The hidden role of heterotrophic bacteria in early carbonate diagenesis

Mónica Sánchez-Román; Viswasanthi Chandra; Sebastian Mulder; Camila Areias; John Reijmer; Volker Vahrenkamp

doi:10.1038/s41598-024-84407-y

The hidden role of heterotrophic bacteria in early carbonate diagenesis

Mónica Sánchez-Román, Viswasanthi Chandra, Sebastian Mulder, Camila Areias, John Reijmer, Volker Vahrenkamp

Research output: Contribution to Journal › Article › Academic › peer-review

Abstract

Microbial impacts on early carbonate diagenesis, particularly the formation of Mg-carbonates at low temperatures, have long eluded scientists. Our breakthrough laboratory experiments with two species of halophilic aerobic bacteria and marine carbonate grains reveal that these bacteria created a distinctive protodolomite (disordered dolomite) rim around the grains. Scanning Electron Microscopy (SEM) and X-ray Diffraction (XRD) confirmed the protodolomite formation, while solid-state nuclear magnetic resonance (NMR) revealed bacterial interactions with carboxylated organic matter, such as extracellular polymeric substances (EPS). We observed a significant carbon isotope fractionation (average δ13C = 11.3‰) and notable changes in Mg/Ca ratios throughout the experiments. Initial medium δ13C was − 18‰, sterile sediments were at 2‰ (n = 12), bacterial-altered sediments were − 6.8‰ (n = 12), and final medium δ13C was − 4.7‰. These results highlight the role of bacteria in driving organic carbon sequestration into Mg-rich carbonates and demonstrate the utility of NMR as a tool for detecting microbial biosignatures. This has significant implications for understanding carbonate diagenesis (dissolution and reprecipitation), climate science, and extraterrestrial research.

Original language	English
Article number	561
Pages (from-to)	1-14
Number of pages	14
Journal	Scientific Reports
Volume	15
Early online date	2 Jan 2025
DOIs	https://doi.org/10.1038/s41598-024-84407-y
Publication status	Published - 2025

Funding

We acknowledge the time and effort devoted by two anonymous reviewers and the editor (Y. He) to improving the quality of this manuscript. B. Brenha, J. Chin, H. Spaa, S. Wieling, and B. Scheffer are greatly acknowledged for their assistance with laboratory work, XRD, SEM-EDS, stable isotopes, NMR analyses and data interpretation during their bachelor thesis projects conducted at the Vrije Universiteit Amsterdam in 2018/2019/2020 under the supervision of MSR. We acknowledge Suzan Verdegaal-Wardemam for her kind assistance with stable C and O isotope analysis. We thank Alessandro Genovese and Edy Abou-Hamad from KAUST imaging and characterization corelabs for assistance with SEM and NMR analyses, respectively. T. Yao is gratefully acknowledged for discussions on NMR data, and Z. Naim for assistance with the figures. We recognize the KAUST VSRP program for supporting Sebastian\u2019s Mulder\u2019s internship at Vrije Universiteit Amsterdam. This work was supported by the Dutch Research Council (NWO) Projects OCENW.KLEIN.037 to MSR, and the Competitive Research Grant (CRG) of the King Abdullah University of Science and Technology (KAUST) Grant OSR Nr. 4097 to VV and MSR. We acknowledge support to VC through KAUST baseline funding to VV. We acknowledge the time and effort devoted by two anonymous reviewers and the editor (Y. He) to improving the quality of this manuscript.\u00A0B. Brenha, J. Chin, H. Spaa, S. Wieling, and B. Scheffer are greatly acknowledged for their assistance with laboratory work, XRD, SEM-EDS, stable isotopes, NMR analyses and data interpretation during their bachelor thesis projects conducted at the Vrije Universiteit Amsterdam in 2018/2019/2020 under the supervision of MSR. We acknowledge Suzan Verdegaal-Wardemam for her kind assistance with stable C and O isotope analysis. We thank Alessandro Genovese and Edy Abou-Hamad from KAUST imaging and characterization corelabs for assistance with SEM and NMR analyses, respectively. T. Yao is gratefully acknowledged for discussions on NMR data, and Z. Naim for assistance with the figures. We recognize the KAUST VSRP program for supporting Sebastian\u2019s Mulder\u2019s internship at Vrije Universiteit Amsterdam. This work was supported by the Dutch Research Council (NWO) Projects OCENW.KLEIN.037 to MSR, and the Competitive Research Grant (CRG) of the King Abdullah University of Science and Technology (KAUST) Grant OSR Nr. 4097 to VV and MSR. We acknowledge support to VC through KAUST baseline funding to VV.

