# Biotic processes involved in the mineralization of tufa deposits

Pierre Boussagol, Emmanuelle Vennin, Madeline Duret, Aline Bonnotte, Élodie Noirot, Chrystel Deulvot, Irina Bundeleva, Pieter Visscher

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Pierre Boussagol, Emmanuelle Vennin, Madeline Duret, Aline Bonnotte, Élodie Noirot, et al. Biotic processes involved in the mineralization of tufa deposits. Jean-Yves Reynaud; Eric Armynot du Châtelet. Short Papers from the 19th French Congress of Sedimentology, 84, Association des Sédimentologistes Français, pp.13-20, 2025, 2-907205-83-8. 10.70665/BCCM2113. hal-05005262

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# BIOTIC PROCESSES INVOLVED IN THE MINERALIZATION OF TUFA DEPOSITS

Pierre BOUSSAGOL<fnref n="1" />, Emmanuelle VENNIN<fnref n="1" />, Madeline DURET<fnref n="2" />, Aline BONNOTTE<fnref n="3" />, Élodie NOIROT<fnref n="3" />, Chrystel DEULVOT<fnref n="3" />, Irina BUNDELEVA<fnref n="1" /> and Pieter VISSCHER<fnref n="4" />

Corresponding author: emmanuelle.vennin@u-bourgogne.fr

**Abstract:** In the Bourgogne-Franche-Comté region, tufa deposits, form in rivers fed by karstic springs, raising questions about their biotic or abiotic origins. These deposits form in calcium carbonate-saturated waters with vegetation and microbial communities. The study aims to understand the bio-physicochemical conditions of tufa formation in rivers, which show diverse carbonate depositional structures. To address this question, a multi-analytical and multi-scale approach are employed, combining microscopy methods (fluorescence, confocal, SEM, and Cryo-SEM), analysis of physico-chemical conditions (pH, conductivity, Ca<fnref n="2" />⁺ concentration, alkalinity), and mineralogical assessments, along with a mapping of the structures to understand the context of their formation. It also assesses the mineralization kinetics revealing a complex interaction between physicochemical and biological processes, always involving microbial activity.

**Keywords:** Rivers, Carbonate mineralization, Microbialite, Exopolymeric substances, Biotic/Abiotic

## 1 INTRODUCTION

Calcium carbonates deposits found in river stream, known as tufa, raise questions about their origins, particularly regarding the role of microbial communities in their formation. Tufa typically forms at ambient temperatures in calcium carbonate-saturated water, often in association with vegetation and photosynthetic microorganisms (Shiraishi et al., 2008; Pedley et al., 2009; Roche et al., 2019). The formation of tufa involves complex interactions between environmental, physicochemical, and biological factors (Ford & Pedley, 1996; Merz-Preiß. & Riding, 1999; Boussagol et al., 2023). Several mechanisms, both biotic and abiotic, have been proposed to explain carbonate precipitation in freshwater environments, with microbial activity, especially cyanobacteria, often playing a key role. However, the debate continues as to whether tufa formation is predominantly biotic or abiotic in origins.

Modern tufa deposits are primarily composed of calcite and influenced by factors such as water flow (depth, velocity, etc.), CO₂ degassing, and climate (precipitation, temperature, humidity, etc.). Tufa often displays lamination characterized by alternating dense and porous layers. Microbial activity, especially from cyanobacteria and biofilms, is closely associated with calcite precipitation, with the degradation of extracellular polymeric substances (EPS) promoting mineral crystal growth. Studies suggest that tufa formation is influenced by seasonal variations, with more efficient production in warmer conditions (Arenas & Jones, 2017). The biogenic origin of carbonates, although less frequently discussed, is sometimes linked to the formation of micrite or small crystals, while sparry crystals are mostly considered abiotic (Pedley et al., 2009). Perri et al. (2012) propose that bacteria may influence carbonate precipitation in rivers through the formation of mineral nanostructures. Three main mechanisms for tufa formation have been identified: abiotic control from CO₂ degassing (Kano et al., 2003), physical control with some biofilm influence (Ford & Pedley, 1996; Merz-Preiß. & Riding, 1999), and biofilm components, like cyanobacteria, contributing to calcite mineralization (Pedley et al., 2009; Dupraz et al., 2009).

The study aims to explore tufa formation in rivers fed by karst springs in Bourgogne-Franche-Comté (France), using multi-analytical approaches, combining microscopy methods (fluorescence, confocal, SEM, and Cryo-SEM), analysis of physico-chemical conditions (pH, conductivity, Ca<fnref n="2" />⁺ concentration, alkalinity), and mineralogical assessments to understand the biotic and abiotic factors involved.

