A non-classical crystallization mechanism of microbially-induced disordered dolomite

May combine two claims.

After 10-day incubation, an XRD peak at 30.76° 2θ (d-spacing 2.904 Å) matched the (104) reflection of (disordered-)dolomite, and Raman bands were consistent with disordered dolomite.

“Notably, the characteristic peak at 30.76° 2θ (corresponding to a d-spacing of 2.904 Å) closely matched the (104) reflection of (disordered-)dolomite (Gregg et al., 2015).”

• Also stated in: § 3.1.2. XRD, Raman and microscopic evidence for precursor ACMC involved in bioprecipitated disordered dolomite · plain

  “In addition, Raman analysis also revealed the presence of four distinct bands (Fig. 3b), which were consistent with those observed in disordered dolomite described in the literature (Fan et al., 2023).”

• cites Gregg et al., 2015 sourceNot checked — no full text of the source
• cites Fan et al., 2023 sourcePartly supported

  Section 2.3 identifies a (104) XRD reflection in the precipitates and classifies the disordered carbonate as protodolomite; Section 2.4 reports Raman bands. But Section 1.5 says the precipitates were collected after 14 days, not 10, and the copy does not report an XRD peak at 30.76° 2θ or a 2.904 Å spacing. Section 2.6 instead gives an approximately 2.910 Å (104) spacing measured by TEM. (LLM, conf=0.88)

  Experimental — accuracy not yet measured

Classified as probably not a substantial claim.

Recent abiotic synthesis experiments have highlighted the potential involvement of the NCC pathway in the precipitation of Ca-Mg carbonates, particularly under high saturation conditions.

“Noticeably, recent abiotic synthesis experiments have highlighted the potential involvement of the NCC pathway in the precipitation of Ca-Mg carbonates, particularly under high saturation conditions.”

• cites Al Disi et al., 2021 sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

Non-classical crystallization is a common route to the formation of carbonate shells and skeletons in invertebrates, as evidenced by transient ACC.

“Growing experimental evidence showed that NCC is a common route to the formation of carbonate shells and skeletons in invertebrates, as evidenced by the presence of transient ACC (Addadi et al., 2003;Gong et al., 2012;Grünewald et al., 2022).”

• cites Addadi et al., 2003 sourceNot checked — no full text of the source
• cites Gong et al., 2012 sourceSupported
• cites Grünewald et al., 2022 sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

This unique feature provides a large surface area that facilitates exchange of solutes between ACMC and surrounding reactive solution.

“This unique feature provides a large surface area that facilitates the exchange of solutes between ACMC and the surrounding reactive solution (Goetschl et al., 2021).”

• cites Goetschl et al., 2021 sourceSupported

Probably not a substantial claim: may not pass S3 (load-bearing).

Dry heating can induce crystallization of ACMC into dolomite through solid-state transformation.

“Dry heating, for example, can induce the crystallization of ACMC into dolomite through solid-state transformation (Sugawara et al., 2022).”

• cites Sugawara et al., 2022 sourceSupported

The quote only partly states this claim.

The growth of strain JBHLT-1 resulted in an increase of pH and alkalinity in the biotic sets.

“The growth of strain JHBH-1 resulted in the increase of pH (Fig. 2a) and alkalinity (Fig. 2b).”

May combine two claims.

In the abiotic sets, pH and alkalinity remained relatively constant.

“Conversely, these parameters remained relatively constant in the abiotic sets.”

May combine two claims.

The amorphous phase collected on day 4 appeared as nano-spheres with an average size of 65 nm, had similar Mg and Ca content, and was identified as dolomite-like ACMC.

“In STEM bright-field mode, the amorphous phase was observed as nano-spheres with an average size of 65 nm (Fig. 4b, c) and showed sensitivity to electron beam irradiation (Fig. 4c).”

• Also stated in: § 3.1.2. XRD, Raman and microscopic evidence for precursor ACMC involved in bioprecipitated disordered dolomite · hedged

  “Semi-quantification of EDS analyses indicated that the amorphous phase had similar levels of Mg and Ca content (Fig. 4b), suggesting it could be identified as dolomite-like ACMC.”

