrestrial ecosystems or arid climate immediately after the severe Permian–Triassic ecologic crisis.

The Bivalvia is an important benthic clade that was relatively less affected than other benthos during the Permian–Triassic (P–Tr) biotic crisis, reporting losses of 85%, 64%, and 32% at the species, genus and family levels, respectively. This clade proliferated immediately after the P–Tr mass extinction (PTME) to become one of the key elements of the ‘Modern Evolutionary Fauna’ following the P–Tr ‘Great Dying’. Global bivalve occurrence data demonstrate that the initial recovery started in the Griesbachian, a substage immediately after the PTME, and are characterized by relatively high origination and low extinction rates. Thus, unlike other fossil groups, bivalves did not significantly engage in the survival interval. The initial Griesbachian recovery is followed by a stepwise recovery during the Dienerian to Spathian. Then, a remarkably rapid radiation occurred in the Anisian, indicated by extremely high proportional origination and extinction rates. Infaunalization has long been considered the most significant adaptation during the Mesozoic Marine Revolution (MMR), which was thought to have commenced in the Early–Middle Triassic. However, the proportion of infauna in communities remained virtually unchanged before and after the P–Tr biotic crisis; additionally there was no significant difference in proportional extinction/origination rates between infaunal and epifaunal taxa at the genus and family levels through the entire P–Tr transition, implying the absence of ecological selectivity, a conclusion that differs from some previous studies. Therefore, if escalating predatory pressure indeed played a crucial role in driving the initial phases of the MMR, infaunalization was not marked prior to the Ladinian. Alternatively, infaunalization may have played a minor role in facilitating the MMR during the entire era. If so, changes in the physical and chemical environment (‘Court Jester’ model) (i.e. amelioration of marine environments in late Early Triassic), rather than biotic processes (‘Red Queen’ model), may be crucial for the origination and initial phases of the MMR during the early Mesozoic.