Biomineralization and Biominerals: Lessons from Mineral-Producing Organisms

A special issue of Minerals (ISSN 2075-163X). This special issue belongs to the section "Biomineralization and Biominerals".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 20520

Special Issue Editors

School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
Interests: mineralization; biomaterials; bioarcheology; synthetic chemistry; palaeobiology; geoscience; materials science; biophysics; biochemistry; smart concrete
Special Issues, Collections and Topics in MDPI journals
Department of Geology, University of Tartu, 50411 Tartu, Estonia
Interests: skeletal micro- and ultrastructures; evolution of mineral composition; biomineralization in serpulids; biomineralization in problematic fossils; aragonite versus calcite seas; ocean acidification
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Living organisms have gone through an evolution, over 3.8 Gyr, to use inorganic matrices to fashion a diverse range of highly organized biological minerals that are ideal for biological functions. For instance, teeth made of calcium phosphate mineral enable mammals to tear, chew food and are also used as a weapon, while bones made of calcium phosphate provide a skeleton to support the body for a perfect framework. Sea urchins use teeth made of a complex arrangement of calcite, calcium carbonate, to grind the seabed in search of food and hollow out holes for sanctuary from predators and waves. The skeletons of deep-sea glass sponges are built of silica-based minerals which, in turn, make exceptional fibre-optic properties. Mollusc shells are made of calcareous, aragonite or calcite, then achieve stiffness and toughness higher than that of their pure inorganic counterparts. Shrimps dactyl club exhibits tough and exceptional damage tolerance properties due to the complex bioapatite-based mineralized structure. As with all these biominerals, the structural design elements are composed of biopolymers, such as collagen, chitin, silk, keratin, and proteoglycans, and are hierarchically assembled in parallel to form microfibrils, fibrils, or fibres, depending upon the particular system involved. The properties of biominerals are far superior compared to human-made materials, and the current understanding of their formation is far from complete. It is indeed necessary to learn from nature. The structural lessons gained from the study of these biocomposites could thus provide important design insights into the fabrication of tough layered inorganic–organic hybrid materials/morphologies that could always have fresh surfaces to do specific jobs. 

Therefore, you are invited to submit manuscripts that focus on biomineralization and biomineral characterization, and biomimetic design that will be highly beneficial to society.

Dr. Oluwatoosin Agbaje
Dr. Olev Vinn
Guest Editors

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Minerals is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2400 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • biomineralization
  • biomaterials
  • apatite structure
  • mollusc shell
  • extracellular matrix
  • fossilized biominerals
  • biomimetic mineralization
  • advanced functional materials
  • lessons from nature
  • materials science

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Published Papers (10 papers)