May combine two claims.

The biotic ACMC sample with 0.5 g/L biomass had a MgCO3 content of 48.77 mol%, qualifying it as dolomite-like ACMC.

“It is interesting to note that the biotic ACMC sample with 0.5 g/L biomass had a MgCO3 content of 48.77 mol%, qualifying it as dolomite-like ACMC.”

May combine two claims.

The Mg content in the biogenic ACMC was the same as that of Ca, indicating a stoichiometry similar to (disordered-)dolomite.

“The Mg content in this biogenic ACMC was found to be the same as that of Ca (Fig. 4b), indicating a stoichiometry similar to (disordered-)dolomite.”

May combine two claims.

In the biomineralization experiments, ACMC emerged at least by day 4 and persisted until day 10.

“In our biomineralization experiments, ACMC was observed to emerge at least by day 4 and persist until day 10 (Fig. 3).”

May combine two claims. The quote only partly states this claim.

By day 30, biogenic dolomite grew into dumbbell-shaped morphologies around 20 μm, with a polycrystalline texture and nano-granular surface.

“By day 30, the biogenic dolomite continued to grow in size, with the emergence of notable dumbbell-shaped morphologies around 20 μm in size (Fig. 4f).”

• Also stated in: § 3.1.2. XRD, Raman and microscopic evidence for precursor ACMC involved in bioprecipitated disordered dolomite · plain

  “This observation was further supported by high-resolution TEM (HRTEM) that showed a polycrystalline texture (Fig. 4h).”

May combine two claims.

As a consequence of microbial activity, concentrations of Ca2+ and Mg2+ decreased gradually over time, indicating bioprecipitation of Ca-Mg carbonate(s) in the biosystems.

“As a consequence of microbial activity, the concentrations of Ca 2+ and Mg 2+ decreased gradually over time (Fig. 2c), indicating the occurrence of bioprecipitation of Ca-Mg carbonate(s) in the biosystems.”

May combine two claims.

Biogenic ACMC induced by strain JBHLT-1 exhibited a stoichiometry similar to dolomite, while abiotic ACMC synthesized under the same conditions had significantly lower Mg content.

“According to Experiment II, it was found that biogenic ACMC induced by strain JBHLT-1 exhibited a stoichiometry similar to dolomite, while abiotic ACMC synthesized under the same conditions had significantly lower Mg content (more details can be found in Section 3.3).”

May combine two claims.

In the biotic sets, pH increased from ca.7.78 to 8.40 at day 30, and solution alkalinity increased from 3.904 to 150.038 mM by day 30.

“Specifically, in the biotic sets, the pH increased from an initial value of ca.7.78 to 8.40 at day 30, and the solution alkalinity increased from 3.904 (at day 0) to 150.038 mM by day 30.”

May combine two claims. The quote only partly states this claim.

After 10-day incubation, bioprecipitates coalesced into spheroids about 4 to 6 μm with granular-texture surfaces and were characterized as poorly-crystalline disordered dolomite.

“After 10-day incubation, the bioprecipitates tended to coalesce into spheroids about 4 to 6 μm and with granular-texture surfaces (Fig. 4e).”

• Also stated in: § 3.1.2. XRD, Raman and microscopic evidence for precursor ACMC involved in bioprecipitated disordered dolomite · plain

  “Based on the EDS result and the earlier XRD data, these bioprecipitates were characterized as poorly-crystalline disordered dolomite.”

May combine two claims.

In Experiment III, transformation of abiotic ACMC occurred via a dissolution-reprecipitation route, resulting in loss of Mg2+ from ACMC as attested by its transformation to high-Mg calcite with a Mg content lower than that of initial ACMC.

“In Experiment III, the transformation of abiotic ACMC occurred via a dissolution-reprecipitation route, resulting in the loss of Mg 2+ from ACMC as attested by its transformation to high-Mg calcite with a Mg content lower than that of the initial ACMC.”

May combine two claims.

At end of 30-day incubation, size of biogenic disordered dolomite significantly increased, accompanied by morphological change into dumbbell shape.

“At the end of the 30-day incubation, the size of biogenic disordered dolomite significantly increased, accompanied by a morphological change into a dumbbell shape (Fig. 4f).”