## 2 MATERIALS AND METHODS

This study adopts a multi-scale approach to investigate calcium carbonate production in river systems by integrating geomorphological, sedimentological, and biological factors.

Detailed mapping of tufa deposits was performed using high-resolution LiDAR data (20 cm resolution from the HD LiDAR program, National Institute of Geographic and Forest Information, Baume-Les-Messieurs).

<footnote n="1">¹Biogéosciences, UMR 6282 CNRS, Université de Bourgogne, 6 Boulevard Gabriel, F-21000, Dijon, France.</footnote>

<footnote n="2">²Department of Geosciences, University of Fribourg, Switzerland</footnote>

<footnote n="3">³Plateforme DimaCell, UMR 1347 Agroécologie, INRAE, Institut Agro, Université de Bourgogne, F-21000 Dijon, France.</footnote>

<footnote n="4">⁴Departments of Marine Sciences & Earth Sciences, University of Connecticut, Storrs, CT 06269, USA. E-mail</footnote>
The mapping is supplemented by field observations, including the identification of areas suitable for observing microbial mats and small structures, such as oncoids, measuring less than 20 cm.

These field observations were combined with physico-chemical analyses of river water, including pH, conductivity, and calcium concentration, which were monitored monthly from July 2023 to May 2024 in Baume-les-Messieurs, and several times per year in Marangea from 2021 to 2024, using a portable multi-parameter probe (ProfiLine 3320 WTW). Water samples were collected for calcium concentration and alkalinity analysis (GET Laboratory, Toulouse, France). The saturation index (SI) for calcite is calculated using PHREEQC software (version 3.6.2) along with the corresponding database (Parkhurst & Wissmeier, 2015), taking into account pH, alkalinity, temperature, and calcium concentration at the time of sampling. This method allows for the identification of river sections where the physico-chemical conditions favor carbonate precipitation, as well as the determination of whether specific times of the year are more conducive to this process.

The results of the physico-chemical analyses conducted on river water, from the source to the downstream, are systematically geolocated and mapped to identify any potential physico-chemical variations along the river's course.

The sedimentological analysis examined tufa formations at macro, meso, and micro scales (Shapiro, 2000; Dupraz et al., 2009) using a range of microscopy techniques. 150 thin sections were observed using polarizing and fluorescence microscopes (Zeiss Axioscope 7, Zeiss group, Oberkachen, Baden-Württemberg, Germany) coupled with a deltaPix camera (DeltaPix, Smoerum, Denmark) processed by DeltaPix InSight software (v.7.0) and scanning electron microscopy (SEM). Five samples were analyzed using confocal microscopy (Leica SP8 with a 10x dry objective, following Gérard et al., 2013 protocol) Five fresh tufa samples, collected in spring 2024, were observed with cryo-SEM (FE-SEM Hitachi SU 8230 with Quorum PP3010T cryo- preparation; DIMACELL platform, university of Burgundy, Dijon, France

# 3 RESULTS AND DISCUSSION

## 3.1 Geological context

This study focuses on Baume-les-Messieurs and Marangea rivers flowing through the French Jura. The Jura is a crescent-shaped fold-and-thrust belt that developed during the Mio-Pliocene at the foreland of the western Alps (Turrini et al., 2009). It features Cenozoic and Mesozoic sedimentary successions, primarily limestone and marl, shaped by compressional tectonics from the Alpine orogeny. The studied rivers flow along uplifted Mesozoic limestone plateaus marked by fault zones and are deeply incised due to intense erosion and glacial processes (Campy, 1982). This geomorphological evolution has led to significant karstification, creating dolines, sinkholes, and subterranean drainage networks (Campy, 1982; Bichet & Campy, 2008; Chauve et al., 1993). The valleys, known as "Reculée," are formed in Jurassic crinoidal and coral limestones, discharging water through springs at the contact with impermeable marl strata. Currently, the rivers erode Quaternary tufa deposits. The Baume-les-Messieurs River (the Dard) is studied over 1,500 meters, showcasing significant slope variation, with an average slope of about 6% (Fig. 1A-B). It features a 30-meter drop over ten meters at the tufa mound, along with several waterfalls. The river's flow is laminar in the first 150 meters and the last 400 meters, while the intermediate section is characterized by turbulent flow in a straight channel (Fig. 1C). The Marangea river (average slope of 11%) is studied over 950 meters (Fig. 1A-B). This river is marked by a perched tufa-mound, located a few meters from the source and features a torrential flow for about 400 meters before becoming calmer and taking on a slightly meandering morphology.