Funders	Funder number
King Abdullah University of Science and Technology
Microsoft Research
Nederlandse Organisatie voor Wetenschappelijk Onderzoek	OCENW.KLEIN.037

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title = "The hidden role of heterotrophic bacteria in early carbonate diagenesis",

abstract = "Microbial impacts on early carbonate diagenesis, particularly the formation of Mg-carbonates at low temperatures, have long eluded scientists. Our breakthrough laboratory experiments with two species of halophilic aerobic bacteria and marine carbonate grains reveal that these bacteria created a distinctive protodolomite (disordered dolomite) rim around the grains. Scanning Electron Microscopy (SEM) and X-ray Diffraction (XRD) confirmed the protodolomite formation, while solid-state nuclear magnetic resonance (NMR) revealed bacterial interactions with carboxylated organic matter, such as extracellular polymeric substances (EPS). We observed a significant carbon isotope fractionation (average δ13C = 11.3‰) and notable changes in Mg/Ca ratios throughout the experiments. Initial medium δ13C was − 18‰, sterile sediments were at 2‰ (n = 12), bacterial-altered sediments were − 6.8‰ (n = 12), and final medium δ13C was − 4.7‰. These results highlight the role of bacteria in driving organic carbon sequestration into Mg-rich carbonates and demonstrate the utility of NMR as a tool for detecting microbial biosignatures. This has significant implications for understanding carbonate diagenesis (dissolution and reprecipitation), climate science, and extraterrestrial research.",

author = "M{\'o}nica S{\'a}nchez-Rom{\'a}n and Viswasanthi Chandra and Sebastian Mulder and Camila Areias and John Reijmer and Volker Vahrenkamp",

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AU - Sánchez-Román, Mónica

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AU - Mulder, Sebastian

AU - Areias, Camila

AU - Reijmer, John

AU - Vahrenkamp, Volker

PY - 2025

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N2 - Microbial impacts on early carbonate diagenesis, particularly the formation of Mg-carbonates at low temperatures, have long eluded scientists. Our breakthrough laboratory experiments with two species of halophilic aerobic bacteria and marine carbonate grains reveal that these bacteria created a distinctive protodolomite (disordered dolomite) rim around the grains. Scanning Electron Microscopy (SEM) and X-ray Diffraction (XRD) confirmed the protodolomite formation, while solid-state nuclear magnetic resonance (NMR) revealed bacterial interactions with carboxylated organic matter, such as extracellular polymeric substances (EPS). We observed a significant carbon isotope fractionation (average δ13C = 11.3‰) and notable changes in Mg/Ca ratios throughout the experiments. Initial medium δ13C was − 18‰, sterile sediments were at 2‰ (n = 12), bacterial-altered sediments were − 6.8‰ (n = 12), and final medium δ13C was − 4.7‰. These results highlight the role of bacteria in driving organic carbon sequestration into Mg-rich carbonates and demonstrate the utility of NMR as a tool for detecting microbial biosignatures. This has significant implications for understanding carbonate diagenesis (dissolution and reprecipitation), climate science, and extraterrestrial research.

AB - Microbial impacts on early carbonate diagenesis, particularly the formation of Mg-carbonates at low temperatures, have long eluded scientists. Our breakthrough laboratory experiments with two species of halophilic aerobic bacteria and marine carbonate grains reveal that these bacteria created a distinctive protodolomite (disordered dolomite) rim around the grains. Scanning Electron Microscopy (SEM) and X-ray Diffraction (XRD) confirmed the protodolomite formation, while solid-state nuclear magnetic resonance (NMR) revealed bacterial interactions with carboxylated organic matter, such as extracellular polymeric substances (EPS). We observed a significant carbon isotope fractionation (average δ13C = 11.3‰) and notable changes in Mg/Ca ratios throughout the experiments. Initial medium δ13C was − 18‰, sterile sediments were at 2‰ (n = 12), bacterial-altered sediments were − 6.8‰ (n = 12), and final medium δ13C was − 4.7‰. These results highlight the role of bacteria in driving organic carbon sequestration into Mg-rich carbonates and demonstrate the utility of NMR as a tool for detecting microbial biosignatures. This has significant implications for understanding carbonate diagenesis (dissolution and reprecipitation), climate science, and extraterrestrial research.

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The hidden role of heterotrophic bacteria in early carbonate diagenesis

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