May combine two claims.

Strain JBHLT-1 possesses the ability to increase solution pH through ammonification of peptone and to elevate solution alkalinity through respiration of yeast extract.

“In general, strain JBHLT-1 possesses the ability to increase solution pH through ammonification of peptone present in the precipitation medium (peptone → NH3 + H2O → NH4 + + OH -) and elevate the solution alkalinity through respiration of yeast extract (yeast extract → CO2 + H2O → HCO3 -+ H + ) (Liu et al., 2019a).”

• cites Liu et al., 2019aNot matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Classified as probably not a substantial claim.

Microbial activity can overcome the kinetic barriers to dolomite nucleation.

“A huge amount of research has been conducted to unravel the mechanisms and kinetics of dolomite crystallization, and one of most exciting achievements is that microbial activity can overcome the kinetic barriers to dolomite nucleation (e.g., Vasconcelos et al., 1995;Roberts et al., 2004;Sánchez-Román et al., 2008;McKenzie and Vasconcelos, 2009;Deng et al., 2010;Bontognali et al., 2014;Petrash et a”

• cites Vasconcelos et al., 1995 sourceNot checked — no full text of the source
• cites Roberts et al., 2004 sourceNot checked — no full text of the source
• cites Sánchez-Román et al., 2008 sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

Amorphous calcium carbonate (ACC) is often observed during the pre-nucleation stages of CaCO3 polymorph crystallization.

“For instance, growing evidence shows that amorphous calcium carbonate (ACC) is often observed during the pre-nucleation stages of CaCO3 polymorph crystallization, such as calcite, aragonite, and vaterite (e.g., Rodriguez-Blanco et al., 2011;Rodriguez-Navarro et al., 2015;Purgstaller et al., 2016).”

• cites Rodriguez-Blanco et al., 2011 sourceNot checked — no full text of the source
• cites Rodriguez-Navarro et al., 2015Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

• cites Purgstaller et al., 2016 sourceNot checked — no full text of the source

May combine two claims.

The microbially-induced growth of disordered dolomite followed a spherulitic growth mechanism, evidenced by a hierarchical structure of coalesced nano-spheres growing into micron-sized spheroids and dumbbells with extended incubation.

“The microbially-induced growth of disordered dolomite appeared to follow a spherulitic growth mechanism, as evidenced by its hierarchical structure composed of coalesced nano-spheres, eventually growing into micron-sized spheroids and dumbbells with extended incubation times.”

May combine two claims.

In the stage of ACMC crystallization, the presence of microbial biomass reduced the dissolution-reprecipitation rate and induced a bias towards a solid-state reaction pathway.

“In the stage of ACMC crystallization, the presence of microbial biomass reduced the dissolution-reprecipitation rate and induced bias towards a solid-state reaction pathway.”

Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Disordered dolomite (with 36-55 mol% Mg2+) possesses the same space group as calcite but has a higher Mg content than Mg-calcite (<36 mol% Mg2+).

“Disordered dolomite (with 36-55 mol% Mg 2+ ) possesses the same space group as calcite, but with a higher Mg content compared with Mg-calcite (<36 mol% Mg 2+ ) (Zhang et al., 2012).”

• cites Zhang et al., 2012 sourceNot checked — no full text of the source

Classified as probably not a substantial claim. May combine two claims.

Microbially-induced dolomites produced in most experimental studies are Mg-Ca disordered and should be termed disordered dolomite or protodolomite stricto senso.

“Since microbially-induced dolomites produced in most experimental studies are Mg-Ca disordered (Gregg et al., 2015), they should be termed as disordered dolomite or protodolomite stricto senso (Zhang et al., 2012;Gregg et al., 2015;Kaczmarek et al., 2017).”

• cites Gregg et al., 2015 sourceNot checked — no full text of the source
• cites Zhang et al., 2012 sourceNot checked — no full text of the source
• cites Kaczmarek et al., 2017 sourceNot checked — no full text of the source

Classified as probably not a substantial claim.

The abiotic controls were identical to the biotic systems except that cells were replaced with an equal volume of medium.