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Research

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22 pages, 10713 KiB  
Article
Imaging of Ancient Microbial Biomarkers within Miocene Dolomite (Kuwait) Using Time-of-Flight Secondary Ion Mass Spectrometry
by Ammar S. Alibrahim, Rana N. S. Sodhi, Michael J. Duane and Maria Dittrich
Minerals 2023, 13(7), 968; https://0-doi-org.brum.beds.ac.uk/10.3390/min13070968 - 21 Jul 2023
Cited by 1 | Viewed by 1242
Abstract
Time-of-Flight–Secondary Ion Mass Spectrometry (ToF-SIMS) using a bismuth liquid metal ion source was utilized to characterize and image microbial biomarkers within dolomite from early-middle Miocene coastal mud volcano outcrops in Kuwait. ToF-SIMS analysis revealed biomarkers of ancient microbial consortia of sulfate reducers and [...] Read more.
Time-of-Flight–Secondary Ion Mass Spectrometry (ToF-SIMS) using a bismuth liquid metal ion source was utilized to characterize and image microbial biomarkers within dolomite from early-middle Miocene coastal mud volcano outcrops in Kuwait. ToF-SIMS analysis revealed biomarkers of ancient microbial consortia of sulfate reducers and methane oxidizers participating in the anaerobic oxidation of methane. The identified lipid biomarkers comprised 17α(H),21β(H)-Norhopane, Hop-17(21)-ene or Hop-22(29)-ene (diploptene), non-isoprenoidal dialkyl glycerol diethers (DAGEs), and Diacylglycerol esters (DGs). The ion µ-scale images of carbonate rocks showed two characteristic styles: (1) high signal intensity of dolomite, halite, and biomarkers, where the biomarkers demonstrate a distinctive co-localization pattern with both dolomite and halite; and (2) a lack of dolomite, halite low signal intensity, and an absence of biomarker co-localization patterns. Our results highlight three remarkable observations. Firstly, the concomitance of dolomite and halite suggests a common source of magnesium and sodium supply, likely from the hypersaline Al-Subiya sabkha. This emphasizes the importance of hypersaline seawater for dolomite formation. Secondly, microbial biomarkers correspond to methane- and sulfate-rich conditions under which dolomite was formed. Lastly, the high intensity of biomarker signals and their association with dolomite and halite indicate that the consortia involved in dolomite formation have preferences for high-salinity conditions. The three observations align with previous studies that have highlighted the importance of methane-sulfate redox, high salinity, and halophilic microbes for dolomite formation. This work is the first to acknowledge ancient microbial biomarkers within Miocene dolomite in Kuwait, which aims to broaden the understanding of the biogeochemical processes triggering dolomite formation in similar environments and ancient geologic settings. Full article
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18 pages, 7512 KiB  
Article
Structure Evolution of CaCO3 Precipitates Formed during the Bacillus cereus Induced Biomineralization
by Lyubov A. Ivanova, Darya A. Golovkina, Elena V. Zhurishkina, Yulia E. Gorshkova, Alexey D. Yapryntsev, Alexander E. Baranchikov, Natalia V. Tsvigun, Gennady P. Kopitsa, Anna A. Kulminskaya and Dmitry V. Lebedev
Minerals 2023, 13(6), 740; https://0-doi-org.brum.beds.ac.uk/10.3390/min13060740 - 30 May 2023
Cited by 1 | Viewed by 1201
Abstract
Biomineralization is a universal process that has implications in a variety of areas, from civil engineering to medicine. While crystallization of amorphous CaCO3 formed in vitro is known to precede the vaterite-calcite/aragonite pathway, this process could be significantly altered when induced by [...] Read more.
Biomineralization is a universal process that has implications in a variety of areas, from civil engineering to medicine. While crystallization of amorphous CaCO3 formed in vitro is known to precede the vaterite-calcite/aragonite pathway, this process could be significantly altered when induced by bacteria, particularly within the extracellular matrix (ECM) of microbial cells. We used a combination of SEM, SANS, SAXS, FTIR and XRD methods to investigate the structure of CaCO3 formed during biomineralization induced by planktonic Bacillus cereus. Formation of precipitates in the presence of CaCl2 and urea was observed both during bacterial growth and in the medium devoid of bacteria and ECM (cell-free system). The pathway for polymorphic transformations of CaCO3 from the amorphous phase to vaterite and further to calcite was confirmed for the bacterium-induced mineralization and did not depend on the concentration of Ca2+ and urea. The structure of CaCO3 sediments differed when formed in cell-free and bacterial systems and varied depending on time and the medium composition. The rate of precipitation was accelerated in the presence of DNA, which had little effect on the solid phase structure in the cell-free system, while strongly affecting the structure and polymorphic composition of the precipitates in bacterial culture. Full article
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16 pages, 7809 KiB  
Article
Calcium Oxalates in Soils within Disturbed Landscapes and Rock on the Territory of Yakutia (Russia), Formation Conditions in a Sharply Continental Cryoarid Climate
by Tatiana I. Vasileva and Yana B. Legostaeva
Minerals 2023, 13(5), 659; https://0-doi-org.brum.beds.ac.uk/10.3390/min13050659 - 10 May 2023
Viewed by 1264
Abstract
The formation of oxalates in soils and rocks under conditions of cryoarid climate, permafrost and taiga vegetation was studied. Whewellite and weddellite were found in four areas associated with the mining industry: on the kimberlite deposit of the Daldyn territory, in the lower [...] Read more.
