The Limagne Basin (Massif Central, France) originated during a major, European-scale, extensive event (European Cenozoic Rift System), which led to the formation of several rift systems in the foreland of the Alps between the Upper Eocene and Pliocene. A fluvio-lacustrine system emplaced in the basin and resulted in a mixed carbonate-siliciclastic sedimentation in which microbial and metazoan buildups occupy an important place. However, microbial deposits are not exclusive to the Cenozoic history of the Limagne Basin; nowadays, in the basin, they still form in association with thermal spring systems. A fieldtrip was carried out in the Limagne Basin as part of the Microbialites: formation, evolution and diagenesis (M-Fed) meeting (October 2019). The objective of this excursion was to assess the diversity of modern and fossil (Chattian to Aquitanian) microbial sediments and structures in three prime locations (the Jussat and Chadrat outcrops and the Grand Gandaillat quarry). A detailed description of the morphologies and fabrics of the buildups and their associated biotic components can be used to discuss the spatio-temporal distribution pattern. Different basin margin models are proposed based on the changes in the distribution, morphology and size of the microbial and metazoan-rich deposits through time. The Jussat outcrop offers novel perspectives to unravel the evolution of the lacustrine/palustrine cycles over time and to establish a long-term paleoenvironmental history of the western margin of the basin during the Aquitanian. These cycles are composed of (i) lacustrine sedimentation comprising microbial and metazoan buildups and organic matter-rich marls reflecting a period of high accommodation, and (ii) palustrine deposits made of mudstones and clayey paleosoils, indicative of a period of low accommodation. It is suggested that climatic, tectonic, volcanic and local parameters (physiography, substrate) control the deposition of the buildups in each of the different cycles. In addition, the modern microbial mats of the Sainte-Marguerite and La Poix outcrops offer an opportunity to constrain the controlling processes at the origin of the mineralization involved in the formation of the microbialites and their preservation in the fossil record.

Le bassin des Limagnes (Massif Central) est issu de la mise en place d’une phase de rifting liée à la géodynamique Ouest-Eropéenne (Rift Ouest Européen) entre l’Eocène Supérieur et le Pliocène. Il représente un lieu privilégier pour étudier les bioconstructions à microbialites et métazoaires qui s’inscrivent dans une sédimentation mixte carbonate-terrigène fluvio-lacustre. Ce secteur bénéficie par ailleurs de la présence de tapis microbiens modernes. L’excursion organisée en octobre 2019, à l’occasion du colloque Microbialites: formation, evolution and diagenesis, dans cette région permet d’observer et d’approcher la diversité et la structuration de sédiments microbiens modernes et fossiles. Une description détaillée de la morphologie, des fabriques des bioconstructions chattiennes et aquitaniennes et de leurs composants biotiques, des affleurements de Jussat et Chadrat et dans la carrière de Grand Gandaillat, fournit un éclairage concernant leur organisation spatio-temporelle. Les changements de distribution, de morphologie et de taille des bioconstructions à microbialites et métazoaires à travers le temps permettent de proposer plusieurs modèles de rampe lacustre. Les cycles palustre/lacustre ont fait l’objet de publication récente, toutefois le site de Jussat offre des conditions d’affleurement exceptionnelles qui soulignent le rôle du climat et de la tectonique dans la mise en place de cette cyclicité. Ces cycles sont organisés en une succession de dépôts : (1) lacustres composés de bioconstructions à microbialites et métazoaires et de marnes riches en matière organique qui indiquent des périodes de forte accommodation et (2) de dépôts palustres boueux et argileux à paléosols soulignant des périodes de faible accommodation. Le climat, la tectonique, le volcanisme mais également des paramètres locaux tels que la physiographie des lacs et le substrat sont impliqués dans la formation des bioconstructions et leur organisation au sein des différents cycles sédimentaires. De plus, les tapis microbiens modernes de Sainte-Marguerite et de La Poix viennent offrir une opportunité de comprendre les processus de minéralisation à l’origine de la formation des microbialites et de leur préservation dans le registre fossile.