“The abiotic controls were identical to the biotic systems, except that cells were replaced with an equal volume of medium.”

Probably not a substantial claim: may not pass S3 (load-bearing).

Disordered dolomite can progressively transform into ordered dolomite under burial conditions.

“Nevertheless, given the metastable nature of disordered dolomite, it can progressively transform into ordered dolomite under burial conditions (Zheng et al., 2021).”

• cites Zheng et al., 2021 sourceNot checked — no full text of the source

May combine two claims.

The size of surface pores in disordered dolomite aggregates matched the cell diameter of strain JBHLT-1, suggesting that microbial cells acted as templates during crystallization.

“Notably, the size of these pores matched the cell diameter of strain JBHLT-1, suggesting that the microbial cells acted as templates during the crystallization process.”

Classified as probably not a substantial claim.

The stoichiometry of disordered dolomite was determined by calculating the position of the (104) peak using a calibrated curve developed by Bischoff et al. (1983).

“The stoichiometry of disordered dolomite was determined by calculating the position of the (104) peak using a calibrated curve developed by Bischoff et al. (1983).”

• cites Bischoff et al., 1983Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S1 (asserted), S3 (load-bearing).

Microorganisms catalyze the formation of low-temperature dolomite by increasing the dehydration rate of Mg2+.

“It has been thought that microorganisms catalyze the formation of low-temperature of dolomite by increasing the dehydration rate of Mg 2+ (Kenward et al., 2013).”

• cites Kenward et al., 2013 sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

The chemical measurements were performed in duplicate.

“The above measurements were performed in duplicate.”

Probably not a substantial claim: may not pass S3 (load-bearing).

All experimental flasks, including both biotic and abiotic systems, were incubated in duplicate.

“All experimental flasks, including both biotic and abiotic systems, were incubated in the dark at 30 °C and shaken at 160 rpm in duplicate.”

Classified as probably not a substantial claim.

Adsorption of hydrophobic organic molecules onto surface of ACMC creates a hydrophobic layer.

“It has been proposed that the adsorption of hydrophobic organic molecules onto the surface of ACMC creates a hydrophobic layer (Yu et al., 2017).”

• cites Yu et al., 2017Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Classified as probably not a substantial claim.

Hydrophobic nature of microbial cells is ascribed to presence of non-polar moieties, such as aromatics and aliphatic regions in surface-associated proteins.

“Specifically, the hydrophobic nature of microbial cells is ascribed to the presence of non-polar moieties, such as aromatics and aliphatic regions in surface-associated proteins.”

• cites van der Mei et al., 1998 sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

At moderate levels of supersaturation, crystals form in equilibrium with their morphology primarily determined by shape of their unit cell.

“At moderate levels of supersaturation (i.e., insufficient driving force), crystals form in equilibrium with their morphology primarily determined by the shape of their unit cell.”

• cites Gránásy et al., 2005Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S3 (load-bearing).

Similar observations have been made in aqueous solution containing lipid vesicles.

“Similar observations have also been made in an aqueous solution containing lipid vesicles (Yu et al., 2017).”

• cites Yu et al., 2017Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

May combine two claims.

This layer limits water content on ACMC surface, which retards dissolution-reprecipitation rate and favors solid-state reaction pathway, thereby retaining Mg levels in Ca-Mg carbonates.

“This layer limits the water content on the ACMC surface, which in turn retards the dissolution-reprecipitation rate and favors the solid-state reaction pathway, thereby retaining the Mg levels in Ca-Mg carbonates.”

• cites Yu et al., 2017Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Probably not a substantial claim: may not pass S3 (load-bearing).

Crystallization of ACMC in mixtures of organic solvent (tetrahydrofuran or dioxane) and water can yield disordered dolomite.

“For instance, Lenders and his colleagues demonstrated that crystallization of ACMC in mixtures of organic solvent (tetrahydrofuran or dioxane) and water can yield disordered dolomite (Lenders et al., 2012).”

• cites Lenders et al., 2012 sourceNot checked — no full text of the source

Probably not a substantial claim: may not pass S3 (load-bearing).

Increasing levels of supersaturation can lead to formation of dendritic polycrystals with highly disequilibrium morphology, often appearing as spherular radial structures.