The formation of oxalates in soils and rocks under conditions of cryoarid climate, permafrost and taiga vegetation was studied. Whewellite and weddellite were found in four areas associated with the mining industry: on the kimberlite deposit of the Daldyn territory, in the lower reaches of the Markha River of the Central Yakut Plain, and on the coastal outcrop of the Allah-Yun Sellah-Khotun ore cluster. Whewellite was found in the upper organic horizon of Skeletic Cryosol (Thixotropic) (sample 151) and as a film on the surface of plant remains of Humic Fluvisols (sample 1663). Weddellite was found as an extensive encrustation on the surface of the soil and vegetation cover of Stagnic Cryosols Reductaquic (sample 984) and on a siltstone outcrop (sample KM-6-21). Calcium oxalates were identified by X-ray phase analysis, photographs of the samples were taken on a polarizing microscope, and the crystal morphology was studied on a scanning electron microscope. To determine the chemical composition of soils and rocks, the classical wet-chemical method was used; the physical properties of the studied samples were studied using a pH meter, the photoelectric colorimetric method, and a synchrotron thermal analysis device. The source of calcium for the formation of salts is the parent layers of the studied soils, represented by carbonate and carbonate clastic rocks, which cause neutral and slightly alkaline environments. High humidity, which is provided by the seasonal thawing of the permafrost, has a key role in the formation of the studied oxalates in Yakutia with a sharply continental cryoarid climate. Based on the studies, it was found that the first two samples are the products of lichen activity, and the third and fourth are at the stage of initial soil formation by micromycetes. In addition, the formation of these oxalates, in our opinion, is the result of the protective function of vegetation, in the first two cases, with a sharp increase in the load on lichens under technogenic impact, and in the second and third cases, when favorable conditions arise for initial soil formation, but under conditions of toxic content of heavy metals and arsenic. Full article
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31 pages, 5297 KiB  
Article
Mineral Paragenesis Precipitating in Salt Flat Pools of Continental Environments Replicated in Microbial Mat Microcosms without Evaporation
by Óscar Cabestrero, Cinthya Tebes-Cayo, Nancy W. Hinman and Cecilia Demergasso
Minerals 2022, 12(5), 646; https://0-doi-org.brum.beds.ac.uk/10.3390/min12050646 - 20 May 2022
Cited by 1 | Viewed by 2215
Abstract
Mineral precipitation can be observed in natural environments, such as lagoons, rivers, springs, and soils. The primary precipitation process has long been believed to be abiotic due to evaporation, leading to phase supersaturation. However, biotic interactions of microbial metabolism, organic compounds, and dissolved [...] Read more.
Mineral precipitation can be observed in natural environments, such as lagoons, rivers, springs, and soils. The primary precipitation process has long been believed to be abiotic due to evaporation, leading to phase supersaturation. However, biotic interactions of microbial metabolism, organic compounds, and dissolved ions leading to mineral precipitation has been shown in laboratory studies using single-organism culture. The increase in pH inducing calcium carbonate precipitation due to oxygenic photosynthesis by Cyanobacteria and the release of ions due to organic matter decomposition by Firmicutes-inducing magnesium carbonate precipitation are recognized examples. As microbes do not live as pure cultures in natural environments but form complex communities, such pure culture lab studies do not reflect natural conditions. In this study, we grew natural complex microbial communities in microcosm conditions using filtered brine as water column and two types of natural gypsum substrates, and we replenished incubations to avoid evaporation. We monitored microbial communities through optical microscopy and analyzed mineral paragenesis in association with and without microbes, using different analytical techniques, such X-ray diffraction, and optical and field emission scanning electron microscopies. To detect changes throughout the experiment, small amounts of water column brine were extracted for physicochemial determinations. We were able to detect mineral paragenesis, avoiding evaporation, including major phases of chemical sedimentary rocks, such as gypsum, calcium carbonate, and some silicates in association to microbes. In addition, we evidenced that the use of natural substrates positively impacts growth of microbial communities, promoting the development of more biomass. This study can be seen as the first attempt and proof of concept of differentiating biotic and abiotic participation in evaporitic deposits, as they can form mineral paragenesis without evaporation. Future studies with microcosm experiments using microbial mats will be needed to establish mineral precipitation induced by micro-organisms and their extracellular polymeric substances (EPS), specifically to replicate mineral paragenesis sedimented from natural brines. Full article
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18 pages, 3621 KiB  
Article
The Problem of the Formation of Boehmite and Gibbsite in Bauxite-Bearing Lateritic Profiles
by Vladimir Mamedov, Natalia Boeva, Marina Makarova, Elena Shipilova and Philimon Melnikov
Minerals 2022, 12(3), 389; https://0-doi-org.brum.beds.ac.uk/10.3390/min12030389 - 21 Mar 2022
Cited by 9 | Viewed by 2857
Abstract
The study of a large amount of factual material about the formation conditions of gibbsite or boehmite and their mutual transformations in lateritic bauxites allowed us to solve the problem of boehmite formation and its spatial and genetic relationship to gibbsite. The boehmite [...] Read more.
The study of a large amount of factual material about the formation conditions of gibbsite or boehmite and their mutual transformations in lateritic bauxites allowed us to solve the problem of boehmite formation and its spatial and genetic relationship to gibbsite. The boehmite formation occurred only during the formation of sedimentary-lateritic bauxites from alluvial and lacustrine sediments that underwent bleaching and resilification at the stage of sediment flooding, as well as on bleached bedrock under sedimentary-lateritic bauxites. The most intense boehmite formation occurred at a depth of 20–30 m from the surface and was accompanied by an alumina input, which was realized here in the form of boehmite along with the gibbsite formation due to the hydrolytic decomposition of kaolinite and partially due to the input alumina. In the upper profiles, the recrystallization of bauxites occurs with the replacement of dissolving boehmite with gibbsite, with a decrease in the total Al2O3 content and an increase in the amount of crystallization water. In classic lateritic bauxites, the boehmite content is highly insignificant; that is, its formation in them practically does not occur or is very much inhibited. Full article
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11 pages, 59669 KiB  
Article
Biofilms and Biominerals in the Lateritic Weathering Crust as Exemplified by the Central Bauxite Deposit (Siberian Platform, Russia)
by Natalia Boeva, Nikolay Bortnikov, Anatoly Slukin, Elena Shipilova, Marina Makarova and Philimon Melnikov