## 3.2 Geomorphological structures

Tufa carbonate concretions in the studied rivers are mainly found on or around geomorphological structures. A tufa mound, often associated with karst springs, is prominent formations (Fig. 1D). This mound develops in areas with steep slopes (over 30%), reaching sizes of over 100 m² and heights exceeding 10 meters. Tufa deposits also form dams across watercourses, varying from simple to successive or crossed structures depending on slope and river conditions (Fig. 1E). Simple dams appear in moderate slopes (2%–30%), while successive dams occur in steeper areas. These dams range from a few centimeters to several meters in height and can extend for hundreds of meters.

## 3.3 Tufa composition

The tufa deposits in the riverbeds composed of calcite, are categorized into three macro-structures: lobates, planar, and oncoids. These structures can be either laminated, which displays planar or concentric layering often based on organic remnants (Fig. 1G-a and H) or non-laminated (i.e., clotted; Fig. 1G-b and I), characterized by high porosity and disorganized structure. Based on microscope analyses, five main components were identified: Biotic components, peloids, micrite, microspar and sparite (mineral classification from Folk (2005); see classification from Vennin et al. (2019) and Fig. 1J).
<figure><img src="image_2.png" /></figure>

Figure 1. (A) Location of the study area. (B) Geological map of the Bourgogne-Franche-Comté region (from BRGM; https://www.brgm.fr/fr/implantation-regionale/bourgogne-franche-comte). The red lines indicate rivers with tufa deposits, while the colored stars represent the location of the two rivers studied in this research (Baume-les Messieurs and Marangea). (C) Topographic maps (LiDAR) of the Baume-Les-Messieurs Reculée. (D) Illustration of the tufa-mound of Baume-Les-Messieurs. (E) Illustration of a succession of crossed complex dams forming across the entire width of the river of Marangea. (F) Illustration of a succession of complex dams in Baume-Les-Messieurs River. (G) Illustration of the two main layering that form tufa deposits, (a) laminated and (b) non laminated clotted. (H) Alternation of dense laminae, composed of sparite and microspar, and porous laminae made of micrite and microspar. (I) Illustration of bryophyte remains encrusted by a mix of micrite and microspar forming clotted layers. Illustration of dense laminae, composed of sparite and microspar, and porous laminae made of micrite and microspar observed with optical microscope (J) and (K) in fluorescence microscopy (green emission 555 nm) displaying high density of microbial filaments. (L) Chlorophyll autofluorescence detected by emission between 610 and 730 nm using confocal microscope, highlighting the presence of numerous microbial filaments. (M) Calcein emission, with the detection window set between 517 and 530 nm. The detection of calcein indicates the presence of free Ca²⁺ ions in the sample surrounding microbial filaments.
Lobate structures (m- to several meters) in tufa deposits are composed of cyanobacteria (Rivularia, Phormidium, Calothrix, etc.) with bryophytes and filamentous green algae, either embedded or on the surface of carbonate structures. During spring and summer, when rivers flow, these structures are covered with thick layers of algae, microbial mats, and decaying plant fragments. Texturally, they have a clotted core made of organic remains, surrounded by alternating layers of micrite and microspar. Microscopic analysis reveals that the clotted core contains peloids, while fan-shaped microbial filaments cluster in micritic and sparitic layers. Planar structures form discontinuous mm to cm-thick calcitic layers on riverbeds, appearing granular and becoming slippery when coated with microbial mats in spring and summer. Microscopy shows they are laminated, with micritic and sparitic layers trapping organic fragments (bryophytes, and leaf and wood fragments) and microbial filaments. Oncoids, found along riverbanks, are multi-cm ovoid carbonate biogenic structures with a clotted core composed of disorganized peloids, micrite, and microspar. The core has high porosity (over 30%) and is covered by a laminated cortex of alternating micrite and microspar laminae (up to 1 mm). Sparite may develop on their surface. Observations in all the studied samples, from scanning electron microscopy (SEM), both conventional and cryogenic, show that the calcite crystals in the tufas exhibit a rhombohedral morphology, characterized by the accumulation of rhombic crystallites forming regular polygons. These crystals can grow larger than 40 µm and display a pyramidal or chevron-shaped granular surface. Cryo-SEM analysis of fresh samples reveals a significant presence of extracellular polymeric substances (EPS), which often degrade during conventional SEM observations. The laminated layers are rich in EPS, creating a spider web-like network (Dupraz et al., 2004; Boussagol et al., 2024), with calcite nucleation occurring at the nodes of degrading EPS. Micritic agglomerates are encapsulated within the EPS matrix and associated with biological remains. In non-laminated samples (i.e. clotted), there is a high concentration of casts from microbial filaments and bryophyte structures, with the internal structure composed of small micrite crystals that form granular walls, later covered by larger micrite and spar crystals.

