Abstract
Microorganisms inhabit almost every natural environment on Earth. Since the beginning of life, microorganisms have played a fundamental role in the geochemical cycling of elements and shaped our current environments. Microorganisms that form minerals, a process known as biomineralization, contribute substantially to these processes. Over half of the essential elements required by living organisms are incorporated into biominerals. More than 60 different biominerals are known in nature, including oxides and hydroxides, carbonates, phosphates, sulfates and sulfides, silicates, and organic crystals.
Biominerals are composite materials that often exhibit superior properties when compared to their abiotically formed counterparts. Their well-designed architectures and hierarchical structures offer structural support and protection, but also fulfill a wide variety of other functions. Biominerals often reflect the physicochemical properties of the environment the biomineral was formed in. Fossilized biominerals are therefore useful tools for paleoceanographic and paleoclimate reconstructions. Biomineralization not only fascinates biologists, it also provides sophisticated models for functional materials in materials science and affects the global aspects of the earth sciences.
The chapter gives an overview over non-siliceous biominerals formed by microorganisms and lists them in tabular form ordered by taxonomic criteria. It features carbonates, oxides and hydroxides, phosphates, sulfur-containing biominerals, and organic crystals.
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References
Adams LF, Ghiorse WC (1986) Physiology and ultrastructure of Leptothrix discophora SS-1. Arch Microbiol 145:126–135. https://doi.org/10.1007/BF00446769
Addadi L, Raz S, Weiner S (2003) Taking advantage of disorder: amorphous calcium carbonate and its roles in biomineralization. Adv Mater 15:959–970. https://doi.org/10.1002/adma.200300381
Anderson OR (1981) Radiolarian fine structure and silica deposition. In: Silicon and siliceous structures in biological systems. Springer, New York, pp 347–379
Anderson OR, Perry CC, Hughes NP (1990) Transmission and scanning electron microscopic evidence for cytoplasmic deposition of strontium sulphate crystals in colonial radiolaria. Philos Trans R Soc London Ser B Biol Sci 329:81–86. https://doi.org/10.1098/rstb.1990.0152
Appanna VD, Anderson SL, Skakoon T (1997) Biogenesis of calcite: a biochemical model. Microbiol Res 152:341–343. https://doi.org/10.1016/S0944-5013(97)80049-3
Ariskina EV (2003) Magnetic inclusions in prokaryotic cells. Microbiology 72:251–258. https://doi.org/10.1023/A:1024231512124
Arnott HJ (1995) Calcium oxalate in fungi. In: Calcium oxalate in biological systems. CRC Press, Boca Raton, pp 73–112
Ascaso C, Galvan J, Ortega C (1976) The pedogenic action of parmelia conspersa, rhizocarpon geographicum and umbilicaria pustulata. Lichenol 8:151–171. https://doi.org/10.1017/S0024282976000236
Ascaso C, Galván J, Rodriguez-Pascual C (1982) The weathering of calcareous rocks by lichens. Pedobiologia (Jena) 24:219–229
Bachmeier KL, Williams AE, Warmington JR, Bang SS (2002) Urease activity in microbiologically-induced calcite precipitation. J Biotechnol 93:171–181. https://doi.org/10.1016/S0168-1656(01)00393-5
Bang SS, Galinat JK, Ramakrishnan V (2001) Calcite precipitation induced by polyurethane-immobilized Bacillus pasteurii. Enzyme Microb Technol 28:404–409. https://doi.org/10.1016/S0141-0229(00)00348-3
Banner FT, Sheehan R, Williams E (1973) The organic skeletons of rotaline foraminifera; a review. J Foraminifer Res 3:30–42. https://doi.org/10.2113/gsjfr.3.1.30
Baran EJ, Monje PV (2010) Oxalate biominerals. In: Biomineralization. John Wiley & Sons, Chichester, pp 219–254
Barea J-M, Richardson AE (2015) Phosphate mobilisation by soil microorganisms BT. In: Lugtenberg B (ed) Principles of plant-microbe interactions: microbes for sustainable agriculture. Springer International Publishing, Cham, pp 225–234
Bargar JR, Tebo BM, Bergmann U et al (2005) Biotic and abiotic products of Mn(II) oxidation by spores of the marine Bacillus sp. strain SG-1. Am Mineral 90:143–154. https://doi.org/10.2138/am.2005.1557
Baumann K-H, Böckel B, Donner B et al (2003) Contribution of calcareous plankton groups to the carbonate budget of south Atlantic surface sediments. In: The south Atlantic in the late quaternary. Springer, Berlin, Heidelberg, pp 81–99
Baumann K-H, Andruleit H, Böckel B et al (2005) The significance of extant coccolithophores as indicators of ocean water masses, surface water temperature, and palaeoproductivity: a review. Paläontologische Zeitschrift 79:93–112. https://doi.org/10.1007/bf03021756
Bauminger ER, Cohen SG, Dickson DPE et al (1980) Mössbauer spectroscopy of Escherichia coli and its iron-storage protein. Biochim Biophys Acta – Protein Struct 623:237–242. https://doi.org/10.1016/0005-2795(80)90252-4
Bazylinski DA (1996) Controlled biomineralization of magnetic minerals by magnetotactic bacteria. Chem Geol 132:191–198. https://doi.org/10.1016/S0009-2541(96)00055-1
Bazylinski D, Frankel R (2003) Biologically controlled mineralization in prokaryotes. Rev Mineral Geochemistry 54:217–247. https://doi.org/10.2113/0540217
Bazylinski DA, Heywood BR, Mann S, Frankel RB (1993) Fe304 and Fe3S4 in a bacterium. Nature 366:218
Bazylinski DA, Schlezinger DR, Howes BH et al (2000) Occurrence and distribution of diverse populations of magnetic protists in a chemically stratified coastal salt pond. Chem Geol 169:319–328. https://doi.org/10.1016/S0009-2541(00)00211-4
Bazylinski DA, Frankel RB, Konhauser KO (2007) Modes of biomineralization of magnetite by microbes. Geomicrobiol J 24:465–475. https://doi.org/10.1080/01490450701572259
Beavon J, Heatley NG (1963) The occurrence of struvite (magnesium ammonium phosphate hexahydrate) in microbial cultures. J Gen Microbiol 31:167–169. https://doi.org/10.1099/00221287-31-1-167
Beger H (1935) Leptothrix echinata, ein neues vorwiegend Magnan fällendes Eisenbakterium. Zentralbl Bakteriol Abt II 92:401–406
Beniash E, Aizenberg J, Addadi L, Weiner S (1997) Amorphous calcium carbonate transforms into calcite during sea urchin larval spicule growth. Proc R Soc B Biol Sci 264:461–465. https://doi.org/10.1098/rspb.1997.0066
Bentov S, Erez J (2006) Impact of biomineralization processes on the Mg content of foraminiferal shells: a biological perspective. Geochemistry, Geophys Geosystems 7(1):Q01P08. https://doi.org/10.1029/2005GC001015@10.1002/(ISSN)1525-2027.PPOXY1
Bentov S, Brownlee C, Erez J (2009) The role of seawater endocytosis in the biomineralization process in calcareous foraminifera. Proc Natl Acad Sci U S A 106:21500–21504. https://doi.org/10.1073/pnas.0906636106
Benzerara K, Menguy N, Guyot F et al (2004) Biologically controlled precipitation of calcium phosphate by Ramlibacter tataouinensis. Earth Planet Sci Lett 228:439–449. https://doi.org/10.1016/j.epsl.2004.09.030
Benzerara K, Skouri-Panet F, Li J et al (2014) Intracellular Ca-carbonate biomineralization is widespread in cyanobacteria. Proc Natl Acad Sci U S A 111:10933–10938. https://doi.org/10.1073/pnas.1403510111
Berg JS, Duverger A, Cordier L et al (2020) Rapid pyritization in the presence of a sulfur/sulfate-reducing bacterial consortium. Sci Rep 10:8264. https://doi.org/10.1038/s41598-020-64990-6
Bernheimer AW (1938) A comparative study of the crystalline inclusions of protozoa. Trans Am Microsc Soc 57:336. https://doi.org/10.2307/3222488
Bersa E (1920) Über das Vorkommen von kohlensaurem Kalk in einer Gruppe von Schwefelbakterien. Sitzungsbericht Akad der Wissenschaften, Math naturwissenschaftliche Klasse, I Abteilung Wien
Bertram MA, Cowen JP (1998) Biomineralization in agglutinating foraminifera: an analytical SEM investigation of external wall composition in three small test forms. Aquat Geochemistry 4:455–468. https://doi.org/10.1023/a:1009648701741
Beveridge TJ, Murray RG (1976) Uptake and retention of metals by cell walls of Bacillus subtilis. J Bacteriol 127:1502–1518. https://doi.org/10.1128/JB.127.3.1502-1518.1976
Bharde A, Wani A, Houche Y et al (2005) Bacterial aerobic synthesis of nanocrystalline magnetite. J Am Chem Soc 127:9326–9327. https://doi.org/10.1021/JA0508469
Bharde A, Parikh RY, Baidakova M et al (2008) Bacteria-mediated precursor-dependent biosynthesis of superparamagnetic iron oxide and iron sulfide nanoparticles. Langmuir 24:5787–5794. https://doi.org/10.1021/la704019p
Bigham JM, Schwertmann U, Pfab G (1996a) Influence of pH on mineral speciation in a bioreactor simulating acid mine drainage. Appl Geochemistry 11:845–849. https://doi.org/10.1016/S0883-2927(96)00052-2
Bigham JM, Schwertmann U, Traina SJ et al (1996b) Schwertmannite and the chemical modeling of iron in acid sulfate waters. Geochim Cosmochim Acta 60:2111–2121. https://doi.org/10.1016/0016-7037(96)00091-9
Blackmon PD, Todd R (1959) Mineralogy of some foraminifera as related to their classification and ecology. J Paleontol 33:1–15. https://doi.org/10.2307/1300802
Blackwelder E (1916) The geologic role of phosphorus. Proc Natl Acad Sci U S A 2:490–495. https://doi.org/10.1073/pnas.2.8.490
Blake RE, Alt JC, Martini AM (2001) Oxygen isotope ratios of PO4: an inorganic indicator of enzymatic activity and P metabolism and a new biomarker in the search for life. Proc Natl Acad Sci U S A 98:2148–2153. https://doi.org/10.1073/pnas.051515898
Blakemore R (1975) Magnetotactic bacteria. Science (80-) 190:377–379. https://doi.org/10.1126/science.170679
Blondeau M, Sachse M, Boulogne C et al (2018) Amorphous calcium carbonate granules form within an intracellular compartment in calcifying cyanobacteria. Front Microbiol 9:1768. https://doi.org/10.3389/fmicb.2018.01768
Boetius A, Ravenschlag K, Schubert CJ et al (2000) A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:623–626. https://doi.org/10.1038/35036572
Boogerd FC, de Vrind JP (1987) Manganese oxidation by Leptothrix discophora. J Bacteriol 169:489–494. https://doi.org/10.1128/JB.169.2.489-494.1987
Borowitzka MA, Larkum AWD, Nockolds CE (1974) A scanning electron microscope study of the structure and organization of the calcium carbonate deposits of algae. Phycologia 13:195–203. https://doi.org/10.2216/i0031-8884-13-3-195.1
Bosselmann F, Epple M (2008) Sulfate-Containing Biominerals. Biomineralization 4:207–217
Böttger U, Meessen J, Martinez-Frias J et al (2014) Raman spectroscopic analysis of the calcium oxalate producing extremotolerant lichen Circinaria gyrosa. Int J Astrobiol 13:19–27. https://doi.org/10.1017/S1473550413000293
Boyan BD, Landis WJ, Knight J et al (1984) Microbial hydroxyapatite formation as a model of proteolipid-dependent membrane-mediated calcification. Scan Electron Microsc 4:1793–1800
Braissant O, Decho AW, Dupraz C et al (2007) Exopolymeric substances of sulfate-reducing bacteria: Interactions with calcium at alkaline pH and implication for formation of carbonate minerals. Geobiology 5:401–411. https://doi.org/10.1111/j.1472-4669.2007.00117.x
Braun M (2002) Gravity perception requires statoliths settled on specific plasma membrane areas in characean rhizoids and protonemata. Protoplasma 219:150–159. https://doi.org/10.1007/s007090200016
Brock J, Schulz-Vogt HN (2011) Sulfide induces phosphate release from polyphosphate in cultures of a marine Beggiatoa strain. ISME J 5:497–506. https://doi.org/10.1038/ismej.2010.135
Brook AJ (1981) Calcium sulphate inclusions in the desmids bambusina and gonatozygon. Br Phycol J 16:267–272. https://doi.org/10.1080/00071618100650281
Brook AJ, Fotheringham A, Bradly J, Jenkins A (1980) Barium accumulation by desmids of the genus closterium (Zygnemophyceae). Br Phycol J 15:261–264. https://doi.org/10.1080/00071618000650251
Brook AJ, Grime GW, Watt F (1988) A study of barium accumulation in desmids using the Oxford scanning proton microprobe (SPM). Nucl Inst Methods Phys Res B 30:372–377. https://doi.org/10.1016/0168-583X(88)90027-4
Brownlee C, Wheeler GL, Taylor AR (2015) Coccolithophore biomineralization: New questions, new answers. Semin Cell Dev Biol 46:11–16. https://doi.org/10.1016/j.semcdb.2015.10.027
Brüchert V, Jørgensen BB, Neumann K et al (2003) Regulation of bacterial sulfate reduction and hydrogen sulfide fluxes in the central Namibian coastal upwelling zone. Geochim Cosmochim Acta 67:4505–4518. https://doi.org/10.1016/S0016-7037(03)00275-8
Brune DC (1995) Isolation and characterization of sulfur globule proteins from Chromatium vinosum and Thiocapsa roseopersicina. Arch Microbiol 163:391–399. https://doi.org/10.1007/BF00272127
