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A scanning electron microscopy study of organic sheets in serpulid tube mineral structures was carried out to discern their function, formation and evolution. The organic sheets may have some taxonomic value in distinguishing the two major clades of serpulids previously identified. The organic sheets in the mineral tube structure occur only in certain taxa belonging to clade A, but not all species in clade A have them. Organic sheets are best developed in genus Spirobranchus. One could speculate that organic sheets have evolved as an adaption to further strengthen the mechanical properties of the tubes in clade A, which contains serpulids with the most advanced mineral tube microstructures. The organic sheets are presumably secreted with at least some mineral phase.

The ultrastructural diversity of the Middle and Late Jurassic serpulid tubes from the Polish Basin has been investigated. The inspection of 12 taxa representing the two major serpulid clades allowed for the identification of three ultrastructure types—irregularly oriented prismatic structure (IOP), spherulitic prismatic structure (SPHP), and simple prismatic structure (SP). Six of the studied species are single-layered and six species possess two distinct layers. Ultrastructural diversity corresponds to certain serpulid clades. The members of Filograninae have single-layered tube walls composed of possibly plesiomorphic, irregularly oriented prismatic structure (IOP). Two-layered tubes occur solely within the clade Serpulinae, where the external, denser layer is built of either the ordered spherulitic (SPHP) or simple prismatic microstructure (SP), and the internal layer is composed of irregularly oriented prismatic structure (IOP). Apart from phylogenetic signals provided by the tube ultrastructure, it can be used in analyzing paleoecological aspects of tube-dwelling polychaetes. Compared to the more primitive, irregularly oriented microstructures of Filograninae, the regularly oriented microstructures of Serpulinae need a higher level of biological control over biomineralization. The advent of the dense outer protective layer (DOL) in serpulids, as well as the general increase in ultrastructure diversity, was likely a result of the evolutionary importance of the tubes for serpulids. Such diversity of the tube ultrastructural fabrics allowed for maximizing functionality by utilizing a variety of morphogenetic programs. The biomineralization system of serpulids remains more complex compared to other tube-dwelling polychaetes. Physiologically more expensive tube formation allows for mechanical strengthening of the tube by building robust, strongly ornamented tubes and firm attachment to the substrate. Contrary to sabellids, which perform a fugitive strategy, an increased tube durability allows serpulids a competitive advantage over other encrusters.

Bryozoans were common benthic invertebrates in the Silurian seas. The large biodiversity among Silurian benthic organisms prompted diversified interactions, and as a result bryozoans hosted many other organisms as symbionts. Here we analyse the cystoporate bryozoan Fistulipora przhidolensis and unidentified trepostomes intergrown with auloporid tabulate corals and putative hydrozoans. The material comes from the uppermost Přídolí Series (Late Silurian) of the Sõrve Peninsula, Saaremaa, Estonia. Our analysis shows that the interaction was beneficial for both organisms—cnidarians benefited from feeding currents created by the host bryozoan, while the latter benefited from the protection from predators by cnidae, it can thus be classified as mutualism. Such associations are common in modern seas. The analysed organisms are typically encrusting when the symbiosis is absent, when intergrown they display erect, branching morphologies, raised over the substratum, thus exploiting a higher suspension-feeding tier. While similar associations were known from the Devonian, we demonstrate that this novel ecological strategy for greater resource exploitation started as early as the latest Silurian.

The frequency of growth increments in the tube wall of the Mesozoic and Cenozoic serpulids is in the range of modern species (i.e. 7–37 growth lines per 50 μm). The growth increments of serpulids do not show correlation with the water temperature and presumably cold water and warm water serpulid species are growing on average with similar speed in terms of number of growth lines per 50 μm. The large serpulid species have usually significantly larger growth increments than smaller species and presumably also grew faster than smaller species. The species with denser skeletons have lower growth rates than species with more porous skeletons. It is possible that serpulids do not have to calcify faster to produce thicker growth increments with lower density.