Confocal microscopy observations revealed significant natural chlorophyll fluorescence in all examined samples, particularly in the outer parts, indicating better preservation of chlorophyll molecules and organelles. Chlorophyll compounds appeared in both laminated and clotted layers, primarily as microbial filaments (Fig. 1L). In laminated structures, these filaments were concentrated in dense laminae of sparite and microspar, oriented perpendicularly to the lamination, while in porous laminae of micrites, they were more disorganized. In clotted layers, chlorophyll was associated with remnants of bryophytes, often reduced to cell walls and some microbial filaments. Calcein staining detected free Ca²⁺ and Mg²⁺ cations, with fluorescence overlapping areas of chlorophyll fluorescence, suggesting that these cations are primarily located on the walls of microbial filaments and bryophyte remains (Fig. 1M). Extracellular polymeric substances, observed in cryo-SEM, enveloped organic remnants in all meso-fabric structures. The EPS likely played a key role in releasing Ca²⁺ ions during degradation, making them detectable through calcine staining. This highlights EPS as a promising candidate for facilitating calcium release.

## 3.4 Biotic control on carbonate production

Observations of non-laminated clotted samples consistently indicated a high concentration of biological compounds, particularly EPS, which coat microbial filaments and surrounding organic materials, including bryophyte remains. These findings correlate with confocal microscopy results, showing free calcium ions around these organic structures. Considering that EPS captures free Ca²⁺ due to negatively charged acidic groups (Dupraz & Visscher, 2005; Shiraishi et al., 2008) they inhibit calcium carbonate (CaCO₃) precipitation (Dupraz & Visscher, 2005; Decho & Gutierrez, 2017). As EPS degrades, calcium can be released, increasing the local concentration of Ca²⁺ and enhancing the saturation index for calcite (SIcalcite) near microbial filaments, which promotes calcite nucleation (Dupraz & Visscher, 2005; Dupraz et al., 2004, 2009) at the nodes formed by degrading EPS and around organic remains (Boussagol et al., 2024).

Cryo-SEM observations (Fig. 2) revealed that micrite crystals, predominantly rhombohedral, consist of an accumulation of rhombic crystallites, akin to structures found in lacustrine carbonate mud deposits formed from EPS degradation (Boussagol et al., 2024). This carbonate mineralization process is crucial in forming the non-laminated, characterized by organic remains encrusted by peloids, micrites, and microspars. Overall, these observations illustrate the significant role of biological processes and EPS degradation in the mineralization of tufa deposits. The porous laminations of laminated layers resemble the composition of clotted structures, indicating a dual biotic influence on carbonate precipitation. Calcium supply arises from the degradation of EPS, crucial for calcite nucleation. Additionally, these carbonates serve as substrates as we observed a new EPS fixation, mineralization, and micrite growth upon previous lithified layers.

Formation of non-laminated clotted layers and porous laminae is linked to microbial and bryophyte development, mainly during spring, summer, and early autumn when chlorophyll production is high. Locally, the micritic fringes are covered with microspar suggesting a change in precipitation conditions and enhanced mineralization. Cryo-SEM observations reveal microspar crystals, ranging from cubic to rhombohedral shapes, often encapsulated in degrading EPS, highlighting the interplay of biotic and physicochemical processes in carbonate deposits.
<figure><img src="image_3.png" /><figcaption>Figure 2. Cryo-SEM illustrations of the relationship between EPS and calcite crystals in a fresh tufa sample. (A) High concentration of EPS forming a veil with diatoms as well as numerous microbial filaments embedded within the microbial matrix; EPS veil takes on a typical spiderweb shape as it degrades (Dupraz et al., 2004). (B) Close-up view of degrading EPS showing the occurrence of numerous calcite nucleation points resulting from the clustering of nano-globules leading to the formation of rhombohedral crystallites. (C) Microspar crystals embedded in the EPS matrix. (D) EPS thread coated with calcite crystals.</figcaption></figure>

In the laminated layers, the occurrence of sparitic laminae in which microbial filaments are observed in an erected and vertical position suggests a progressive precipitation of some of the sparites. This implies that the formation of sparites may be contemporaneous with the development of the filaments, evoking a mixed precipitation process involving biotic factors. This is consistent with sparite crystal morphology, whose walls display trigonal, pyramidal, and chevron growths, which are generally associated with biotic influence (Pedley et al., 2009; Roche et al., 2019). In contrast, sparites lacking filaments might result from more physico-chemical processes, associated with an increase in ionic concentration. However, it cannot be ruled out that the calcium released from the degradation of EPS partially contributes to the formation of sparites in the absence of filaments. Therefore, the presence of larger crystals and microspar in dense laminae implies a more efficient carbonate production process. These layers are preferentially observed in higher hydrodynamic setting of the river (main channel and during increasing drainage), driven by enhanced CO₂ degassing. Seasonal droughts may contribute to increased Ca²⁺ concentrations and evaporation, favoring higher calcite saturation indices.