Bundeleva IA, Shirokova LS, Pokrovsky OS et al (2014) Experimental modeling of calcium carbonate precipitation by cyanobacterium Gloeocapsa sp. Chem Geol 374–375:44–60. https://doi.org/10.1016/j.chemgeo.2014.03.007
Burford EP, Fomina M, Gadd GM (2003) Fungal involvement in bioweathering and biotransformation of rocks and minerals. Mineral Mag 67:1127–1155. https://doi.org/10.1180/0026461036760154
Burford EP, Hillier S, Gadd GM (2006) Biomineralization of fungal hyphae with calcite (CaCO3) and calcium oxalate mono- and dihydrate in carboniferous limestone microcosms. Geomicrobiol J 23:599–611. https://doi.org/10.1080/01490450600964375
Bütschli O (1906) On the chemical nature of the skeleton substance of Acantharia. Zool Anz 30:784–789
Cacchio P, Ercole C, Cappuccio G, Lepidi A (2003) Calcium carbonate precipitation by bacterial strains isolated from a limestone cave and from a loamy soil. Geomicrobiol J 20:85–98. https://doi.org/10.1080/01490450303883
Cam N, Benzerara K, Georgelin T et al (2016) Selective uptake of alkaline earth metals by cyanobacteria forming intracellular carbonates. Environ Sci Technol 50:11654–11662. https://doi.org/10.1021/acs.est.6b02872
Cartwright JHE, Checa AG, Gale JD et al (2012) Calcium carbonate polyamorphism and its role in biomineralization: how many amorphous calcium carbonates are there? Angew Chemie Int Ed 51:11960–11970. https://doi.org/10.1002/anie.201203125
Cayeux L (1936) Existence de nombreuses bactéries dans les phosphates sédimentaires de tout âge. CR Acad Sci 203:1198–1200
Chan CS, Fakra SC, Edwards DC et al (2009) Iron oxyhydroxide mineralization on microbial extracellular polysaccharides. Geochim Cosmochim Acta 73:3807–3818. https://doi.org/10.1016/J.GCA.2009.02.036
Chan Y, Lacap DC, Lau MCY et al (2012) Hypolithic microbial communities: between a rock and a hard place. Environ Microbiol 14:2272–2282. https://doi.org/10.1111/j.1462-2920.2012.02821.x
Châtellier X, Fortin D, West MM et al (2001) Effect of the presence of bacterial surfaces during the synthesis of Fe oxides by oxidation of ferrous ions. Eur J Mineral 13:705–714. https://doi.org/10.1127/0935-1221/2001/0013-0705
Cheng ZY, Fernández-Remolar DC, Izawa MRM et al (2016) Oxalate formation under the hyperarid conditions of the Atacama desert as a mineral marker to provide clues to the source of organic carbon on Mars. J Geophys Res Biogeosciences 121:1593–1604. https://doi.org/10.1002/2016JG003439
Chisholm JE, Jones GC, Purvis OW (1987) Hydrated copper oxalate, moolooite, in lichens. Mineral Mag 51:715–718. https://doi.org/10.1180/minmag.1987.051.363.12
Chuo SC, Mohamed SF, Mohd Setapar SH et al (2020) Insights into the current trends in the utilization of bacteria for microbially induced calcium carbonate precipitation. Materials (Basel) 13:4993. https://doi.org/10.3390/ma13214993
Clark BM, St. Clair LL, Mangelson NF et al (2001) Characterization of mycobiont adaptations in the foliose lichen Xanthoparmelia chlorochroa (Parmeliaceae). Am J Bot 88:1742–1749. https://doi.org/10.2307/3558348
Clode PL, Saunders M, Maker G et al (2009) Uric acid deposits in symbiotic marine algae. Plant, Cell Environ 32:170–177. https://doi.org/10.1111/j.1365-3040.2008.01909.x
Cockell CS, Osinski GR, Banerjee NR et al (2010) The microbe-mineral environment and gypsum neogenesis in a weathered polar evaporite. Geobiology 8:293–308. https://doi.org/10.1111/j.1472-4669.2010.00240.x
Cosmidis J, Benzerara K, Guyot F et al (2015) Calcium-phosphate biomineralization induced by alkaline phosphatase activity in escherichia coli: localization, kinetics, and potential signatures in the fossil record. Front Earth Sci 3:84. https://doi.org/10.3389/feart.2015.00084
Couradeau E, Benzerara K, Gérard E et al (2012) An early-branching microbialite cyanobacterium forms intracellular carbonates. Science (80-) 336:459–462. https://doi.org/10.1126/science.1216171
Creutz CE, Mohanty S, Defalco T, Kretsinger R (2002) Purine composition of the crystalline cytoplasmic inclusions of paramecium tetraurelia. Protist 153:39–45. https://doi.org/10.1078/1434-4610-00081
Crowe SA, O’Neill AH, Kulczycki E et al (2007) Reductive dissolution of trace metals from sediments. Geomicrobiol J 24:157–165. https://doi.org/10.1080/01490450701457329
Da Silva S, Bernet N, Delgenès J, Moletta R (2000) Effect of culture conditions on the formation of struvite by Myxococcus xanthus. Chemosphere 40:1289–1296. https://doi.org/10.1016/S0045-6535(99)00224-6
Dahl C (2020) A biochemical view on the biological sulfur cycle. In: Environmental technologies to treat sulphur pollution: principles and engineering, vol 2. IWA Publishing, London, pp 55–96
Dahl C, Prange A (2006) Bacterial sulfur globules: occurrence, structure and metabolism. In: Inclusions in prokaryotes. Springer-Verlag, Berlin, pp 21–51
Daoud J, Karamanev D (2006) Formation of jarosite during Fe2+ oxidation by Acidithiobacillus ferrooxidans. Miner Eng 19:960–967. https://doi.org/10.1016/J.MINENG.2005.10.024
David CN, Easterbrook K (1971) Ferritin in the fungus Phycomyces. J Cell Biol 48:15–28. https://doi.org/10.1083/jcb.48.1.15
Daye M, Klepac-Ceraj V, Pajusalu M et al (2019) Light-driven anaerobic microbial oxidation of manganese. Nature 576:311–314. https://doi.org/10.1038/s41586-019-1804-0
de Araujo FFT, Pires MA, Frankel RB, Bicudo CEM (1986) Magnetite and magnetotaxis in algae. Biophys J 50:375–378. https://doi.org/10.1016/S0006-3495(86)83471-3
Lins de Barros HGP, Esquivel DMS, Danon J (1981) Magnetotactic algae. Centro Brasileiro de Pesquisas Fisicas
de la Torre MA, Gomez-Alarcon G (1994) Manganese and iron oxidation by fungi isolated from building stone. Microb Ecol 27:177–188. https://doi.org/10.1007/BF00165816
De Muynck W, De Belie N, Verstraete W (2010) Microbial carbonate precipitation in construction materials: a review. Ecol Eng 36:118–136. https://doi.org/10.1016/j.ecoleng.2009.02.006
de Nooijer LJ, Spero HJ, Erez J et al (2014) Biomineralization in perforate foraminifera. Earth-Science Rev 135:48–58. https://doi.org/10.1016/J.EARSCIREV.2014.03.013
de Oliveira LFC, Edwards HGM, Feo-Manga JC et al (2002) FT-Raman spectroscopy of three foliicolous lichens from costa rican rainforests. Lichenol 34:259–266. https://doi.org/10.1006/lich.2002.0396
de Vienne DM (2016) Lifemap: exploring the entire tree of life. PLOS Biol 14:e2001624. https://doi.org/10.1371/journal.pbio.2001624
Decelle J, Martin P, Paborstava K et al (2013) Diversity, ecology and biogeochemistry of cyst-forming acantharia (radiolaria) in the oceans. PLoS One 8. https://doi.org/10.1371/journal.pone.0053598
Deflandre G (1953) Ordre de Testacealobosa (Desaedeleer, 1934), Teataceafilosa (Desadeller, 1934), Thalamia (Haeckel, 1862) ou Thecamebiens (Rhizopoda Testata). In: Grassé P-P (ed) Traité de Zoologie. Masson, Paris, pp 97–148
Demény A, Németh P, Czuppon G et al (2016) Formation of amorphous calcium carbonate in caves and its implications for speleothem research. Sci Rep 6:39602. https://doi.org/10.1038/srep39602
DeSa R, Hastings JW, Vatter AE (1963) Luminescent “crystalline” particles: an organized subcellular bioluminescent system. Science 141:1269–1270. https://doi.org/10.1126/science.141.3587.1269
DeSa R, Hastings JW, Hole W et al (1968) The characterization of scintillons. Bioluminescent particles from the marine dinoflagellate, Gonyaulax polyedra. J Gen Physiol 51:105–122. https://doi.org/10.1085/jgp.51.1.105
Diaz J, Ingall E, Benitez-Nelson C et al (2008) Marine polyphosphate: a key player in geologic phosphorus sequestration. Science (80-) 320:652–655. https://doi.org/10.1126/science.1151751
Diaz MR, Eberli GP, Blackwelder P et al (2017) Microbially mediated organomineralization in the formation of ooids. Geology 45:771–774. https://doi.org/10.1130/G39159.1
Ding J, Gao J, Wu X et al (2007) Jarosite-type precipitates mediated by YN22, Sulfobacillus thermosulfidooxidans, and their influences on strain. Trans Nonferrous Met Soc China 17:1038–1044. https://doi.org/10.1016/S1003-6326(07)60222-2
Dittrich M, Sibler S (2010) Calcium carbonate precipitation by cyanobacterial polysaccharides. Geol Soc London, Spec Publ 336:51–63. https://doi.org/10.1144/SP336.4
Dittrich M, Müller B, Mavrocordatos D, Wehrli B (2003) Induced calcite precipitation by cyanobacterium synechococcus. Acta Hydrochim Hydrobiol 31:162–169. https://doi.org/10.1002/aheh.200300486
Docampo R, de Souza W, Miranda K et al (2005) Acidocalcisomes – conserved from bacteria to man. Nat. Rev. Microbiol. 3:251–261
Donald R, Southam G (1999) Low temperature anaerobic bacterial diagenesis of ferrous monosulfide to pyrite. Geochim Cosmochim Acta 63:2019–2023. https://doi.org/10.1016/S0016-7037(99)00140-4
Dorozhkin SV, Epple M (2002) Biological and medical significance of calcium phosphates. Angew Chem Int Ed Engl 41:3130–3146. https://doi.org/10.1002/1521-3773(20020902)41:17<3130::AID-ANIE3130>3.0.CO;2-1
Doyle WL, Doyle MM (1940) The structure of zooxanthellae. Pap Tortugas Lab XXXII:129–142
Dutton MV, Evans CS (1996) Oxalate production by fungi: its role in pathogenicity and ecology in the soil environment. Can J Microbiol 42:881–895. https://doi.org/10.1139/m96-114
Duverger A, Berg JS, Busigny V et al (2020) Mechanisms of pyrite formation promoted by sulfate-reducing bacteria in pure culture. Front Earth Sci 8:457. https://doi.org/10.3389/feart.2020.588310
Edwards HGM, Farwell DW, Seaward MRD (1991) Raman spectra of oxalates in lichen encrustations on Renaissance frescoes. Spectrochim Acta Part A Mol Spectrosc 47:1531–1539. https://doi.org/10.1016/0584-8539(91)80247-G
Edwards HGM, Farwell DW, Jenkins R, Seaward MRD (1992) Vibrational Raman spectroscopic studies of calcium oxalate monohydrate and dihydrate in lichen encrustations on renaissance frescoes. J Raman Spectrosc 23:185–189. https://doi.org/10.1002/jrs.1250230310
Edwards HGM, Farwell DW, Seaward MRD (1997) Ft-raman spectroscopy of dirina massiliensis f. Sorediata encrustations growing on diverse substrata. Lichenol 29:83–90. https://doi.org/10.1006/lich.1996.0062
Egal M, Casiot C, Morin G et al (2009) Kinetic control on the formation of tooeleite, schwertmannite and jarosite by Acidithiobacillus ferrooxidans strains in an As(III)-rich acid mine water. Chem Geol 265:432–441. https://doi.org/10.1016/j.chemgeo.2009.05.008
Ehrlich HL (1966) Reactions with manganese by bacteria from marine ferromanganese nodules. Dev Ind Microbiol 7:279–286
Emerson D, Ghiorse WC (1992) Isolation, cultural maintenance, and taxonomy of a sheath-forming strain of Leptothrix discophora and characterization of manganese-oxidizing activity associated with the sheath. Appl Environ Microbiol 58:4001–4010. https://doi.org/10.1128/aem.58.12.4001-4010.1992
Emerson D, Garen RE, Ghiorse WC (1989) Formation of Metallogenium-like structures by a manganese-oxiding fungus. Arch Microbiol 151:223–231. https://doi.org/10.1007/BF00413134
Englander CM, Corden ME (1971) Stimulation of mycelial growth of Endothia parasitica by heavy metals. Appl Microbiol 22:1012–1016
Ennever J, Summers FE (1975) Calcification by Candida albicans. J Bacteriol 122:1391–1393. https://doi.org/10.1128/JB.122.3.1391-1393.1975
Ennever J, Vogel JJ, Streckfuss JL (1971) Synthetic medium for calcification of Bacterionema matruchotii. J Dent Res 50:1327–1330. https://doi.org/10.1177/00220345710500054101
Ennever J, Streckfuss JL, Takazoe I (1973) Calcification of bacillary and streptococcal variants of bacterionema matruchotii. J Dent Res 52:305–308. https://doi.org/10.1177/00220345730520021901
Enyedi NT, Makk J, Kótai L et al (2020) Cave bacteria-induced amorphous calcium carbonate formation. Sci Rep 10:8696. https://doi.org/10.1038/s41598-020-65667-w
Erdman JA, Gough LP, White RW (1977) Calcium oxalate as source of high ash yields in the terricolous lichen parmelia chlorochroa. Bryologist 80:334. https://doi.org/10.2307/3242479
Erez J (2003) The source of ions for biomineralization in foraminifera and their implications for paleoceanographic proxies. Rev Mineral Geochemistry 54:115–149. https://doi.org/10.2113/0540115
Faivre D, Schüler D (2008) Magnetotactic bacteria and magnetosomes. Chem Rev 108:4875–4898. https://doi.org/10.1021/cr078258w
Farina M, Esquivel DMS, de Barros HGPL (1990) Magnetic iron-sulphur crystals from a magnetotactic microorganism. Nature 343:256–258. https://doi.org/10.1038/343256a0
Fauré-Fremiet E, Gauchery M (1957) Concrétions Minérales Intracytoplasmiques chez les Ciliés. J Protozool 4:96–109. https://doi.org/10.1111/j.1550-7408.1957.tb02493.x
Feng XH, Zhu M, Ginder-Vogel M et al (2010) Formation of nano-crystalline todorokite from biogenic Mn oxides. Geochim Cosmochim Acta 74:3232–3245. https://doi.org/10.1016/j.gca.2010.03.005
Fischer A (1884) Über das Vorkommen von Gypskristallen bei den Desmidieen. Jahrb Wiss Bot 14:133–184