“However, increasing the levels of supersaturation can lead to the formation of dendritic polycrystals with highly disequilibrium morphology, often appearing as spherular radial structures (Gránásy et al., 2005).”

• cites Gránásy et al., 2005Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Classified as probably not a substantial claim.

Microbes have both hydrophilic and hydrophobic properties due to presence of various functional groups on surface of cell wall and within EPS.

“It has been well documented that microbes have both hydrophilic and hydrophobic properties due to the presence of various functional groups on the surface of cell wall and within EPS (van der Mei et al., 1998;Al Disi et al., 2019;Zheng et al., 2021).”

• cites van der Mei et al., 1998 sourceNot checked — no full text of the source
• cites Al Disi et al., 2019 sourceNot checked — no full text of the source
• cites Zheng et al., 2021 sourceNot checked — no full text of the source

May combine two claims.

Conversion of ACMC to disordered dolomite can be interpreted to most likely have occurred through solid-state transformation instead of dissolution-reprecipitation process, explaining why Mg content of resulting crystalline byproduct remained high.

“In this regard, the conversion of ACMC to disordered dolomite can be interpreted to most likely have occurred through a solid-state transformation instead of the dissolution-reprecipitation process, explaining why in this case the Mg content of the resulting crystalline byproduct remained high (Fig. 9).”

• AssumptionRests on an assumption: The energy difference between ACMC and disordered dolomite is the driving force of the solid-state reaction.

Probably not a substantial claim: may not pass S3 (load-bearing).

A similar mechanism may be involved in ACMC transformation in presence of microbes.

“A similar mechanism may be involved in the ACMC transformation in the presence of microbes.”

May combine two claims.

Through three sets of experiments, microbially-induced disordered dolomite proceeded through spherulitic growth, with ACMC serving as a transient phase.

“Through three sets of experiments, we demonstrated that microbially-induced disordered dolomite proceeded through spherulitic growth, with ACMC serving as a transient phase.”

Classified as probably not a substantial claim. May combine two claims.

Solution saturation commonly acts as thermodynamic driving force that governs crystal growth rate and impacts its shape.

“Because solution saturation commonly acts as the thermodynamic driving force that not only governs the crystal growth rate but also impacts its shape (Gránásy et al., 2005).”

• cites Gránásy et al., 2005Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

Classified as probably not a substantial claim.

Spherulitic growth is known for its rapid process, where new nanoparticles continuously nucleate on surface of pre-existing particles.

“Spherulitic growth is known for its rapid process, where new nanoparticles continuously nucleate on the surface of pre-existing particles (Rodriguez-Blanco et al., 2011).”

• cites Rodriguez-Blanco et al., 2011 sourceNot checked — no full text of the source

May combine two claims.

Nanoparticle aggregates have been observed in Holocene dolomites, as well as in some ancient dolomites.

“Nanoparticle aggregates have been observed in Holocene dolomites (e.g., Bontognali et al., 2010;Nyirö-Kása et al., 2018;Raudsepp et al., 2022), as well as in some ancient dolomites (Perri and Tucker, 2007;Sánchez-Román et al., 2008;Sun et al., 2023).”

• cites Bontognali et al., 2010Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

• cites Perri and Tucker, 2007 sourceNot checked — no full text of the source
• cites Sun et al., 2023Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

May combine two claims.

This particular microscopic morphology is indicative of fluid chemistry conditions under which dolomite is formed and cannot serve as a biosignature.

“Therefore, this particular microscopic morphology is indicative of fluid chemistry conditions under which dolomite is formed and cannot serve as a biosignature.”

Probably not a substantial claim: may not pass S1 (asserted), S3 (load-bearing). May combine two claims.

This unique morphology and texture were considered as potential biomarkers suggesting microbial activity or presence of fossilized bacteria or viruses.

“This unique morphology and texture were considered as potential biomarkers suggesting microbial activity or the presence of fossilized bacteria or viruses (e.g., Perri and Tucker, 2007;Sun et al., 2023).”

• cites Perri and Tucker, 2007 sourceNot checked — no full text of the source
• cites Sun et al., 2023Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.