Minerals 2021, 11(11), 1184; https://doi.org/10.3390/min11111184 - 26 Oct 2021
Cited by 4 | Viewed by 1414
Abstract
The study of lateritic bauxite by electron microscopy revealed abundant products of interaction between organic matter and minerals. Abundant biomineral films of different genesis and composition were found, including Al, Fe, Al-Fe, Al-Si, Al-Fe-Si, sorbed rare and rare-earth elements (REE). The evolution of [...] Read more.
The study of lateritic bauxite by electron microscopy revealed abundant products of interaction between organic matter and minerals. Abundant biomineral films of different genesis and composition were found, including Al, Fe, Al-Fe, Al-Si, Al-Fe-Si, sorbed rare and rare-earth elements (REE). The evolution of these films from amorphous to crystallized and the conversion into druse crystals of gibbsite, hematite, kaolinite etc. was traced. New data were obtained on mineralization of deposits of wood, roots, biofilms and bacteria in tropical conditions. Mono- and multilayer films were identified. Different composition biofilms occurred before and after seasonal monsoon rains. The mineral composition of the films is influenced by micro-local conditions and the introduction of chemical elements, including rare and rare-earth elements, with capillary water during the dry seasons. The products of biomineralization are microscopic in size, but are of universal and global importance to all weathered rocks and associated bauxite deposits. Full article
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25 pages, 6413 KiB  
Article
First Report of Small Shelly Fossils from the Cambrian Miaolingian Limestones (Zhangxia and Hsuzhuang Formations) in Yiyang County, Henan Province of North China
by Yazhou Hu, Lars E. Holmer, Yue Liang, Xiaolin Duan and Zhifei Zhang
Minerals 2021, 11(10), 1104; https://0-doi-org.brum.beds.ac.uk/10.3390/min11101104 - 09 Oct 2021
Cited by 3 | Viewed by 2119
Abstract
Small Shelly Fossils (SSFs) from the Cambrian are widely distributed and well known across different paleocontinents of the world. However, middle Cambrian SSFs from North China Platform have only rarely been documented until now. In this paper, we presented the first report on [...] Read more.
Small Shelly Fossils (SSFs) from the Cambrian are widely distributed and well known across different paleocontinents of the world. However, middle Cambrian SSFs from North China Platform have only rarely been documented until now. In this paper, we presented the first report on SSFs from bioclastic and oolitic limestones of the Zhangxia and Hsuzhuang formations of Henan province, North China. The carbonate-hosted fauna includes brachiopods (Micromitra sp., M. modesta, Eoobolus sp., and Schizopholis sp.), helcionellids (Oelandiellaaccordionata and O. aliciae), hyolithids, Hyolithellus sp., Chancelloriaeros, sponge spicules, echinoderm ossicles, and chancelloriid sclerites. In terms of preservation, the brachiopod shell valves of M. modesta appeared to be homogeneous, consisting of tightly packed phosphate grains. Eoobolus sp. is composed of primary layer and secondary baculate, both of which consist of tightly compacted phosphate grains. Schizopholis sp. has multiple-lamellar phosphatized microstructures that distinctly differ from the other brachiopods recovered from the Longwanggou section. A similar multiple-lamellar microstructure was also revealed in conchs of Hyolithellus, with tightly compacted phosphate grains. The argillaceous shell of Oelandiellaaccordionata and O. aliciae, and the calcitic inner molds of hyolith did not preserve any shell structure. The helcionellids O. accordionata and O. aliciae and the brachiopod M. modesta were reported for the first time from North China. The fauna is most similar to the middle Cambrian faunas of Australia, in the brachiopod and mollusk components; it is also similar in composition of brachiopods and mollusks to coeval faunas from South China. The new fauna of SSFs in the Yiyang Longwanggou Section indicated that the Hsuzhuang and Zhangxia formations are late Drumian to middle Guzhuangian in age, most likely correlating with the Murrawong Creek Formation of Australia. Full article
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12 pages, 2954 KiB  
Article
Effect of Ca2+ Replacement with Cu2+ Ions in Brushite on the Phase Composition and Crystal Structure
by Mazen Alshaaer, Juma’a Al-Kafawein, Ahmed S. Afify, Nagat Hamad, Ghassan Saffarini and Khalil Issa
Minerals 2021, 11(10), 1028; https://0-doi-org.brum.beds.ac.uk/10.3390/min11101028 - 22 Sep 2021
Cited by 4 | Viewed by 1903
Abstract
The gradual replacement of Ca2+ with Cu2+ ions in brushite (CaHPO4·2H2O) has been extensively studied and discussed. The approach adopted in this work has not been systematically explored in previous studies. This novel approach may prove beneficial [...] Read more.
The gradual replacement of Ca2+ with Cu2+ ions in brushite (CaHPO4·2H2O) has been extensively studied and discussed. The approach adopted in this work has not been systematically explored in previous studies. This novel approach may prove beneficial for the production of Ca1−xCuxHPO4·nH2O materials with desired properties suitable for medical applications. Solutions of sodium dihydrogen orthophosphate dihydrate, NaH2PO4·2H2O, calcium nitrate tetrahydrate, Ca(NO3)2·4H2O, copper nitrate trihydrate, Cu(NO3)2·3H2O, ammonium hydroxide solution, and diluted HCl were used for the preparation of these materials. At low Cu/Ca molar ratios (up to 0.25) in the starting solution, biphasic phosphate minerals were formed: brushite and sampleite. When the Cu/Ca molar ratio increases gradually from 0.67 to 1.5, sampleite-like mineral precipitates. Powdered XRD (X-ray diffraction), thermogravimetric (TG) analysis, and SEM (scanning electron microscopy) techniques were employed for the study of the microstructure of the produced materials for different degrees of Ca replacement with Mg. It is found that the Cu/Ca ratio in the starting solution can be adjusted to obtain materials with tailored composition. Thus, a new method of sampleite-like synthesis as a rare mineral is introduced in this study. Both phosphate minerals brushite and sampleite-like minerals are attractive as precursors of bioceramics and biocements. The search for such products that may decrease the possibility of post prosthetic or implant infection can be crucial in preventing devastating post-surgical complications. Full article
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Review