### 3.5 Biotic vs physicochemical processes

As illustrated in figure 3, tufa deposit formation is a complex process influenced by multiple factors, particularly the calcite saturation index (IScalcite), which is determined by the physico-chemical conditions of water and watershed characteristics (Shiraishi et al., 2008; Roche et al., 2019; Kano et al., 2003). CO₂ degassing, evaporation, water agitation, evaporation, and photosynthesis raise pH and promote calcium carbonate precipitation (Jacobson & Usdowski, 1975; Herman & Lorah, 1988). High concentrations of Ca²⁺, driven by water from karstic aquifer, temperature, and exopolysaccharides (EPS), further enhance this process (Pentecost, 1975; Shiraishi et al., 2008; Arenas et al., 2014; Bouton et al., 2020). The occurrence of EPS has been observed in all samples analyzed by Cryo-SEM (Fig. 2E), showing that the nucleation points of calcite and their growing are associated with EPS degradation (Boussagol et al., 2024). Calcium release is generally observed around microbial and algal filaments, which explains their encrustation by micrites and
microspars, the main components of clotted layers and porous laminae in laminated layers suggesting a more 'biotic' control. The interaction of abiotic and biotic factors, such as the photosynthetic role of microbial filaments and EPS, contributes to different carbonate components, ranging from sparite crystals and clots layers. Despite the distinction between "more abiotic" and "more biotic" poles, both processes are intertwined, with microbial filaments potentially influencing even the most abiotic sparite formations. The formation of tufa appears to lie along a biotic-abiotic gradient, with no clear dominance of one over the other, as both processes can lead to similar precipitation outcomes through varied pathways, such as the rise in pH or Ca²⁺ concentration (Boussagol, 2024). Thus, carbonate deposits reflect a mix of physicochemical and biological influences. As observed in modern lacustrine micrite sediments (Boussagol et al., 2024), the precipitation of micrite associated with ESP decay, may conduce to maintain mineralization during the early diagenesis (Boussagol, 2024).

<figure><img src="image_4.png" /><figcaption>Figure 2. (A) Summary diagram showing the processes involved in the formation of continental carbonate deposits. (B) Microstructure of a speleothem sampled from the Baume-les-Messieurs cave and observed under optical microscopy. (C) Laminated layer sampled from a tufa dam in Marangea. (D) "Clotted" layer sampled from a waterfall, mainly composed of encrusted organic remains (Marangea). (E) Cryo-SEM illustration of a tufa sample showing the presence of calcite nucleation points that form at the nodes of EPS during their degradation (Baume-les-Messieurs).</figcaption></figure>

## 4 CONCLUSION

The study of tufa deposits in karstic aquifer fed rivers highlights several key findings regarding calcite carbonate precipitation and early diagenetic processes: (1) Microbial Role: Microscopic studies show microbial filaments and extracellular polymeric substances (EPS) play a crucial role in calcite nucleation, creating mineralization sites. The degradation of EPS may contribute to local increases in Ca²⁺ concentration, favoring calcite precipitation in the tufa formation. (2) Biotic-Abiotic Gradient: tufa formation occurs along a gradient where both biotic (microbial) and abiotic factors interact.

## 5 ACKNOWLEDGMENT

This work is a contribution from the SEDS team in the Biogéosciences Laboratory (uB, Dijon, France) to the project Carbostock-Envergure/OSU THETA and Stock-car/OSU THETA. The authors sincerely thank Dr. Concepčion Arenas Abad for her constructive comments, which helped improving the quality of this manuscript. The authors warmly thank DimaCell Facility Imaging Center (INRAE, UBFC, France) which manages and maintains the analytical equipment used in this study. We also thank Lucie Masson (Bourgogne Franche-Comté University, Dijon) for preparing the thin sections, Ludovic Bruno for the DRX
analyses and Alex Pourprix and Arnaud Grivel for their participation as master student in the field acquisition.
We thank geosciences Environnement laboratory (Toulouse, France) for waters analysis.

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