Flemming H-C, Wingender J (2010) The biofilm matrix. Nat Rev Microbiol 8:623–633. https://doi.org/10.1038/nrmicro2415
Flies CB, Peplies J, Schüler D (2005) Combined approach for characterization of uncultivated magnetotactic bacteria from various aquatic environments. Appl Environ Microbiol 71:2723–2731. https://doi.org/10.1128/AEM.71.5.2723-2731.2005
Folk RL (2005) Nannobacteria and the formation of framboidal pyrite: textural evidence. J Earth Syst Sci 114:369–374. https://doi.org/10.1007/BF02702955
Fomina M, Ford E, Burford EP, Gadd GM (2006) Fungal dissolution and transformation of minerals: significance for nutrient and metal mobility. In: Fungi in biogeochemical cycles. UNESCO/Cambridge University Press, Cambridge, pp 236–266
Fortin D, Southam G, Beveridge TJ (1994) Nickel sulfide, iron-nickel sulfide and iron sulfide precipitation by a newly isolated Desulfotomaculum species and its relation to nickel resistance. FEMS Microbiol Ecol 14:121–132. https://doi.org/10.1111/j.1574-6941.1994.tb00099.x
Frankel RB, Bazylinski DA (2009) Magnetosomes and magneto-aerotaxis. In: Contributions to microbiology. KARGER, Basel, pp 182–193
Frankel RB, Blakemore RP, Wolfe RS (1979) Magnetite in freshwater magnetotactic bacteria. Science (80-) 203:1355–1356. https://doi.org/10.1126/science.203.4387.1355
Frankel RB, Papaefthymiou GC, Blakemore RP, O’Brien W (1983) Fe3O4 precipitation in magnetotactic bacteria. Biochim Biophys Acta - Mol Cell Res 763:147–159. https://doi.org/10.1016/0167-4889(83)90038-1
Frankel RB, Papaefthymiou GC, Blakemore RP (1985) Mössbauer spectroscopy of iron biomineralization products in magnetotactic bacteria. Springer, Boston, MA, pp 269–287
Fredrickson JK, Zachara JM, Kennedy DW et al (1998) Biogenic iron mineralization accompanying the dissimilatory reduction of hydrous ferric oxide by a groundwater bacterium. Geochim Cosmochim Acta 62:3239–3257. https://doi.org/10.1016/S0016-7037(98)00243-9
Fresnel J, Galle P, Gayral P (1979) Résultats de la microanalyse des cristaux vacuolaires chez deux Chromophytes unicellulaires marines: Exanthemachrysis gayraliae, Pavlova sp.(Prymnésiophycées, Pavlovacées). Comptes rendus Hebd des seances Ser D Sci Nat
Friedmann EI (1979) The genus Geitleria (Cyanophyceae or Cyanobacteria): Distribution of G. calcarea and G. floridana n. sp. Plant Syst Evol 131:169–178. https://doi.org/10.1007/BF00984251
Frost RL, Yang J, Ding Z (2003) Raman and FTIR spectroscopy of natural oxalates: implications for the evidence of life on Mars. Chinese Sci Bull 48:1844–1852. https://doi.org/10.1007/BF03184066
Gadd GM (1993) Interactions of fungi with toxic metals. New Phytol 124:25–60. https://doi.org/10.1111/j.1469-8137.1993.tb03796.x
Gadd GM (1999) Fungal production of citric and oxalic acid: importance in metal speciation, physiology and biogeochemical processes. Adv Microb Physiol 41:47–92. https://doi.org/10.1016/S0065-2911(08)60165-4
Gadd GM, Bahri-Esfahani J, Li Q et al (2014) Oxalate production by fungi: significance in geomycology, biodeterioration and bioremediation. Fungal Biol Rev 28:36–55. https://doi.org/10.1016/J.FBR.2014.05.001
Gal A, Sviben S, Wirth R et al (2017) Trace-element incorporation into intracellular pools uncovers calcium-pathways in a coccolithophore. Adv Sci 4:1700088. https://doi.org/10.1002/advs.201700088
Gal A, Sorrentino A, Kahil K et al (2018) Native-state imaging of calcifying and noncalcifying microalgae reveals similarities in their calcium storage organelles. Proc Natl Acad Sci 115:11000–11005. https://doi.org/10.1073/PNAS.1804139115
Galdenzi S, Maruoka T (2003) Gypsum deposits in the Frasassi Caves, central Italy. J Cave Karst Stud 65:111–125
Galván J, Pascual CR, Ascaso C (1981) The pedogenic action of lichens in metamorphic rocks. Pedobiologia (Jena) 21:60–73
Gayral P, Fresnel J (1979) Exanthemachrysis-Gayraliae Lepailleur (Prymnesiophyceae, Pavlovales)-Ultrastructure and taxonomic discussion. Protistologica 15:271–282
Gharieb MM, Sayer JA, Gadd GM (1998) Solubilization of natural gypsum (CaSO4.2H2O) and the formation of calcium oxalate by Aspergillus niger and Serpula himantioides. Mycol Res 102:825–830. https://doi.org/10.1017/S0953756297005510
Ghiorse WC, Chapnick SD (1983, 1981) Metal-depositing bacteria and the distribution of manganese and iron in swamp waters (Leptothrix). Environ Biogeochem Proc 5th Int Symp Stock:367–376
Ghiorse WC, Hirsch P (1979) An ultrastructural study of iron and manganese deposition associated with extracellular polymers of pedomicrobium-like budding bacteria. Arch Microbiol 123:213–226. https://doi.org/10.1007/BF00406653
Glasauer S, Langley S, Beveridge TJ (2002) Intracellular iron minerals in a dissimilatory iron-reducing bacterium. Science (80-) 295:117–119. https://doi.org/10.1126/SCIENCE.1066577
Glasauer S, Weidler PG, Langley S, Beveridge TJ (2003) Controls on Fe reduction and mineral formation by a subsurface bacterium. Geochim Cosmochim Acta 67:1277–1288. https://doi.org/10.1016/S0016-7037(02)01199-7
Goldhammer T, Brüchert V, Ferdelman TG, Zabel M (2010) Microbial sequestration of phosphorus in anoxic upwelling sediments. Nat Geosci 3:557–561. https://doi.org/10.1038/ngeo913
Goldstein ST (1999) Foraminifera: A biological overview. In: Modern Foraminifera. Springer Netherlands, Dordrecht, pp 37–55
Gollapudi UK, Knutson CL, Bang SS, Islam MR (1995) A new method for controlling leaching through permeable channels. Chemosphere 30:695–705. https://doi.org/10.1016/0045-6535(94)00435-W
Golubic S, Campbell SE (1981) Biogenically formed aragonite concretions in marine rivularia. In: Phanerozoic stromatolites. Springer, Berlin, Heidelberg, pp 209–229
Gómez F, Kiriakoulakis K, Lara E (2017) Achradina pulchra, a Unique Dinoflagellate (Amphilothales, Dinophyceae) with a Radiolarian-like Endoskeleton of Celestite (Strontium Sulfate). Acta Protozologica 56:71–76. https://doi.org/10.4467/16890027AP.17.006.7481
González-Muñoz MT, Entrena M, Omar NB et al (1994) Production of syngenetic minerals with struvite by myxococcus coralloides D. Geomicrobiol J 12:279–283. https://doi.org/10.1080/01490459409377995
González-Muñoz MT, BenChekroun K, Ben Aboud A et al (2000) Bacterially induced Mg-calcite formation: Role of Mg2+ in development of crystal morphology. J Sediment Res 70:559–564. https://doi.org/10.1306/2DC40928-0E47-11D7-8643000102C1865D
González-Muñoz MT, Fernández-Luque B, Martínez-Ruiz F et al (2003) Precipitation of barite by Myxococcus xanthus: Possible implications for the biogeochemical cycle of barium. Appl Environ Microbiol 69:5722–5725. https://doi.org/10.1128/AEM.69.9.5722-5725.2003
Gooday AJ, Nott JA (1982) Intracellular barite crystals in two xenophyophores, aschemonella ramuliformis and galatheammina sp. (Protozoa: Rhizopoda) with comments on the taxonomy of A. Ramuliformis. J Mar Biol Assoc United Kingdom 62:595–605. https://doi.org/10.1017/S0025315400019779
Gramp JP, Sasaki K, Bigham JM et al (2006) Formation of covellite (CuS) under biological sulfate-reducing conditions. Geomicrobiol J 23:613–619. https://doi.org/10.1080/01490450600964383
Gramp JP, Bigham JM, Sasaki K, Tuovinen OH (2007) Formation of Ni- and Zn-sulfides in cultures of sulfate-reducing bacteria. Geomicrobiol J 24:609–614. https://doi.org/10.1080/01490450701758239
Gramp JP, Wang H, Bigham JM et al (2009) Biogenic Synthesis and Reduction of Fe(III)-hydroxysulfates. Geomicrobiol J 26:275–280. https://doi.org/10.1080/01490450902892597
Gramp JP, Bigham JM, Jones FS, Tuovinen OH (2010) Formation of Fe-sulfides in cultures of sulfate-reducing bacteria. J Hazard Mater 175:1062–1067. https://doi.org/10.1016/J.JHAZMAT.2009.10.119
Graustein WC, Cromack K, Sollins P (1977) Calcium oxalate: Occurrence in soils and effect on nutrient and geochemical cycles. Science (80-) 198:1252–1254. https://doi.org/10.1126/science.198.4323.1252
Gray ND (2006) The unique role of intracellular calcification in the genus achromatium. In: Inclusions in prokaryotes. Springer-Verlag, Berlin/Heidelberg, pp 299–309
Gray N, Head I (2014) The family achromatiaceae. In: Rosenberg E, DeLong EF, Lory S et al (eds) The prokaryotes. Springer, Berlin, Heidelberg, pp 1–14
Gray ND, Howarth R, Pickup RW et al (1999) Substrate uptake by uncultured bacteria from the genus Achromatium determined by microautoradiography. Appl Environ Microbiol 65:5100–5106. https://doi.org/10.1128/aem.65.11.5100-5106.1999
Gray ND, Comaskey D, Miskin IP et al (2004) Adaptation of sympatric Achromatium spp. to different redox conditions as a mechanism for coexistence of functionally similar sulphur bacteria. Environ Microbiol 6:669–677. https://doi.org/10.1111/j.1462-2920.2004.00607.x
Greenfield LJ (2006) Metabolism and concentration of calcium and magnesium and precipitation of calcium carbonate by a marine bacterium. Ann N Y Acad Sci 109:23–45. https://doi.org/10.1111/j.1749-6632.1963.tb13459.x
Grenabo L, Brorson J-E, Hedelin H, Pettersson S (1984) Ureaplasma urealyticum-induced crystallization of magnesium ammonium phosphate and calcium phosphates in synthetic urine. J Urol 132:795–799. https://doi.org/10.1016/S0022-5347(17)49876-4
Griffith DP (1978) Struvite stones. Kidney Int 13:372–382. https://doi.org/10.1038/KI.1978.55
Gros O (2017) First description of a new uncultured epsilon sulfur bacterium colonizing marine mangrove sediment in the Caribbean: Thiovulum sp. strain karukerense. FEMS Microbiol Lett 364(18):fnx172. https://doi.org/10.1093/femsle/fnx172
Grote G, Krumbein WE (1992) Microbial precipitation of manganese by bacteria and fungi from desert rock and rock varnish. Geomicrobiol J 10:49–57. https://doi.org/10.1080/01490459209377903
Groth I, Schumann P, Laiz L et al (2001) Geomicrobiological study of the Grotta dei Cervi, Porto Badisco, Italy. Geomicrobiol J 18:241–258. https://doi.org/10.1080/01490450152467778
Grover JE, Rope AF, Kaneshiro ES (1997) The occurrence of biogenic calcian struvite, (Mg, Ca)NH4PO4.6H2O, as intracellular crystals in paramecium. J Eukaryot Microbiol 44:366–373. https://doi.org/10.1111/j.1550-7408.1997.tb05679.x
Grünberg K, Wawer C, Tebo BM, Schüler D (2001) A large gene cluster encoding several magnetosome proteins is conserved in different species of magnetotactic bacteria. Appl Environ Microbiol 67:4573. https://doi.org/10.1128/AEM.67.10.4573-4582.2001
Gur D, Palmer BA, Weiner S, Addadi L (2017) Light manipulation by guanine crystals in organisms: biogenic scatterers, mirrors, multilayer reflectors and photonic crystals. Adv Funct Mater 27:1616–3028. https://doi.org/10.1002/adfm.201603514
Gussone N, Eisenhauer A, Heuser A et al (2003) Model for kinetic effects on calcium isotope fractionation (δ44Ca) in inorganic aragonite and cultured planktonic foraminifera. Geochim Cosmochim Acta 67:1375–1382. https://doi.org/10.1016/S0016-7037(02)01296-6
Haferburg G, Kloess G, Schmitz W, Kothe E (2008) “Ni-struvite” – A new biomineral formed by a nickel resistant Streptomyces acidiscabies. Chemosphere 72:517–523. https://doi.org/10.1016/j.chemosphere.2008.02.050
Hallberg R (1965) Notes on biosynthesis of pyrite. Stock Contrib Geol 13:35–37
Hallberg RO (1972) Iron and zinc sulfides formed in a continuous culture of sulfate-reducing bacteria. Neues Jahrb für Mineral Monatshefte 11:481–500
Hallberg R, Ferris FG (2004) Biomineralization by Gallionella. Geomicrobiol J 21:325–330. https://doi.org/10.1080/01490450490454001
Hallberg KB, Johnson DB (2005) Biological manganese removal from acid mine drainage in constructed wetlands and prototype bioreactors. Sci Total Environ 338:115–124. https://doi.org/10.1016/J.SCITOTENV.2004.09.011
Hallberg RO, Wadsten T (1980) Crystal data of a new phosphate compound from microbial experiments on iron sulfide mineralization. Am Mineral 65:200–204
Hammes F, Seka A, De Knijf S, Verstraete W (2003) A novel approach to calcium removal from calcium-rich industrial wastewater. Water Res 37:699–704. https://doi.org/10.1016/S0043-1354(02)00308-1
Hansen HCB, Poulsen IF (1999) Interaction of synthetic sulphate green rust with phosphate and the crystallization of vivianite. Clays Clay Miner 47:312–318. https://doi.org/10.1346/ccmn.1999.0470307
Harouaka K, Mansor M, Macalady JL, Fantle MS (2016) Calcium isotopic fractionation in microbially mediated gypsum precipitates. Geochim Cosmochim Acta 184:114–131. https://doi.org/10.1016/j.gca.2016.03.003
Harrison PM, Andrews SC, Ford GC et al (1987) Ferritin and bacterioferritin: iron sequestering molecules from man to microbe. Iron Transp Microbes, Plants Anim:445–475
Hastings D, Emerson S (1986) Oxidation of manganese by spores of a marine bacillus: Kinetic and thermodynamic considerations. Geochim Cosmochim Acta 50:1819–1824. https://doi.org/10.1016/0016-7037(86)90141-9