Polychaete annelids are a very important group of calcifiers in the modern oceans. They can produce calcite, aragonite, and amorphous phosphates. Serpulids possess very diverse tube ultra-structures, several unique to them. Serpulid tubes are composed of aragonite or calcite or a mixture of both polymorphs. The serpulid tubes with complex oriented microstructures, such as lamello fibrillar, are exclusively calcitic, whereas tubes with prismatic structures can be composed either of calcite or aragonite. In serpulids, the calcareous opercula also have complex microstructures. Evolutionarily, calcitic serpulid taxa belong to one clade and the aragonitic taxa belong to another clade. Modern ocean acidification affects serpulid biomineralization. Serpulids are capable of biomineralization in extreme environments, such as the deepest part (hadal zone) of the ocean. The tubes of calcareous sabellids are aragonitic and have two layers, the inner irregular spherulitic prismatic layer and the outer spherulitic layer. The tube wall of cirratulids is composed of aragonitic lamellae with a spherulitic prismatic structure. In some other polychaetes, biominerals are formed in different parts of the animal body, such as chaetae or body shields, or occur within the body as granule-shaped or rod-shaped inclusions.

The occurrence of echinoderm and ptilodictyid bryozoan holdfasts on the surface of Darriwilian calcareous sandstone in northwestern Estonia indicates that it was lithified before encrustation. Pelmatozoans outnumber the bryozoans and cover a larger area of the hardground although both are very sparse. The hardground is very sparsely encrusted (0.37% of the total area studied) and lacks signs of bioerosion.

The earliest bioeroded inorganic hard substrates in the Ordovician of Estonia appear in the Dapingian. Hardgrounds are also known from the Sandbian and Katian. Most of the bioerosion of inorganic hard substrates occurs as the boring Trypanites Mägdefrau, 1932 along with some possible Gastrochaenolites borings. North American hardground borings are more diverse than those in Baltica. In contrast to a worldwide trend of increasing boring intensity, the Estonian record seems to show no increase in boring intensities during the Middle and Late Ordovician. Hardgrounds seem to be more common during the temperate climate interval of the Ordovician calcite sea in Estonia (seven hardgrounds during 15 my) than in the part with a tropical climate (four hardgrounds during 12 my). Bioerosion is mostly associated with carbonate hardgrounds, but cobbles and pebbles broken from the hardgrounds are also often penetrated by Trypanites borings. The general diversity of boring ichnotaxa in Baltica increased from one ichnospecies in the Cambrian to seven by the end of Ordovician, showing the effect of the GOBE on bioeroding ichnotaxa. The diversity of inorganic hard substrate borers increased by only two times. This difference can be explained by the wider environmental distribution of organic as compared to inorganic substrates in the Ordovician seas of Baltica, and their more continuous temporal availability, which may have caused increased specialization of several borers. The inorganic substrates may have been bioreroded only by the generalists among boring organisms.

Late Pridoli Cruziana traces have recently been found in carbonate shelf sediments of the Ohesaare Formation on Saaremaa Island, Estonia. Cruziana isp is interpreted here as a locomotory trace (repichnia) of an arthropod, possibly a trilobite. Cruziana traces previously known from the Silurian of Baltica differ from Cruziana isp, indicating that, the diversity of Cruziana traces in the late Silurian of Baltica was higher than previously thought.

A paleoecological study of stromatoporoid endobionts was carried out to discern the relationships between symbiotic rugosans and their stromatoporoid hosts. The earliest endobiotic rugosan symbiont Palaeophyllum sp. in Baltica has only been found in the stromatoporoid Ecclimadictyon astrolaxum from Saaremaa, Estonia. The rugosans are vertically oriented inside the stromatoporoid skeleton. Numerous rugosans have their corallites open at the upper, external surface of stromatoporoids, but many are completely embedded within the stromatoporoids. Stromatoporoid hosts were presumably beneficial for rugosans as elevated substrates on a sea floor that offered a higher tier for feeding. Relative substrate stability in the hydrodynamically active shallow waters may have also been beneficial for the rugosans.

Phosphatic biomineralization is unknown in modern species of Scyphozoa (Cnidaria). However, some extinct groups of Scyphozoa, such as conulariids and Sphenothallus, were capable of secreting phosphatic exoskeletons. Both conulariids and Sphenothallus used apatite to improve the mechanical properties of their skeletons, which offered better protection than the non-biomineralized periderms. The skeletons of conulariids and Sphenothallus have a lamellar microstructure. The shell lamellae of conulariids are often pierced by tiny pores. Several apatitic mineral structures have been described in conulariids and Sphenothallus, including plywood-like structures. Different lattice parameters of the apatite indicate that the biomineralization mechanisms of the phosphatic cnidarians Sphenothallus and conulariids differed from each other.