Abstract Diverse biogenic and abiogenic processes produce calcite speleothems. From a biogenic perspective, cave microbes mediate a wide range of destructive and constructive processes that collectively influence the growth of calcite speleothems and their internal fabrics. Destructive processes include substrate breakdown by dissolution, boring and residue micrite production, whereas constructive processes include microbe calcification, trapping and binding of detrital particles to substrates, and microbial induced calcite precipitation. Biogenesis can be established from: (1) the presence of mineralized microbes; (2) fabrics, such as stromatolite-like structures, that can be attributed to microbial activity; and/or (3) geochemical proxies (carbon and oxygen isotopes, lipid biomarkers) considered indicative of microbe activity. Such criteria have, for example, been used to demonstrate microbial involvement in the formation of pool fingers, stalactites/stalagmites, cave pisoliths and moonmilk. Nevertheless, absolute proof of microbial biogenesis in calcitic speleothems is commonly difficult because taphonomic processes and/or diagenetic processes commonly mask evidence of microbial activity. The assumption that calcitic speleothems are abiogenic, which has been tacitly assumed in many studies, is dangerous as there is clear evidence that microbes thrive in most caves and can directly and indirectly influence calcite precipitation in many different ways.

Abstract Devonian reef systems are thought to represent the greatest phase of global reef development in the Phanerozoic. Despite this, ecological and environmental controls on the sedimentary nature of these vast systems have scarcely been investigated and remain enigmatic. The Late Devonian (Frasnian) Alexandra Reef System, exposed in the Northwest Territories of Canada, developed on a ramp that was situated on the western margin of Laurussia. The system consists of two reef complexes. The second reef complex developed basinwards of the first after sea level fell ~ 17 m. In contrast to stromatoporoid (± coral)-dominated reef facies in the first reef complex and the upper part of the second reef complex, reef facies in the lower part of the second reef complex are dominated by stromatoporoid-microbe associations. These include significant renalcid boundstone and stromatolite accumulations that are not found elsewhere in the reef system. It is concluded that the occurrence of the stromatoporoid-microbe reef facies indicates that a shift in the reef environment from oligotrophic to mesotrophic conditions took place. The mechanisms of nutrification were linked to the platform geometry, sea-level position, and oceanographic system, indicating that on carbonate ramps, systems tracts of falling sea level (forced regression) and sea-level lowstand may be particularly susceptible to nutrification. A nutrient-gradient model developed to explain different types of reef facies in the Alexandra Reef System indicates that trophic resources were an important control on the composition of Devonian reef-building communities, and that Devonian reefs and carbonate platforms were not highly susceptible to nutrient-invoked drowning.