Hastings DW, Russell AD, Emerson SR (1998) Foraminiferal magnesium in globeriginoides sacculifer as a paleotemperature proxy. Paleoceanography 13:161–169. https://doi.org/10.1029/97PA03147
Hausmann K, Walz B (1979) Feinstrukturelle und mikroanalytische Untersuchungen an den Kristallen und Lithosomen des Ciliaten Euplotes vannus. Protoplasma 99:67–77
Head IM, Gray ND, Clarke KJ et al (1996) The phylogenetic position and ultrastructure of the uncultured bacterium Achromatium oxaliferum. Microbiology 142:2341–2354. https://doi.org/10.1099/00221287-142-9-2341
Head IM, Gray ND, Babenzien H-D, Oliver Glöckner F (2000a) Uncultured giant sulfur bacteria of the genus Achromatium. FEMS Microbiol Ecol 33:171–180. https://doi.org/10.1111/j.1574-6941.2000.tb00739.x
Head IM, Gray ND, Howarth R et al (2000b) Achromatium oxaliferum understanding the unmistakable. In: Advances in microbial ecology. Kluwer Academic/Plenum Publishers, New York, pp 1–40
Hedley RH, Ogden CG, Mordan NJ (1976) Manganese in the shell of Centropyxis (Rhizopodea: Protozoa). Cell Tissue Res 171:543–549. https://doi.org/10.1007/BF00220245
Hemleben C, Be AWH, Anderson OR, Tuntivate S (1977) Test morphology, organic layers and chamber formation of the planktonic foraminifer Globorotalia menardii (d’Orbigny). J Foraminifer Res 7:1–25. https://doi.org/10.2113/gsjfr.7.1.1
Hemmersbach R, Voormanns R, Bromeis B et al (1998) Comparative studies of the graviresponses of Paramecium and Loxodes. Adv Sp Res 21:1285–1289. https://doi.org/10.1016/S0273-1177(97)00400-6
Hepperle D, Krienitz L, Hepperle D (1996) The extracellular calcification of zoospores of phacotus lenticularis (chlorophyta, chlamydomonadales). Eur J Phycol 31:11–21. https://doi.org/10.1080/09670269600651141
Herbert RB, Benner SG, Pratt AR, Blowes DW (1998) Surface chemistry and morphology of poorly crystalline iron sulfides precipitated in media containing sulfate-reducing bacteria. Chem Geol 144:87–97. https://doi.org/10.1016/S0009-2541(97)00122-8
Heywood BR, Bazylinski DA, Garratt-Reed A et al (1990) Controlled biosynthesis of greigite (Fe3S4) in magnetotactic bacteria. Naturwissenschaften 77:536–538. https://doi.org/10.1007/BF01139266
Hirschler A, Lucas J, Hubert J-C (1990a) Bacterial involvement in apatite genesis. FEMS Microbiol Lett 73:211–220. https://doi.org/10.1111/j.1574-6968.1990.tb03943.x
Hirschler A, Lucas J, Hubert J (1990b) Apatite genesis: A biologically induced or biologically controlled mineral formation process? Geomicrobiol J 8:47–56. https://doi.org/10.1080/01490459009377877
Hollande A, Martoja R (1974) Identification du cristalloide des isospores de radiolaires a un cristal de celestine (SrSO4). Determination de la constitution du cristalloide par voie cytochimique et a l’aide de la microsonde electronique et du microanalyseur par emission ionique secon. Protistologica 10:603–609
Horner HT, Tiffany LH, Cody AM (1983) Formation of calcium oxalate crystals associated with apothecia of the discomycete dasyscypha capitata. Mycologia 75:423–435. https://doi.org/10.1080/00275514.1983.12023706
Howarth R, Unz RF, Seviour EM et al (1999) Phylogenetic relationships of filamentous sulfur bacteria (Thiothrix spp. and Eikelboom type 021N bacteria) isolated from wastewater treatment plants and description of Thiothrix eikelboomii sp. nov., Thiothrix unzii sp. nov., Thiothrix fructosivorans sp. Int J Syst Evol Microbiol 49:1817–1827. https://doi.org/10.1099/00207713-49-4-1817
Huang J, Zhang H (2020) Redox reactions of iron and manganese oxides in complex systems. Front Environ Sci Eng 14:76. https://doi.org/10.1007/s11783-020-1255-8
Hubert G, Rieder N, Schmitt G, Send W (1975) Bariumanreicherung in den Müllerschen Körperchen der Loxodidae (Ciliata, Holotricha)/Accumulation of Barium in Müller’s Bodies of the Loxodidae (Ciliata, Holotricha). Zeitschrift für Naturforsch C 30:422–422b. https://doi.org/10.1515/znc-1975-5-622
Huddleson IF, Winter OB (1927) Magnesium ammonium phosphate crystals in aerobic cultures of brucella abortus and brucella melitensis. J Infect Dis 40:476–478
Hughes NP, Perry CC, Anderson OR, Williams RJP (1989) Biological minerals formed from strontium and barium sulphates. III. The morphology and crystallography of strontium sulphate crystals from the colonial radiolarian, Sphaerozoum punctatum. Proc R Soc London B Biol Sci 238:223–233. https://doi.org/10.1098/rspb.1989.0078
Hunger S, Benning LG (2007) Greigite: a true intermediate on the polysulfide pathway to pyrite. Geochem Trans 8:1. https://doi.org/10.1186/1467-4866-8-1
Ikogou M, Ona-Nguema G, Juillot F et al (2017) Long-term sequestration of nickel in mackinawite formed by Desulfovibrio capillatus upon Fe(III)-citrate reduction in the presence of thiosulfate. Appl Geochemistry 80:143–154. https://doi.org/10.1016/J.APGEOCHEM.2017.02.019
Isenberg HD, Lavine LS, Moss ML et al (2006) Calcification in a marine coccolithophorid. Ann N Y Acad Sci 109:49–64. https://doi.org/10.1111/j.1749-6632.1963.tb13461.x
Ivarson KC (1973) Microbiological formation of basic ferric sulfates. Can J Soil Sci 53:315–323. https://doi.org/10.4141/cjss73-046
Ivarson KC, Hallberg RO (1976) Formation of mackinawite by the microbial reduction of jarosite and its application to tidal sediments. Geoderma 16:1–7. https://doi.org/10.1016/0016-7061(76)90089-6
Jackson TA, Keller WD (1970) A comparative study of the role of lichens and “inorganic” processes in the chemical weathering of Recent Hawaiian lava flows. Am J Sci 269:446–466. https://doi.org/10.2475/ajs.269.5.446
Jackson BP, Williams PL, Lanzirotti A, Bertsch PM (2005) Evidence for biogenic pyromorphite formation by the nematode caenorhabditis elegans. Environ Sci Technol 39:5620–5625. https://doi.org/10.1021/ES050154K
Jamieson JC (1953) Phase equilibrium in the system calcite-aragonite. J Chem Phys 21:1385–1390. https://doi.org/10.1063/1.1699228
Jantschke A, Pinkas I, Hirsch A et al (2019) Anhydrous β-guanine crystals in a marine dinoflagellate: structure and suggested function. J Struct Biol 207:12–20. https://doi.org/10.1016/j.jsb.2019.04.009
Jantschke A, Pinkas I, Schertel A et al (2020) Biomineralization pathways in calcifying dinoflagellates: uptake, storage in MgCaP-rich bodies and formation of the shell. Acta Biomater 102:427–439. https://doi.org/10.1016/j.actbio.2019.11.042
Jarvis WR, Barrie SD, Traquair JA, Stoessl A (1990) Morphological and chemical studies of Penicillium oxalicum, newly identified as a pathogen on greenhouse cucumbers. Can J Bot 68:21–25. https://doi.org/10.1139/b90-003
Javor BJ, Wilmot DB, Vetter RD (1990) pH-Dependent metabolism of thiosulfate and sulfur globules in the chemolithotrophic marine bacterium Thiomicrospira crunogena. Arch Microbiol 154:231–238. https://doi.org/10.1007/BF00248960
Jogler C, Niebler M, Lin W et al (2010) Cultivation-independent characterization of ‘Candidatus Magnetobacterium bavaricum’ via ultrastructural, geochemical, ecological and metagenomic methods. Environ Microbiol 12:2466–2478. https://doi.org/10.1111/j.1462-2920.2010.02220.x
Johnson DB, Hallberg KB (2003) The microbiology of acidic mine waters. Res. Microbiol. 154:466–473
Jones AR (1967) Calcium and phosphorus accumulation in spirostomum ambiguum. J Protozool 14:220–225. https://doi.org/10.1111/j.1550-7408.1967.tb01987.x
Jones B, Peng X (2012) Amorphous calcium carbonate associated with biofilms in hot spring deposits. Sediment Geol 269–270:58–68. https://doi.org/10.1016/J.SEDGEO.2012.05.019
Jones D, McHardy WJ, Wilson MJ (1976) Ultrastructure and chemical composition of spines in Mucorales. Trans Br Mycol Soc 66:153–157. https://doi.org/10.1016/S0007-1536(76)80106-4
Jones D, Wilson MJ, Tait JM (1980) Weathering of a basalt by pertusaria corallina. Lichenol 12:277–290. https://doi.org/10.1017/S002428298000028X
Jones D, Wilson MJ, Laundon JR (1982) Observations on the location and form of lead in stereocaulon vesuvianum. Lichenol 14:281–286. https://doi.org/10.1017/S0024282982000516
Jürgensen A, Widmeyer JR, Gordon RA et al (2004) The structure of the manganese oxide on the sheath of the bacterium Leptothrix discophora: An XAFS study. Am Mineral 89:1110–1118. https://doi.org/10.2138/am-2004-0724
Kajander EO, Ciftçioglu N (1998) Nanobacteria: an alternative mechanism for pathogenic intra- and extracellular calcification and stone formation. Proc Natl Acad Sci U S A 95:8274–8279. https://doi.org/10.1073/pnas.95.14.8274
Kamptner E (1950) Über den Aufbau des Kalkgehäuses von Phacotus Lendneri Chod. Österreichische Bot Zeitschrift 97:391–402
Kang CH, Choi JH, Noh JG et al (2014) Microbially induced calcite precipitation-based sequestration of strontium by sporosarcina pasteurii WJ-2. Appl Biochem Biotechnol 174:2482–2491. https://doi.org/10.1007/s12010-014-1196-4
Kato C, Bartlett DH (1997) The molecular biology of barophilic bacteria. Extremophiles 1:111–116
Kawaguchi R, Burgess JG, Matsunaga T (1992) Phylogeny and 16s rRNA sequence of Magnetospirillum sp. AMB-1, an aerobic magnetic bacterium. Nucleic Acids Res 20:1140. https://doi.org/10.1093/nar/20.5.1140
Kennedy CB, Scott SD, Ferris FG (2004) Hydrothermal phase stabilization of 2-line ferrihydrite by bacteria. Chem Geol 212:269–277. https://doi.org/10.1016/J.CHEMGEO.2004.08.017
Keul N, Langer G, Thoms S et al (2017) Exploring foraminiferal Sr/Ca as a new carbonate system proxy. Geochim Cosmochim Acta 202:374–386. https://doi.org/10.1016/j.gca.2016.11.022
Keupp H (1981) Die kalkigen dinoflagellaten-zysten der borealen unter-kreide (unter-hauterivium bis unter-albium). Facies 5:1–190
Khan SR (1995) Calcium oxalate in biological systems. CRC Press, Boca Raton
Kim HS, Stair PC (2004) Bacterially produced manganese oxide and todorokite: UV Raman spectroscopic comparison. J Phys Chem B 108:17019–17026. https://doi.org/10.1021/jp048810a
Kim HS, Pastén PA, Gaillard JF, Stair PC (2003) Nanocrystalline todorokite-like manganese oxide produced by bacterial catalysis. J Am Chem Soc 125:14284–14285. https://doi.org/10.1021/ja0375784
Kish A, Miot J, Lombard C et al (2016) Preservation of archaeal surface layer structure during mineralization. Sci Rep 6:26152. https://doi.org/10.1038/srep26152
Klaveness D (1999) Metallogenium — A Microbial Enigma. In: Enigmatic microorganisms and life in extreme environments. Springer, Netherlands, pp 539–548
Kleinjan WE, de Keizer A, Janssen AJH (2003) Biologically produced sulfur BT. In: Steudel R (ed) Elemental sulfur and sulfur-rich compounds I. Springer, Berlin, Heidelberg, pp 167–188
Kletzin A, Urich T, Müller F et al (2004) Dissimilatory oxidation and reduction of elemental sulfur in thermophilic archaea. J Bioenerg Biomembr 36:77–91. https://doi.org/10.1023/B:JOBB.0000019600.36757.8c
Knauer K, Jabusch T, Sigg L (1999) Manganese uptake and Mn(II) oxidation by the alga Scenedesmus subspicatus. Aquat Sci 61:44–58. https://doi.org/10.1007/pl00001321
Kolo K, Claeys P (2005) In vitro formation of Ca-oxalates and the mineral glushinskite by fungal interaction with carbonate substrates and seawater. Biogeosciences 2:277–293. https://doi.org/10.5194/bg-2-277-2005
Komeili A, Vali H, Beveridge TJ, Newman DK (2004) Magnetosome vesicles are present before magnetite formation, and MamA is required for their activation. Proc Natl Acad Sci U S A 101:3839–3844. https://doi.org/10.1073/pnas.0400391101
Kopetzky-Rechtperg O (1949) Zellbau und zelleinschlüsse bei conjugaten, besonders desmidiales. Protoplasma 39:106–112
Kopp C, Pernice M, Domart-Coulon I et al (2013) Highly dynamic cellular-level response of symbiotic coral to a sudden increase in environmental nitrogen. MBio 4:e00052–e00013. https://doi.org/10.1128/mBio.00052-13
Kornberg A, Rao NN, Ault-Riche D (1999) Inorganic polyphosphate: a molecule of many functions. Annu Rev Biochem 68:89–125
Krauss F, Schäfer W, Schmidt A (1984) Formation of elemental sulfur by chlorella fusca during growth on l-cysteine ethylester. Plant Physiol 74:176–182. https://doi.org/10.1104/pp.74.1.176
Kreger DR (1957) X-ray interferences of barium sulphate in Fungi and Algae. Nature 180:867–868. https://doi.org/10.1038/180867b0
Kreger DR, Boeré H (1969) Some observations on barium sulphate in Spirogyra. Acta Bot Neerl 18:143–151. https://doi.org/10.1111/j.1438-8677.1969.tb00579.x
Krejci MR, Finney L, Vogt S, Joester D (2011a) Selective sequestration of strontium in desmid green algae by biogenic co-precipitation with barite. ChemSusChem 4:470–473. https://doi.org/10.1002/cssc.201000448
Krejci MR, Wasserman B, Finney L et al (2011b) Selectivity in biomineralization of barium and strontium. J Struct Biol 176:192–202. https://doi.org/10.1016/j.jsb.2011.08.006