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28 pages, 4770 KiB  
Review
Comparative Study of Formation Conditions of Fe-Mn Ore Microbialites Based on Mineral Assemblages: A Critical Self-Overview
by Márta Polgári and Ildikó Gyollai
Minerals 2022, 12(10), 1273; https://0-doi-org.brum.beds.ac.uk/10.3390/min12101273 - 09 Oct 2022
Cited by 7 | Viewed by 1432
Abstract
The role of biogenicity in the mineral world is larger than many might assume. Biological processes and physical and chemical processes interact both at the Earth’s surface and far underground, leading to the formation of banded iron and manganese deposits, among others. Microbial [...] Read more.
The role of biogenicity in the mineral world is larger than many might assume. Biological processes and physical and chemical processes interact both at the Earth’s surface and far underground, leading to the formation of banded iron and manganese deposits, among others. Microbial mats can form giant sedimentary ore deposits, which include enrichment of further elements. This article reviews the ways in which microbially-mediated processes contribute to mineralization, the importance of mineralized microbial textural features, and the methods that must be used to obtain high-resolution datasets. If the chosen methodology and/or the size dimension of investigation is not appropriate, then it is not possible to recognize that a system is microbially mediated, and the conclusion will be incomplete. We call attention to variable authigenic mineralization as the result of complex mineralization of cells and extracellular polymeric substances in the starving basins, which form giant ore deposits together with ore-forming minerals. Microbial mats and other biosignatures can serve as indicators of environmental reconstruction in ore formations. We suggest tests and analyses that will allow the potential role of biomineralization to be properly investigated for a more comprehensive view of formation processes and their implications. Full article
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15 pages, 5640 KiB  
Review
Biomineralization in Polychaete Annelids: A Review
by Olev Vinn
Minerals 2021, 11(10), 1151; https://0-doi-org.brum.beds.ac.uk/10.3390/min11101151 - 19 Oct 2021
Cited by 13 | Viewed by 2809
Abstract
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 [...] Read more.
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. Full article
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