Krumbein WE (1974) On the precipitation of aragonite on the surface of marine bacteria. Naturwissenschaften 61:167. https://doi.org/10.1007/BF00602591
Krumbein WE (1979) Photolithotropic and chemoorganotrophic activity of bacteria and algae as related to beachrock formation and degradation (gulf of Aqaba, Sinai). Geomicrobiol J 1:139–203. https://doi.org/10.1080/01490457909377729
Kukkadapu RK, Zachara JM, Fredrickson JK, Kennedy DW (2004) Biotransformation of two-line silica-ferrihydrite by a dissimilatory Fe(III)-reducing bacterium: formation of carbonate green rust in the presence of phosphate. Geochim Cosmochim Acta 68:2799–2814. https://doi.org/10.1016/J.GCA.2003.12.024
Kulaev I, Kulakovskaya T (2000) Polyphosphate and phosphate pump. Annu Rev Microbiol 54:709–734
Kulaev IS, Vagabov VM (1983) Polyphosphate metabolism in micro-organisms. In: Advances in microbial physiology. Elsevier, Amsterdam, pp 83–171
Kulaev IS, Vagabov V, Kulakovskaya T (2005) The biochemistry of inorganic polyphosphates. John Wiley & Sons
La Rivière JWM, Schmidt K (1992) Morphologically conspicuous sulfur-oxidizing eubacteria. In: Balows A, Trüper HG, Dworkin M et al (eds) The prokaryotes. Springer, New York, NY, pp 3934–3947
Lane DJ, Harrison AP, Stahl D et al (1992) Evolutionary relationships among sulfur- and iron-oxidizing eubacteria. J Bacteriol 174:269–278. https://doi.org/10.1128/jb.174.1.269-278.1992
Larkin JM, Strohl WR (1983) Beggiatoa, thiothrix, and thioploca. Annu Rev Microbiol 37:341–367. https://doi.org/10.1146/annurev.mi.37.100183.002013
Lazaroff N, Sigal W, Wasserman A (1982) Iron oxidation and precipitation of ferric hydroxysulfates by resting thiobacillus ferrooxidans cells. Appl Environ Microbiol 43:924–938. https://doi.org/10.1128/aem.43.4.924-938.1982
Lefèvre CT, Menguy N, Abreu F et al (2011) A cultured greigite-producing magnetotactic bacterium in a novel group of sulfate-reducing bacteria. Science (80-) 334:1720–1723. https://doi.org/10.1126/science.1212596
Leleu M, Goni J (1974) Sur la formation biogéochimique de stalactites de galène. Miner Depos 9:27–32. https://doi.org/10.1007/BF00203275
Leleu M, Gugalski T, Goni J (1975) Synthése de wurtzite par voie bactérienne. Miner Depos 10:323–329. https://doi.org/10.1007/BF00207891
Lemloh ML, Marin F, Herbst F et al (2013) Genesis of amorphous calcium carbonate containing alveolar plates in the ciliate Coleps hirtus (Ciliophora, Prostomatea). J Struct Biol 181:155–161. https://doi.org/10.1016/j.jsb.2012.12.001
Lerner SP, Gleeson MJ, Griffith DP (1989) Infection stones. J Urol 141:753–758. https://doi.org/10.1016/S0022-5347(17)41002-0
Levi-Kalisman Y, Raz S, Weiner S et al (2002) Structural differences between biogenic amorphous calcium carbonate phases using X-ray absorption spectroscopy. Adv Funct Mater 12:43–48. https://doi.org/10.1002/1616-3028(20020101)12:1<43::AID-ADFM43>3.0.CO;2-C
Levine ND, Corliss JO, Cox FEG et al (1980) A newly revised classification of the protozoa*. J Protozool 27:37–58. https://doi.org/10.1111/j.1550-7408.1980.tb04228.x
Li J, Benzerara K, Bernard S, Beyssac O (2013) The link between biomineralization and fossilization of bacteria: Insights from field and experimental studies. Chem. Geol. 359:49–69
Li J, Margaret Oliver I, Cam N et al (2016a) Biomineralization patterns of intracellular carbonatogenesis in cyanobacteria: molecular hypotheses. Minerals 6:10. https://doi.org/10.3390/min6010010
Li Z, Wang F, Bai T et al (2016b) Lead immobilization by geological fluorapatite and fungus Aspergillus niger. J Hazard Mater 320:386–392. https://doi.org/10.1016/j.jhazmat.2016.08.051
Li C, Li Q, Wang Z et al (2019) Environmental fungi and bacteria facilitate lecithin decomposition and the transformation of phosphorus to apatite. Sci Rep 9:1–8. https://doi.org/10.1038/s41598-019-51804-7
Lian B, Hu Q, Chen J et al (2006) Carbonate biomineralization induced by soil bacterium Bacillus megaterium. Geochim Cosmochim Acta 70:5522–5535. https://doi.org/10.1016/J.GCA.2006.08.044
Liang X, Hillier S, Pendlowski H et al (2015) Uranium phosphate biomineralization by fungi. Environ Microbiol 17:2064–2075. https://doi.org/10.1111/1462-2920.12771
Lin W, Paterson GA, Zhu Q et al (2017) Origin of microbial biomineralization and magnetotaxis during the Archean. Proc Natl Acad Sci U S A 114:2171–2176. https://doi.org/10.1073/pnas.1614654114
Lovley DR, Stolz JF, Nord GL, Phillips EJP (1987) Anaerobic production of magnetite by a dissimilatory iron-reducing microorganism. Nature 330:252–254
Lowenstam H (1981) Minerals formed by organisms. Science (80-) 211:1126–1131. https://doi.org/10.1126/science.7008198
Lowenstam HA, Weiner S (1989) On biomineralization. Oxford University Press on Demand, Oxford
Lv JJ, Ma F, Li FC et al (2017) Vaterite induced by Lysinibacillus sp. GW-2 strain and its stability. J Struct Biol 200:97–105. https://doi.org/10.1016/j.jsb.2017.09.008
Maclean LCW, Tyliszczak T, Gilbert PUPA et al (2008) A high-resolution chemical and structural study of framboidal pyrite formed within a low-temperature bacterial biofilm. Geobiology 6:471–480. https://doi.org/10.1111/j.1472-4669.2008.00174.x
Maier S, Murray RGE (1965) The fine structure of Thioploca ingrica and a comparison with Beggiatoa. Can J Microbiol 11:645–655. https://doi.org/10.1139/m65-087
Mangenot G (1932) Sur le pigment et le calcaire chez Fuligo septica Gmel. CR Soc Biol (Paris) 111:936
Mann S (2001) Biomineralization: principles and concepts in bioinorganic materials chemistry. Oxford University Press on Demand, Oxford
Mann H, Mann S, Fyfe WS (1987) Aragonite crystals in Spirogyra sp. (Chlorophyta). J Phycol 23:506–509. https://doi.org/10.1111/j.1529-8817.1987.tb02539.x
Mann S, Sparks NHC, Frankel RB et al (1990) Biomineralization of ferrimagnetic greigite (Fe3S4) and iron pyrite (FeS2) in a magnetotactic bacterium. Nature 343:258–261. https://doi.org/10.1038/343258a0
Mansor M, Harouaka K, Gonzales MS et al (2018) Transport-induced spatial patterns of sulfur isotopes (δ 34 S) as biosignatures. Astrobiology 18:59–72. https://doi.org/10.1089/ast.2017.1650
Manton I, Oates K (1980) Polycrater galapagensis gen. Et sp. nov., a putative coccolithophorid from the Galapagos islands with an unusual aragonitic periplast. Br Phycol J 15:95–103. https://doi.org/10.1080/00071618000650111
Marnocha CL, Levy AT, Powell DH et al (2016) Mechanisms of extracellular S0 globule production and degradation in Chlorobaculum tepidum via dynamic cell–globule interactions. Microbiology 162:1125. https://doi.org/10.1099/MIC.0.000294
Marnocha CL, Sabanayagam CR, Modla S et al (2019) Insights into the mineralogy and surface chemistry of extracellular biogenic S0 globules produced by chlorobaculum tepidum. Front Microbiol 10:271. https://doi.org/10.3389/fmicb.2019.00271
Martignier A, Pacton M, Filella M et al (2017) Intracellular amorphous carbonates uncover a new biomineralization process in eukaryotes. Geobiology 15:240–253. https://doi.org/10.1111/gbi.12213
Martignier A, Filella M, Pollok K et al (2018) Marine and freshwater micropearls: biomineralization producing strontium-rich amorphous calcium carbonate inclusions is widespread in the genus Tetraselmis (Chlorophyta). Biogeosciences 15:6591–6605. https://doi.org/10.5194/bg-15-6591-2018
Marzec B, Walker JM, Panagopoulou M et al (2019) Three-dimensional architecture and surface functionality of coccolith base plates. J Struct Biol 208:127–136. https://doi.org/10.1016/j.jsb.2019.08.007
Matsunaga T, Nakamura C, Burgess JG, Sode K (1992) Gene transfer in magnetic bacteria: transposon mutagenesis and cloning of genomic DNA fragments required for magnetosome synthesis. J Bacteriol 174:2748–2753. https://doi.org/10.1128/jb.174.9.2748-2753.1992
McLean RJC, Nickel JC, Cheng K-J et al (1988) The ecology and pathogenicity of urease-producing bacteria in the urinary tract. CRC Crit Rev Microbiol 16:37–79. https://doi.org/10.3109/10408418809104467
Mehta N, Benzerara K, Kocar BD, Chapon V (2019) Sequestration of Radionuclides Radium-226 and Strontium-90 by Cyanobacteria forming intracellular calcium carbonates. Environ Sci Technol 53:12639–12647. https://doi.org/10.1021/acs.est.9b03982
Meindl U (1984) Nachweis von Bariumsulfat in den Kristallen kultivierterZellen von Micrasterias denticulata mittels energie-dispersiver Röntgenanalyse (EDAX). Phyt 24:273–276
Meldrum FC, O’Shaughnessy C (2020) Crystallization in confinement. Adv Mater 32:2001068. https://doi.org/10.1002/adma.202001068
Milucka J, Ferdelman TG, Polerecky L et al (2012) Zero-valent sulphur is a key intermediate in marine methane oxidation. Nature 491:541–546. https://doi.org/10.1038/nature11656
Miot J, Benzerara K, Morin G et al (2009a) Iron biomineralization by anaerobic neutrophilic iron-oxidizing bacteria. Geochim Cosmochim Acta 73:696–711. https://doi.org/10.1016/j.gca.2008.10.033
Miot J, Benzerara K, Obst M et al (2009b) Extracellular iron biomineralization by photoautotrophic iron-oxidizing bacteria. Appl Environ Microbiol 75:5586–5591. https://doi.org/10.1128/AEM.00490-09
Miot J, Bernard S, Bourreau M et al (2017) Experimental maturation of Archaea encrusted by Fe-phosphates. Sci Rep 7:1–11. https://doi.org/10.1038/s41598-017-17111-9
Miyata N, Tani Y, Maruo K et al (2006) Manganese(IV) oxide production by Acremonium sp. strain KR21-2 and extracellular Mn(II) oxidase activity. Appl Environ Microbiol 72:6467–6473. https://doi.org/10.1128/AEM.00417-06
Mojzeš P, Gao L, Ismagulova T et al (2020) Guanine, a high-capacity and rapid-turnover nitrogen reserve in microalgal cells. Proc Natl Acad Sci U S A 117:32722–32730. https://doi.org/10.1073/pnas.2005460117
Mojzsis SJ, Arrhenius G (1998) Phosphates and carbon on Mars: Exobiological implications and sample return considerations. J Geophys Res Planets 103:28495–28511. https://doi.org/10.1029/98JE02141
Mojzsis SJ, Arrhenius G, McKeegan KD et al (1996) Evidence for life on Earth before 3,800 million years ago. Nature 384:55–59. https://doi.org/10.1038/384055a0
Monteil CL, Benzerara K, Menguy N et al (2020) Intracellular amorphous Ca-carbonate and magnetite biomineralization by a magnetotactic bacterium affiliated to the Alphaproteobacteria. ISME J 15:1–18. https://doi.org/10.1038/s41396-020-00747-3
Monteiro FM, Bach LT, Brownlee C et al (2016) Why marine phytoplankton calcify. Sci. Adv. 2:e1501822
Moorer WR, Ten Cate JM, Buijs JF (1993) Calcification of a cariogenic Streptococcus and of Corynebacterium (Bacterionema) matruchotii. J Dent Res 72:1021–1026. https://doi.org/10.1177/00220345930720060501
Morgan JJ (2005) Kinetics of reaction between O2 and Mn(II) species in aqueous solutions. Geochim Cosmochim Acta 69:35–48. https://doi.org/10.1016/j.gca.2004.06.013
Morin G, Juillot F, Casiot C et al (2003) Bacterial formation of Tooeleite and Mixed Arsenic(III) or Arsenic(V)−Iron(III) Gels in the Carnoulès Acid Mine Drainage, France. A XANES, XRD, and SEM study. Environ Sci Technol 37(9):1705–1712. https://doi.org/10.1021/ES025688P
Morita RY (1980) Calcite precipitation by marine bacteria∗. Geomicrobiol J 2:63–82. https://doi.org/10.1080/01490458009377751
Moudříková Š, Nedbal L, Solovchenko A, Mojzeš P (2017) Raman microscopy shows that nitrogen-rich cellular inclusions in microalgae are microcrystalline guanine. Algal Res 23:216–222. https://doi.org/10.1016/j.algal.2017.02.009
Müller J (1858) Über die thalassicollen, polycystinen und acanthometren des mittelmeeres. F. Dümmler, Berlin
Nathan Y, Bremner JM, Loewenthal RE, Monteiro P (1993) Role of bacteria in phosphorite genesis. Geomicrobiol J 11:69–76. https://doi.org/10.1080/01490459309377935
Neal AL, Techkarnjanaruk S, Dohnalkova A et al (2001) Iron sulfides and sulfur species produced at hematite surfaces in the presence of sulfate-reducing bacteria. Geochim Cosmochim Acta 65:223–235. https://doi.org/10.1016/S0016-7037(00)00537-8
Nealson KH (1978) The isolation and characterization of marine bacteria which catalyze manganese oxidation. In: Krumbein WE (ed) Environmental biogeochemistry and geomicrobiology, vol 3. Ann Arbor Press, Ann Arbor, Michigan, pp 847–885
Nealson KH, Ford J (1980) Surface enhancement of bacterial manganese oxidation: implications for aquatic environments. Geomicrobiol J 2:21–37. https://doi.org/10.1080/01490458009377748
Nealson KH, Tebo BM, Rosson RA (1988) Occurrence and mechanisms of microbial oxidation of manganese. Adv Appl Microbiol 33:279–318. https://doi.org/10.1016/S0065-2164(08)70209-0
Nelson B, Struble J, McCarthy G (1991) In vitro production of struvite by Bacillus pumilus. Can J Microbiol 37:978–983. https://doi.org/10.1139/m91-169
Nelson YM, Lion LW, Ghiorse WC, Shuler ML (1999) Production of biogenic Mn oxides by leptothrix discophora SS-1 in a chemically defined growth medium and evaluation of their Pb adsorption characteristics. Appl Environ Microbiol 65:175–180. https://doi.org/10.1128/AEM.65.1.175-180.1999
Nelson YM, Lion LW, Shuler ML, Ghiorse WC (2002) Effect of oxide formation mechanisms on lead adsorption by biogenic manganese (Hydr)oxides, Iron (Hydr)oxides, and their mixtures. https://doi.org/10.1021/ES010907C
Neugebauer DC, Machemer H (1997) Is there an orientation-dependent excursion of the Muller body in the “statocystoid” of Loxodes? Cell Tissue Res 287:577–582. https://doi.org/10.1007/s004410050780
Niedermeier M, Gierlinger N, Lütz-Meindl U (2018) Biomineralization of strontium and barium contributes to detoxification in the freshwater alga Micrasterias. J Plant Physiol 230:80–91. https://doi.org/10.1016/j.jplph.2018.08.008
Nriagu JO (1972) Stability of vivianite and ion-pair formation in the system fe3(PO4)2-H3PO4H3PO4-H2o. Geochim Cosmochim Acta 36:459–470. https://doi.org/10.1016/0016-7037(72)90035-X
Nudelman F, Sommerdijk NAJM (2012) Biomineralization as an inspiration for materials chemistry. Angew Chemie Int Ed 51:6582–6596. https://doi.org/10.1002/anie.201106715
O’Brien GW, Harris JR, Milnes AR, Veeh HH (1981) Bacterial origin of East Australian continental margin phosphorites. Nature 294:442–444. https://doi.org/10.1038/294442a0
O’Loughlin EJ (2008) Effects of electron transfer mediators on the bioreduction of lepidocrocite (γ-FeOOH) by Shewanella putrefaciens CN32. Environ Sci Technol 42:6876–6882. https://doi.org/10.1021/es800686d
O’Loughlin EJ, Boyanov MI, Flynn TM et al (2013) Effects of bound phosphate on the bioreduction of lepidocrocite (γ-FeOOH) and maghemite (γ-Fe 2 O 3) and formation of secondary minerals. Environ Sci Technol 47:9157–9166. https://doi.org/10.1021/es400627j
O’Reilly S, Hochella MF (2003) Lead sorption efficiencies of natural and synthetic Mn and Fe-oxides. Geochim Cosmochim Acta 67:4471–4487. https://doi.org/10.1016/S0016-7037(03)00413-7
Obst M, Dynes JJ, Lawrence JR et al (2009) Precipitation of amorphous CaCO3 (aragonite-like) by cyanobacteria: A STXM study of the influence of EPS on the nucleation process. Geochim Cosmochim Acta 73:4180–4198. https://doi.org/10.1016/j.gca.2009.04.013
Odintsova EV, Jannasch HW, Mamone JA, Langworthy TA (1996) Thermothrix azorensis sp. nov., an obligately chemolithoautotrophic, sulfur-oxidizing, thermophilic bacterium. Int J Syst Bacteriol 46:422–428. https://doi.org/10.1099/00207713-46-2-422
Odum HT (1951) Notes on the strontium content of sea water, celestite radiolaria, and strontianite snail shells. Science (80-) 114:211–213. https://doi.org/10.1126/science.114.2956.211
Ogden CG, Hedley RH (1980) An atlas of freshwater testate amoebae. Oxford University Press, British Museum (Natural History), Oxford
Oggerin M, Tornos F, Rodríguez N et al (2013) Specific jarosite biomineralization by Purpureocillium lilacinum, an acidophilic fungi isolated from Río Tinto. Environ Microbiol 15:2228–2237. https://doi.org/10.1111/1462-2920.12094
Omar NB, Entrena M, González-Muñoz MT et al (1994) Effects of pH and phosphate on the production of struvite by Myxococcus xanthus. Geomicrobiol J 12:81–90. https://doi.org/10.1080/01490459409377974
Omelon S, Ariganello M, Bonucci E et al (2013) A review of phosphate mineral nucleation in biology and geobiology. Calcif Tissue Int 93:382–396. https://doi.org/10.1007/s00223-013-9784-9
Ondracek K (1936) Über die Bedingungen der Kristallausscheidung im Zellsaft der Desmidiaceen. Planta 26:222–225
Otte S, Kuenen JG, Nielsen LP et al (1999) Nitrogen, carbon, and sulfur metabolism in natural thioploca samples. Appl Environ Microbiol 65:3148–3157. https://doi.org/10.1128/AEM.65.7.3148-3157.1999
Paasche E (1962) Coccolith formation. Nature 193:1094–1095
Pan Y, Li N, Mu J et al (2015) Biogenic magnetic nanoparticles from Burkholderia sp. YN01 exhibiting intrinsic peroxidase-like activity and their applications. Appl Microbiol Biotechnol 99:703–715. https://doi.org/10.1007/s00253-014-5938-6
Parmar N, Warren LA, Roden EE, Ferris FG (2000) Solid phase capture of strontium by the iron reducing bacteria Shewanella algae strain BrY. Chem Geol 169:281–288. https://doi.org/10.1016/S0009-2541(00)00208-4
Pasteris JD, Freeman JJ, Goffredi SK, Buck KR (2001) Raman spectroscopic and laser scanning confocal microscopic analysis of sulfur in living sulfur-precipitating marine bacteria. Chem Geol 180:3–18. https://doi.org/10.1016/S0009-2541(01)00302-3
Pattaragulwanit K, Brune DC, Trüper HG, Dahl C (1998) Molecular genetic evidence for extracytoplasmic localization of sulfur globules in Chromatium vinosum. Arch Microbiol 169:434–444. https://doi.org/10.1007/s002030050594
Pautard FGE (1958) Bone salts in unicellular organisms. BBA - Biochim Biophys Acta 28:514–520. https://doi.org/10.1016/0006-3002(58)90513-4
Pautard FGE (1959) Hydroxyapatite as a developmental feature of Spirostomum ambiguum. BBA - Biochim Biophys Acta 35:33–46. https://doi.org/10.1016/0006-3002(59)90332-4
Pautard FGE (1970) Calcification in unicellular organisms. In: Biological calcification: cellular and molecular aspects. Springer US, Boston, MA, pp 105–201
Peat A, Banbury GH (1968) Occurrence of ferritin-like particles in a fungus. Planta 79:268–270. https://doi.org/10.1007/BF00396033
Pentecost A, Spiro B, Williamson B (2010) A Note on the Relationship Between Some Saxicolous Lichens and Manganese Ore in North Wales, UK. Geomicrobiol J 27:349–352. https://doi.org/10.1080/01490451003707668
Perfil’ev BV, Gabe DR (1965) The use of the microbial landscape method to investigate bacteria which concentrate manganese and iron in bottom deposits. In: Applied capillary microscopy. Consultants Bureau, New York
Perfil’ev BV, Gabe DR (1969) Capillary methods of investigating micro-organisms. University of Toronto Press, Toronto
Pfennig N, Trüper HG (1992) The family chromatiaceae. In: The prokaryotes. Springer, New York, NY, pp 3200–3221
Phillips AJ, Gerlach R, Lauchnor E et al (2013) Engineered applications of ureolytic biomineralization: a review. Biofouling 29:715–733. https://doi.org/10.1080/08927014.2013.796550
Picard A, Gartman A, Clarke DR, Girguis PR (2018) Sulfate-reducing bacteria influence the nucleation and growth of mackinawite and greigite. Geochim Cosmochim Acta 220:367–384. https://doi.org/10.1016/J.GCA.2017.10.006
Pobeguin T (1954) Contribution a l’étude des carbonates de calcium précipitation du calcaire par les végétaux comparaison avec le monde animal. Ann des Sci Nat Bot 15:29–109
Pokorny KS, Gold K (1973) Two morphological types of particulate inclusions in marine dinoflagellates. J Phycol 9:218–224. https://doi.org/10.1111/j.1529-8817.1973.tb04083.x
Pósfai M, Buseck PR, Bazylinski DA, Frankel RB (1998) Reaction sequence of iron sulfide minerals in bacteria and their use as biomarkers. Science (80-) 280:880–883. https://doi.org/10.1126/science.280.5365.880
Pósfai M, Moskowitz BM, Arató B et al (2006) Properties of intracellular magnetite crystals produced by Desulfovibrio magneticus strain RS-1. Earth Planet Sci Lett 249:444–455. https://doi.org/10.1016/J.EPSL.2006.06.036
Post JE (1999) Manganese oxide minerals: crystal structures and economic and environmental significance. Proc Natl Acad Sci 96:3447–3454. https://doi.org/10.1073/PNAS.96.7.3447
Powell MD, Arnott HJ (1985) Calcium oxalate crystal production in two members of the Mucorales. Scan Electron Microsc 1:183
Power IM, Wilson SA, Thom JM et al (2007) Biologically induced mineralization of dypingite by cyanobacteria from an alkaline wetland near Atlin, British Columbia, Canada. Geochem Trans 8:13. https://doi.org/10.1186/1467-4866-8-13
Prange A, Chauvistré R, Modrow H et al (2002) Quantitative speciation of sulfur in bacterial sulfur globules: X-ray absorption spectroscopy reveals at least three different species of sulfur. Microbiology 148:267–276. https://doi.org/10.1099/00221287-148-1-267
Pringsheim EG (1946) On iron flagellates. Philos Trans R Soc Lond B Biol Sci 232:311–342. https://doi.org/10.1098/rstb.1946.0004
Purvis OW (1984) The occurrence of copper oxalate in lichens growing on copper sulphide-bearing rocks in Scandinavia. Lichenol 16:197–204. https://doi.org/10.1017/S0024282984000347
Ramanan R, Kannan K, Deshkar A et al (2010) Enhanced algal CO2 sequestration through calcite deposition by Chlorella sp. and Spirulina platensis in a mini-raceway pond. Bioresour Technol 101:2616–2622. https://doi.org/10.1016/j.biortech.2009.10.061
Reitner J, Peckmann J, Blumenberg M et al (2005) Concretionary methane-seep carbonates and associated microbial communities in Black Sea sediments. Palaeogeogr Palaeoclimatol Palaeoecol 227:18–30. https://doi.org/10.1016/j.palaeo.2005.04.033
Rhee YJ, Hillier S, Gadd GM (2012) Lead transformation to pyromorphite by fungi. Curr Biol 22:237–241. https://doi.org/10.1016/j.cub.2011.12.017
Richardson LL, Stolzenbach KD (1995) Phytoplankton cell size and the development of microenvironments. FEMS Microbiol Ecol 16:185–192. https://doi.org/10.1111/j.1574-6941.1995.tb00282.x
Richardson LL, Aguilar C, Nealson KH (1988) Manganese oxidation in pH and O2 microenvironments produced by phytoplankton. Limnol Oceanogr 33:352–363. https://doi.org/10.4319/lo.1988.33.3.0352
Rickard D (1969) The microbiological formation of iron sulphides. Stock Contrib to Geol 20:49–66
Rieder N, Ott HA, Pfundstein P, Schoch R (1982) X-ray microanalysis of the mineral contents of some protozoa. J Protozool 29:15–18. https://doi.org/10.1111/j.1550-7408.1982.tb02875.x
Rivadeneyra MA, Ramos-Cormenzana A, García-Cervigón A (1983) Bacterial formation of struvite. Geomicrobiol J 3:151–163. https://doi.org/10.1080/01490458309377792
Rivadeneyra MA, Perez-Garcia I, Salmeron V, Ramos-Cormenzana A (1985) Bacterial precipitation of calcium carbonate in presence of phosphate. Soil Biol Biochem 17:171–172. https://doi.org/10.1016/0038-0717(85)90111-7
Rivadeneyra M, Delgado G, Ramos-Cormenzana A, Delgado R (1998) Biomineralization of carbonates by Halomonas eurihalina in solid and liquid media with different salinities: crystal formation sequence. Res Microbiol 149:277–287. https://doi.org/10.1016/S0923-2508(98)80303-3
Rivadeneyra MA, Delgado G, Soriano M et al (2000) Precipitation of carbonates by Nesterenkonia halobia in liquid media. Chemosphere 41:617–624. https://doi.org/10.1016/S0045-6535(99)00496-8
Robbins EI, Corley TL (2005) Microdynamics and seasonal changes in manganese oxide epiprecipitation in Pinal Creek, Arizona. Hydrobiologia 534:165–180. https://doi.org/10.1007/s10750-004-1503-0
Robinson H (1889) On the formation of struvite by microorganisms. Proc Camb Phil Soc 6:360–362
Rodriguez-Blanco JD, Sand KK, Benning LG (2017) ACC and vaterite as intermediates in the solution-based crystallization of CaCO3. In: New perspectives on mineral nucleation and growth. Springer International Publishing, Berlin, pp 93–111
Rodriguez-Navarro C, Jimenez-Lopez C, Rodriguez-Navarro A et al (2007) Bacterially mediated mineralization of vaterite. Geochim Cosmochim Acta 71:1197–1213. https://doi.org/10.1016/J.GCA.2006.11.031
Roh Y, Zhang CL, Vali H et al (2003) Biogeochemical and environmental factors in Fe biomineralization: Magnetite and siderite formation. Clays Clay Miner 51:83–95. https://doi.org/10.1346/CCMN.2003.510110
Roh Y, Chon C-M, Moon J-W (2007) Metal reduction and biomineralization by an alkaliphilic metal-reducing bacterium, Alkaliphilus metalliredigens (QYMF). Geosci J 11:415–423. https://doi.org/10.1007/BF02857056
Rosson RA, Nealson KH (1982) Manganese binding and oxidation by spores of a marine bacillus. J Bacteriol 151:1027–1034. https://doi.org/10.1128/jb.151.2.1027-1034.1982
Rothe M, Kleeberg A, Hupfer M (2016) The occurrence, identification and environmental relevance of vivianite in waterlogged soils and aquatic sediments. Earth-Science Rev 158:51–64. https://doi.org/10.1016/J.EARSCIREV.2016.04.008
Rott E, Holzinger A, Gesierich D et al (2010) Cell morphology, ultrastructure, and calcification pattern of Oocardium stratum, a peculiar lotic desmid. Protoplasma 243:39–50. https://doi.org/10.1007/s00709-009-0050-y
Rouf MA, Stokes JL (1964) Morphology, nutrition and physiology of Sphaerotilus discophorus. Arch Mikrobiol 49:132–149. https://doi.org/10.1007/BF00422137
Ruiz FA, Marchesini N, Seufferheld M et al (2001) The polyphosphate bodies of chlamydomonas reinhardtii possess a proton-pumping pyrophosphatase and are similar to acidocalcisomes. J Biol Chem 276:46196–46203. https://doi.org/10.1074/jbc.M105268200
Rust GW (1935) Colloidal primary copper ores at cornwall mines, Southeastern Missouri. J Geol 43:398–426. https://doi.org/10.1086/624318
Rusznyák A, Akob DM, Nietzsche S et al (2012) Calcite biomineralization by bacterial isolates from the recently discovered pristine karstic herrenberg cave. Appl Environ Microbiol 78:1157–1167. https://doi.org/10.1128/AEM.06568-11
Salman V, Yang T, Berben T et al (2015) Calcite-accumulating large sulfur bacteria of the genus Achromatium in Sippewissett Salt Marsh. ISME J 9:2503–2514. https://doi.org/10.1038/ismej.2015.62
Sánchez-Román M, Fernández-Remolar D, Amils R et al (2014) Microbial mediated formation of Fe-carbonate minerals under extreme acidic conditions. Sci Rep 4:1–7. https://doi.org/10.1038/srep04767
Sánchez-Román M, Puente-Sánchez F, Parro V, Amils R (2015) Nucleation of Fe-rich phosphates and carbonates on microbial cells and exopolymeric substances. Front Microbiol 6:1024. https://doi.org/10.3389/fmicb.2015.01024
Santelli CM, Webb SM, Dohnalkova AC, Hansel CM (2011) Diversity of Mn oxides produced by Mn(II)-oxidizing fungi. Geochim Cosmochim Acta 75:2762–2776. https://doi.org/10.1016/j.gca.2011.02.022
Saratovsky I, Wightman PG, Pastén PA et al (2006) Manganese oxides: Parallels between abiotic and biotic structures. J Am Chem Soc 128:11188–11198. https://doi.org/10.1021/ja062097g
Saratovsky I, Gurr SJ, Hayward MA (2009) The Structure of manganese oxide formed by the fungus Acremonium sp. strain KR21-2. Geochim Cosmochim Acta 73:3291–3300. https://doi.org/10.1016/j.gca.2009.03.005
Sarret G, Manceau A, Cuny D et al (1998) Mechanisms of lichen resistance to metallic pollution. Environ Sci Technol 32:3325–3330. https://doi.org/10.1021/ES970718N
Sawayama M, Suzuki T, Hashimoto H et al (2011) Isolation of a leptothrix strain, OUMS1, from ocherous deposits in groundwater. Curr Microbiol 63:173–180. https://doi.org/10.1007/s00284-011-9957-6
Sayer JA, Gadd GM (1997) Solubilization and transformation of insoluble inorganic metal compounds to insoluble metal oxalates by Aspergillus niger. Mycol Res 101:653–661. https://doi.org/10.1017/S0953756296003140
Sayer JA, Cotter-Howells JD, Watson C et al (1999) Lead mineral transformation by fungi. Curr Biol 9:691–694. https://doi.org/10.1016/S0960-9822(99)80309-1
Schewiakoff W (1893) Über einen neuen bacterienähnlichen Organismus des Süsswassers. University Heidelberg, Heidelberg
Schiebel R (2002) Planktic foraminiferal sedimentation and the marine calcite budget. Global Biogeochem Cycles 16:3-1-3-21. https://doi.org/10.1029/2001gb001459
Schieber J (2002a) Sedimentary pyrite: a window into the microbial past. Geology 30:531. https://doi.org/10.1130/0091-7613(2002)030<0531:SPAWIT>2.0.CO;2
Schieber J (2002b) The role of an organic slime matrix in the formation of pyritized burrow trails and pyrite concretions. Palaios 17:104–109. https://doi.org/10.1669/0883-1351(2002)017<0104:TROAOS>2.0.CO;2
Schlegel I, Krienitz L, Hepperle D (2000) Variability of calcification of Phacotus lenticularis (Chlorophyta, Chlamydomonadales) in nature and culture. Phycologia 39:318–322. https://doi.org/10.2216/i0031-8884-39-4-318.1
Schmalenberger A, Duran AL, Bray AW et al (2015) Oxalate secretion by ectomycorrhizal Paxillus involutus is mineral-specific and controls calcium weathering from minerals. Sci Rep 5:1–14. https://doi.org/10.1038/srep12187
Schmidt WJ (1949) No Title. Giess Naturwissenschaft Vor 6:1–71
Schmitter RE (1971) The fine structure of Gonyaulax polyedra, a bioluminescent marine dinoflagellate. J Cell Sci 9:147–173
Schönleber K (1936) Scytonema Julianum. Beitrage zur normalen und pathologischen Cytologie und Cytogenese der Blaualgen. Arch für Protistenkd 88:36–68
Schopf JM, Ehlers EG, Stiles DV, Birle JD (1965) Fossil iron bacteria preserved in pyrite. Proc Am Philos Soc 109:288–308
Schröder HC, Müller WEG (2012) Inorganic polyphosphates: biochemistry, biology, biotechnology. Springer Science & Business Media, Berlin
Schröter K, Läuchli A, Sievers A (1975) Mikroanalytische Identifikation von Bariumsulfat-Kristallen in den Statolithen der Rhizoide von Chara fragilis, Desv. Planta 122:213–225. https://doi.org/10.1007/BF00385269
Schüler D (2004) Molecular analysis of a subcellular compartment: the magnetosome membrane in Magnetospirillum gryphiswaldense. Arch Microbiol 181:1–7. https://doi.org/10.1007/s00203-003-0631-7
Schultheiss D, Schüler D (2003) Development of a genetic system for Magnetospirillum gryphiswaldense. Arch Microbiol 179:89–94. https://doi.org/10.1007/s00203-002-0498-z
Schultze-Lam S, Harauz G, Beveridge TJ (1992) Participation of a cyanobacterial S layer in fine-grain mineral formation. J Bacteriol 174:7971. https://doi.org/10.1128/JB.174.24.7971-7981.1992
Schulz HN, Schulz HD (2005) Large sulfur bacteria and the formation of phosphorite. Science 307:416–418. https://doi.org/10.1126/science.1103096
Schulz HN, Brinkhoff T, Ferdelman TG et al (1999) Dense populations of a giant sulfur bacterium in Namibian shelf sediments. Science 284:493–495. https://doi.org/10.1126/science.284.5413.493
Schulz-Baldes M, Lewin RA (1975) Manganese encrustation of zygospores of a Chlamydomonas (chlorophyta: Volvocales). Science (80-) 188:1119–1120. https://doi.org/10.1126/science.188.4193.1119
Schulze FE (1907) Die Xenophyophoren, eine besondere Gruppe der Rhizopoden. Wissen-schaftliche Ergebnisse der Dtsch Tiefsee-Expedition auf dem Dampfer’ Vald 1898–1899 11:1–55
Schulze FE, Thierfelder H (1905) Bariumsulfat in Meerestieren (Xenophyophora, F.E. Sch.). Sitzungsberichte der Gesellschaft Naturforschender Freunde zu Berlin 7–10
Schweisfurth R (1971) Manganoxidierende Pilze I. Vorkommen, Isolierungen und mikroskopische Untersuchungen. Z Allg Mikrobiol 11:415–430. https://doi.org/10.1002/jobm.19710110506
Seifan M, Berenjian A (2019) Microbially induced calcium carbonate precipitation: a widespread phenomenon in the biological world. Appl Microbiol Biotechnol 103:4693–4708. https://doi.org/10.1007/s00253-019-09861-5
Shimkets LJ, Dworkin M, Reichenbach H (2006) The myxobacteria. In: Dworkin M, Falkow S, Rosenberg E et al (eds) The prokaryotes. Springer, New York, NY, pp 31–115
Shinano H, Sakai M (1975) Effect of magnesium ion concentration on the types of crystals deposited by marine bacteria in sea water. Bull Jap Soc, Sci Fish 41:913
Sievers A, Schmitz M (1982) Röntgen-mikroanalyse von barium, schwefel und strontium in statolithen-kompartimenten von chrara-rhizoiden. Ber Dtsch Bot Ges 95:353–360. https://doi.org/10.1111/j.1438-8677.1982.tb02871.x
Simmons SL, Sievert SM, Frankel RB et al (2004) Spatiotemporal distribution of marine magnetotactic bacteria in a seasonally stratified coastal salt pond. Appl Environ Microbiol 70:6230–6239. https://doi.org/10.1128/AEM.70.10.6230-6239.2004
Smirnov A, Suzina N, Chudinova N et al (2005) Formation of insoluble magnesium phosphates during growth of the archaea Halorubrum distributum and Halobacterium salinarum and the bacterium Brevibacterium antiquum. FEMS Microbiol Ecol 52:129–137. https://doi.org/10.1016/j.femsec.2004.10.012
Smits MM, Bonneville S, Benning LG et al (2012) Plant-driven weathering of apatite – the role of an ectomycorrhizal fungus. Geobiology 10:445–456. https://doi.org/10.1111/j.1472-4669.2012.00331.x
Soldo AT, Godoy GA, Larin F (1978) Purine-excretory nature of refractile bodies in the marine ciliate parauronema acutum*. J Protozool 25:416–418. https://doi.org/10.1111/j.1550-7408.1978.tb03917.x
Sorokin DY, Lysenko AM, Mityushina LL et al (2001) Thioalkalimicrobium aerophilum gen. nov., sp. nov. and Thioalkalimicrobium sibericum sp. nov., and Thioalkalivibrio versutus gen. nov., sp. nov., Thioalkalivibrio nitratis sp. nov. and Thioalkalivibrio denitrificans sp. nov., novel obligately alkaliphilic. Int J Syst Evol Microbiol 51:565–580. https://doi.org/10.1099/00207713-51-2-565
Spero HJ (1988) Ultrastructural examination of chamber morphogenesis and biomineralization in the planktonic foraminifer Orbulina universa. Mar Biol 99:9–20. https://doi.org/10.1007/BF00644972
Spero HJ, Williams DF (1988) Extracting environmental information from planktonic foraminiferal δ13C data. Nature 335:717–719. https://doi.org/10.1038/335717a0
Spivack AJ, You CF, Smith HJ (1993) Foraminiferal boron isotope ratios as a proxy for surface ocean pH over the past 21 Myr. Nature 363:149–151. https://doi.org/10.1038/363149a0
Spring S, Bazylinski DA (2006) Magnetotactic bacteria. In: The prokaryotes. Springer, New York, NY, pp 842–862
Spring S, Amann R, Ludwig W et al (1993) Dominating role of an unusual magnetotactic bacterium in the microaerobic zone of a freshwater sediment. Appl Environ Microbiol 59:2397–2403
Stabnikov V, Jian C, Ivanov V, Li Y (2013) Halotolerant, alkaliphilic urease-producing bacteria from different climate zones and their application for biocementation of sand. World J Microbiol Biotechnol 29:1453–1460. https://doi.org/10.1007/s11274-013-1309-1
Stanley W, Southam G (2018) The effect of gram-positive (Desulfosporosinus orientis) and gram-negative (Desulfovibrio desulfuricans) sulfate-reducing bacteria on iron sulfide mineral precipitation. Can J Microbiol 64:629–637. https://doi.org/10.1139/cjm-2017-0545
Steudel R, Holdt G, Göbel T, Hazeu W (1987) Chromatographic separation of higher polythionates SnO62⊖(n= 3…22) and their detection in cultures of thiobacillus ferroxidans; Molecular composition of bacterial sulfur secretions. Angew Chemie Int Ed English 26:151–153. https://doi.org/10.1002/anie.198701511
Stevenson EI, Hermoso M, Rickaby REM et al (2014) Controls on stable strontium isotope fractionation in coccolithophores with implications for the marine Sr cycle. Geochim Cosmochim Acta 128:225–235. https://doi.org/10.1016/j.gca.2013.11.043
Stiefel EI, Watt GD (1979) Azotobacter cytochrome b557.5 is a bacterioferritin. Nature 279:81–83. https://doi.org/10.1038/279081a0
Stocks-Fischer S, Galinat JK, Bang SS (1999) Microbiological precipitation of CaCO3. Soil Biol Biochem 31:1563–1571. https://doi.org/10.1016/S0038-0717(99)00082-6
Streckfuss JL, Smith WN, Brown LR, Campbell MM (1974) Calcification of selected strains of Streptococcus mutans and Streptococcus sanguis. J Bacteriol 120:502–506. https://doi.org/10.1128/JB.120.1.502-506.1974
Strohl WR, Geffers I, Larkin JM (1981) Structure of the sulfur inclusion envelopes from four beggiatoas. Curr Microbiol 6:75–79. https://doi.org/10.1007/BF01569007
Sun J, Chen L, Wang X et al (2012) Synthesis of struvite crystals by using bacteria Proteus mirabilis. Synth React Inorganic, Met Nano-Metal Chem 42:445–448. https://doi.org/10.1080/15533174.2011.611850
Sutter HP, Jones EBG, Walchli O (1983) Mechanism of copper tolerance in Poria placenta (Fr.) Cke. and Poria vaillantii (Pers.) Fr. Mater und Org Mater Org 18:241–262
Sutter HP, Jones EBG, Walchli O (1984) Occurrence of crystalline hyphal sheaths in Poria placenta (Fr.) Cke. J Inst Wood Sci 10:19–23
Sviben S, Gal A, Hood MA et al (2016) A vacuole-like compartment concentrates a disordered calcium phase in a key coccolithophorid alga. Nat Commun 7:11228. https://doi.org/10.1038/ncomms11228
Svihla G, Dainko JL, Schlenk F (1963) Ultraviolet microscopy of purine compounds in the yeast vacuole. J Bacteriol 85:399–409. https://doi.org/10.1128/JB.85.2.399-409.1963
Takazoe I, Nakamura T (1965) The relation between metachromatic granules and intracellular calcification of Bacterionema matruchotii. Bull Tokyo Dent Coll 35:29
Tangen K, Brand LE, Blackwelder PL, Guillard RRL (1982) Thoracosphaera heimii (Lohmann) Kamptner is a dinophyte: Observations on its morphology and life cycle. Mar Micropaleontol 7:193–212. https://doi.org/10.1016/0377-8398(82)90002-0
Tani Y, Ohashi M, Miyata N et al (2004) Sorption of Co(II), Ni(II), and Zn(II) on biogenic manganese oxides produced by a Mn-Oxidizing Fungus, Strain KR21-2. J Environ Sci Heal Part A 39:2641–2660. https://doi.org/10.1081/ESE-200027021
Tappan HN (1980) The paleobiology of plant protists. Freeman, San Francisco
Taylor DL (1968) In situ studies on the cytochemistry and ultrastructural of a symbiotic marine dinoflagellate. J Mar Biol Ass U K 48:349–366
Taylor AR, Brownlee C, Wheeler G (2017) Coccolithophore cell biology: chalking up progress. Ann Rev Mar Sci 9:283–310. https://doi.org/10.1146/annurev-marine-122414-034032
Tebo BM, Bargar JR, Clement BG et al (2004) Biogenic manganese oxides: properties and mechanisms of formation. Annu Rev Earth Planet Sci 32:287–328. https://doi.org/10.1146/annurev.earth.32.101802.120213
Tebo BM, Ghiorse WC, van Waasbergen LG et al (2019) Bacterially mediated mineral formation: Insights into manganese(II) oxidation from molecular genetic and biochemical studies. In: Geomicrobiology: interactions between microbes and minerals. Mineralogical Society of America, Washington DC, pp 225–266
Templeton AS, Trainor TP, Spormann AM et al (2003) Sorption versus Biomineralization of Pb(II) within Burkholderia cepacia Biofilms. Environ Sci Technol 37:300–307. https://doi.org/10.1021/es025972g
Tendal OS (1972) A monograph of the Xenophyophoria (Rhizopodea, Protozoa). Galathea Rep 12:7–100
Teske A, Nelson DC (2006) The genera beggiatoa and thioploca. In: The prokaryotes. Springer, New York, pp 784–810
Teske A, Ramsing NB, Küver J, Fossing H (1995) Phylogeny of thioploca and related filamentous sulfide-oxidizing bacteria. Syst Appl Microbiol 18:517–526. https://doi.org/10.1016/S0723-2020(11)80412-1
Thode HG, Macnamara J, Fleming WH (1953) Sulphur isotope fractionation in nature and geological and biological time scales. Geochim Cosmochim Acta 3:235–243. https://doi.org/10.1016/0016-7037(53)90042-8
Thompson JB, Ferris FG (1990) Cyanobacterial precipitation of gypsum, calcite, and magnesite from natural alkaline lake water. Geology 18:995. https://doi.org/10.1130/0091-7613(1990)018<0995:CPOGCA>2.3.CO;2
Thompson IA, Huber DM, Guest CA, Schulze DG (2005) Fungal manganese oxidation in a reduced soil. Environ Microbiol 7:1480–1487. https://doi.org/10.1111/j.1462-2920.2005.00842.x
Tiessen H (2008) Phosphorus in the global environment. Springer, Dordrecht, pp 1–7
Torriani-Gorini A, Yagil E, Silver S (1994) Phosphate in microorganisms: cellular and molecular biology. Zondervan, Grand Rapids
Traquair JA (1987) Oxalic acid and calcium oxalate produced by Leucostoma cincta and L. persoonii in culture and in peach bark tissues. Can J Bot 65:1952–1956. https://doi.org/10.1139/b87-267
Tuason MMS, Arocena JM (2009) Calcium oxalate biomineralization by Piloderma fallax in response to various levels of calcium and phosphorus. Appl Environ Microbiol 75:7079–7085. https://doi.org/10.1128/AEM.00325-09
Urbanus JFLM, van den Ende H, Koch B (1978) Calcium oxalate crystals in the wall of mucor mucedo. Mycologia 70:829–842. https://doi.org/10.1080/00275514.1978.12020288
Vainshtein M, Suzina N, Sorokin V (1997) A new type of magnet-sensitive inclusions in cells of photosynthetic purple bacteria. Syst Appl Microbiol 20:182–186. https://doi.org/10.1016/S0723-2020(97)80064-1
Vainshtein M, Kudryashova E, Suzina N et al (1998) Functions of non-crystal magnetosomes in bacteria. In: Hoover RB (ed) Instruments, methods, and missions for astrobiology. SPIE, Bellingham, WA, pp 280–288
Vainshtein M, Suzina N, Kudryashova E, Ariskina E (2002) New magnet-sensitive structures in bacterial and archaeal cells. Biol Cell 94:29–35. https://doi.org/10.1016/S0248-4900(02)01179-6
Vainshtein M, Belova N, Kulakovskaya T et al (2014) Synthesis of magneto-sensitive iron-containing nanoparticles by yeasts. J Ind Microbiol Biotechnol 41:657–663. https://doi.org/10.1007/s10295-014-1417-4
Vali H, Weiss B, Li Y-L et al (2004) Formation of tabular single-domain magnetite induced by Geobacter metallireducens GS-15. Proc Natl Acad Sci 101:16121–16126. https://doi.org/10.1073/PNAS.0404040101
Van Driessche AES, Stawski TM, Kellermeier M (2019) Calcium sulfate precipitation pathways in natural and engineered environments. Chem Geol 530:119274. https://doi.org/10.1016/j.chemgeo.2019.119274
Van Lith Y, Warthmann R, Vasconcelos C, Mckenzie JA (2003a) Sulphate-reducing bacteria induce low-temperature Ca-dolomite and high Mg-calcite formation. Geobiology 1:71–79. https://doi.org/10.1046/j.1472-4669.2003.00003.x
Van Lith Y, Warthmann R, Vasconcelos C, McKenzie JA (2003b) Microbial fossilization in carbonate sediments: a result of the bacterial surface involvement in dolomite precipitation. Sedimentology 50:237–245. https://doi.org/10.1046/j.1365-3091.2003.00550.x
Vasconcelos C, McKenzie JA, Bernasconi S et al (1995) Microbial mediation as a possible mechanism for natural dolomite formation at low temperatures. Nature 377:220–222. https://doi.org/10.1038/377220a0
Verrecchia EP (2000) Fungi and sediments. In: Microbial sediments. Springer, Berlin, Heidelberg, pp 68–75
Verrecchia EP, Dumont J-L, Rolko KE (1990) Do fungi building limestones exist in semi-arid regions? Sci Nat 77:584–586
Vetter RD (1985) Elemental sulfur in the gills of three species of clams containing chemoautotrophic symbiotic bacteria: a possible inorganic energy storage compound. Mar Biol 88:33–42. https://doi.org/10.1007/BF00393041
Villalobos M, Toner B, Bargar J, Sposito G (2003) Characterization of the manganese oxide produced by Pseudomonas putida strain MnB1. Geochim Cosmochim Acta 67:2649–2662. https://doi.org/10.1016/S0016-7037(03)00217-5
Wacey D, Kilburn MR, Saunders M et al (2015) Uncovering framboidal pyrite biogenicity using nano-scale CNorg mapping. Geology 43:27–30. https://doi.org/10.1130/G36048.1
Wadsten T, Moberg R (1985) Calcium oxalate hydrates on the surface of lichens. Lichenol 17:239–245. https://doi.org/10.1017/S0024282985000305
Walker JM, Marzec B, Lee RBY et al (2019) Polymorph selectivity of coccolith-associated polysaccharides from Gephyrocapsa Oceanica on calcium carbonate formation in vitro. Adv Funct Mater 29:1807168. https://doi.org/10.1002/adfm.201807168
Wall D, Guillard RRL, Dale B et al (1970) Calcitic resting cysts in Peridinium trochoideum (Stein) Lemmermann, an autotrophic marine dinoflagellate. Phycologia 9:151–156. https://doi.org/10.2216/i0031-8884-9-2-151.1
Wallander H (2000) Uptake of P from apatite by Pinus sylvestris seedlings colonised by different ectomycorrhizal fungi. Plant Soil 218(2):249–256. https://doi.org/10.1023/A:1014936217105
Wallner J (1933) Oocardium stratum Naeg., eine wichtige tuffbildende Alge Südbayerns. Planta 20:287–293. https://doi.org/10.1007/BF01909569
Warthmann R, van Lith Y, Vasconcelos C et al (2000) Bacterially induced dolomite precipitation in anoxic culture experiments. Geology 28:1091. https://doi.org/10.1130/0091-7613(2000)28<1091:BIDPIA>2.0.CO;2
Webb SM, Tebo BM, Bargar JR (2005) Structural characterization of biogenic Mn oxides produced in seawater by the marine bacillus sp. strain SG-1. Am Mineral 90:1342–1357. https://doi.org/10.2138/am.2005.1669
Weiner S, Dove PM (2003) An overview of biomineralization processes and the problem of the vital effect. Rev Mineral Geochemistry 54:1–29. https://doi.org/10.2113/0540001
Wendler JE, Bown P (2013) Exceptionally well-preserved Cretaceous microfossils reveal new biomineralization styles. Nat Commun 4:2052. https://doi.org/10.1038/ncomms3052
West GS, Griffiths BM (1913) The lime-sulphur bacteria of the genus hillhousia. Ann Bot (Lond) 27:83–91. https://doi.org/10.1093/oxfordjournals.aob.a089453
Whitney KD, Arnott HJ (1986) Morphology and development of calcium oxalate deposits in Gilbertella persicaria (Mucorales). Mycologia 78:42. https://doi.org/10.2307/3793375
Wierzchos J, Cámara B, De los Ríos A et al (2011) Microbial colonization of Ca-sulfate crusts in the hyperarid core of the atacama desert: implications for the search for life on Mars. Geobiology 9:44–60. https://doi.org/10.1111/j.1472-4669.2010.00254.x
Wilbur KM, Watabe N (1963) Experimental studies on calcification in molluscs and the alga coccolithus huxleyi. Ann N Y Acad Sci 109:82–112. https://doi.org/10.1111/j.1749-6632.1963.tb13463.x
Wilcock JR, Perry CC, Williams RJP, Mantoura RFC (1988) Crystallographic and morphological studies of the celestite skeleton of the acantharian species Phyllostaurus siculus. Proc R Soc London Ser B Biol Sci 233:393–405. https://doi.org/10.1098/rspb.1988.0029
Wilcock JR, Perry CC, Williams RJP, Brook AJ (1989) Biological minerals formed from strontium and barium sulphates. II. Crystallography and control of mineral morphology in desmids. Proc R Soc B Biol Sci 238:203–221. https://doi.org/10.1098/rspb.1989.0077
Wilkin RT, Barnes HL (1997) Formation processes of framboidal pyrite. Geochim Cosmochim Acta 61:323–339. https://doi.org/10.1016/S0016-7037(96)00320-1
Williams KH, Ntarlagiannis D, Slater LD et al (2005) Geophysical imaging of stimulated microbial biomineralization. Environ Sci Technol 39(19):7592–7600. https://doi.org/10.1021/ES0504035
Wilson MJ, Jones D (1984) The occurrence and significance of manganese oxalate in Pertusaria corallina (Lichenes). Pedobiologia (Jena) 26:373–379
Wilson MJ, Jones D, Russell JD (1980) Glushinskite, a naturally occurring magnesium oxalate. Mineral Mag 43:837–840. https://doi.org/10.1180/minmag.1980.043.331.02
Winogradsky S (1887) Über Schwefelbakterien. Bot Zeitung 45:489–610
Wu J, Wang HF, Bin WX et al (2017) Design and characterization of a microbial self-healing gel for enhanced oil recovery. RSC Adv 7:2578–2586. https://doi.org/10.1039/c6ra25814j
Yamashita H, Kobiyama A, Koike K (2009) Do uric acid deposits in zooxanthellae function as eye-spots? PLoS One 4:e6303. https://doi.org/10.1371/journal.pone.0006303
Yang M, Zhan Y, Zhang S et al (2020) Biological materials formed by Acidithiobacillus ferrooxidans and their potential applications. 3 Biotech 10:475. https://doi.org/10.1007/s13205-020-02463-3
Yates KK, Robbins LL (1998) Production of carbonate sediments by a unicellular green alga. Am Mineral 83:1503–1509. https://doi.org/10.2138/am-1998-1111
Yoshida H, Yamamoto K, Murakami Y et al (2008) The development of Fe-nodules surrounding biological material mediated by microorganisms. Environ Geol 55:1363–1374. https://doi.org/10.1007/s00254-007-1087-x
Young JR (2003) Biomineralization within vesicles: the calcite of coccoliths. Rev Mineral Geochem 54:189–215. https://doi.org/10.2113/0540189
Zachara JM, Fredrickson JK, Li S-M et al (1998) Bacterial reduction of crystalline Fe (super 3+) oxides in single phase suspensions and subsurface materials. Am Mineral 83:1426–1443. https://doi.org/10.2138/am-1998-11-1232
Zamarreño DV, Inkpen R, May E (2009) Carbonate crystals precipitated by freshwater bacteria and their use as a limestone consolidant. Appl Environ Microbiol 75:5981–5990. https://doi.org/10.1128/AEM.02079-08
Zavarzin GA (1961) Symbiotic culture of a new manganese-oxidizing microorganism. Mikrobiologiia 30:393–395
Zavarzin GA (1962) Symbiotic oxidation of manganese by two species of Pseudomonas. Microbiology 31:481–482
Zavarzin GA (1981) The genus metallogenium. In: The prokaryotes. Springer, Berlin, Heidelberg, pp 524–528
Zegeye A, Huguet L, Abdelmoula M et al (2007) Biogenic hydroxysulfate green rust, a potential electron acceptor for SRB activity. Geochim Cosmochim Acta 71:5450–5462. https://doi.org/10.1016/J.GCA.2007.08.025
Zhang C, Liu S, Phelps TJ et al (1997) Physiochemical, mineralogical, and isotopic characterization of magnetite-rich iron oxides formed by thermophilic iron-reducing bacteria. Geochim Cosmochim Acta 61:4621–4632. https://doi.org/10.1016/S0016-7037(97)00257-3
Zhang C, Vali H, Romanek CS et al (1998) Formation of single-domain magnetite by a thermophilic bacterium. Am Mineral 83:1409–1418. https://doi.org/10.2138/am-1998-1103
Zhang J, Lion LW, Nelson YM et al (2002) Kinetics of Mn(II) oxidation by Leptothrix discophora SS1. Geochim Cosmochim Acta 66:773–781. https://doi.org/10.1016/S0016-7037(01)00808-0
Zhang C, Lv J, Li F, Li X (2017a) Nucleation and Growth of Mg-Calcite Spherulites Induced by the Bacterium Curvibacter lanceolatus Strain HJ-1. Microsc Microanal 23:1189–1196. https://doi.org/10.1017/S1431927617012715
Zhang J, Zhou A, Liu Y et al (2017b) Microbial network of the carbonate precipitation process induced by microbial consortia and the potential application to crack healing in concrete. Sci Rep 7:1–10. https://doi.org/10.1038/s41598-017-15177-z
Zhou C, Vannela R, Hayes KF, Rittmann BE (2014) Effect of growth conditions on microbial activity and iron-sulfide production by Desulfovibrio vulgaris. J Hazard Mater 272:28–35. https://doi.org/10.1016/J.JHAZMAT.2014.02.046
Ziegler S, Ackermann S, Majzlan J, Gescher J (2009) Matrix composition and community structure analysis of a novel bacterial pyrite leaching community. Environ Microbiol 11:2329–2338. https://doi.org/10.1111/j.1462-2920.2009.01959.x
Zonneveld KAF, Meier KJS, Esper O et al (2005) The (palaeo-) environmental significance of modern calcareous dinoflagellate cysts: a review. Atlantic 79:61–77. https://doi.org/10.1007/BF03021754
Zou Z, Habraken WJEM, Matveeva G et al (2019) Solid-state chemistry: a hydrated crystalline calcium carbonate phase: Calcium carbonate hemihydrate. Science (80-) 363:396–400. https://doi.org/10.1126/science.aav0210
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Jantschke, A. (2022). Non-silicate Minerals (Carbonates, Oxides, Phosphates, Sulfur-Containing, Oxalates, and Other Organic Crystals) Induced by Microorganisms. In: Berenjian, A., Seifan, M. (eds) Mineral Formation by Microorganisms. Microbiology Monographs, vol 36. Springer, Cham. https://doi.org/10.1007/978-3-030-80807-5_6
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