The accumulation and preservation of lacustrine microbial carbonates in both recent systems (e.g. Lake Tanganyika, Kenya; Casanova and Hillaire-Marcel, 1992; Cohen et al., 1997; Great Salt Lake, USA, e.g.Carozzi, 1962; Bouton et al., 2016; Vanden Berg, 2019; Vennin et al., 2019) and ancient systems (e.g. Green River Formation, USA; Seard et al., 2013; Chidsey et al., 2015) have been the focus of numerous studies with the aim to better constrain their petrology and isotopic composition with regards to the sedimentary and geodynamic context and to ultimately understand the processes leading to their formation. Microbial deposits have been at the center of interest of many studies since the discovery of extensive examples of these associated with petroleum reservoirs and, in particular, because of the rush to find the best modern and/or fossil analogues (e.g.Paik, 2005; Seard et al., 2013; He et al., 2015; Chidsey et al., 2015; Gong et al., 2017; Adiya et al., 2017; Roche et al., 2018). Lacustrine microbialites have been linked to economically significant petroleum systems, especially prolific in the Lower Cretaceous “pre-salt” systems found offshore Brazil and Angola (Awramik and Buchheim, 2012; Wasson et al., 2012; Mello et al., 2013; Muniz and Bosence, 2015; Gomes et al., 2020) and the Eocene Green River Formation within the Uinta Basin in Utah, USA (Bradley, 1924; Loewen et al., 1999; Leggitt and Cushman, 2001; Leggitt et al., 2007; Seard et al., 2013; Chidsey et al., 2015; Hurst et al., 2018). The Limagne Basin, located in the French Massif Central, shares numerous geodynamical (e.g., a normal fault system framework linked to a rifting system and volcanic activity; Davison, 2007) and sedimentological (diverse and abundant lacustrine microbialites; Bertrand-Sarfati et al., 1966; Donsimoni and Giot, 1977; Freytet, 2000; Wattinne et al., 2003; Roche et al., 2018) characteristics with the South-Atlantic “pre-salt” basins and therefore represents an exceptional analogue.

The Limagne Basin originated from a rifting phase linked to a major, continental-scale, extensive geodynamic event (European Cenozoic Rift System) affecting the foreland of the Alps between the Upper Eocene and Pliocene. It represents an unsurpassed location to investigate the sedimentary dynamics of microbial and metazoan buildups deposited as part of a fluvio-lacustrine mixed carbonate-siliciclastic sedimentary system during the Oligocene and Miocene. Additionally, is that extensive microbial mats still currently form associated with the thermal activity of the region, which in turn is directly linked to the tertiary geodynamic framework? Despite showing great similarities with the world-famous Eocene buildups of the Green River Formation (e.g. morphologies, composition, distribution, associated sedimentation and presence of hydrocarbons), the buildups of the Limagne Basin have attracted less interest, even though their existence has been reported for a long time (D’Halloy, 1812). Most of the previous studies were limited to a detailed description of the morphology and composition of these buildups and fail to include the spatial and temporal evolution or the paleo-environmental significance of these deposits. After characterizing the various microbial buildups, and reconstructing the associated paleo-environments, Wattinne et al. (2003) and Wattinne (2004) suggested that the morphologies and distribution of the bioconstructions were mostly controlled by the organisms (microbes vs. metazoans) involved in the buildups, the available space and the fluctuations of the shorelines. However, this work was mainly concentrated in the northern part of the Limagne Basin. Based on the detailed investigations carried out on microbial and metazoan buildups preserved in the southern and central Limagne basins, Roche et al. (2018) showed that the sedimentary cycles were mostly driven by a superimposition of regional (climatic, tectono-volcanism) and local factors, controlling the chemical and physical changes of the waterbody, the vegetation covers and the physiography of the lake margin. Over a large scale, climate and tectonics directly affect the morphology of lakes and their watersheds and then are considered as first-order factors controlling sedimentation. When coupled, these two major factors may strongly and quickly impact base level variations and therefore accommodation in lacustrine environments (Bohacs et al., 2013). The hydrology of the lake is also a determining factor in the onset of sedimentation and intense carbonate precipitation (Owen and Crossley, 1992). Although often neglected, dissolved solids produced by weathering processes contribute significantly to the sedimentary dynamics of basins, supporting chemical and/or biological precipitation. Dissolved solids are delivered to the basin by surface flow through local rivers and also from subsurface flow through faults. The chemistry of the lake mostly results from the balance between the inputs and outputs of dissolved solids and the precipitation/evaporation ratio (Bouton et al., 2019). The precipitation of solid matter from the dissolved load of the lakes occurs either abiotically (driven by inorganic thermodynamics and reaction kinetics) or biotically (as a consequence of metabolism). Inorganic and/or organic mediated carbonate precipitation processes occur in lacustrine settings as a function of water chemistry, carbonate supersaturation, skeletal biota, vegetation, algae and microorganisms (Pedley, 1990, 2014; Riding, 2008, 2011; Pentecost, 2005; Dupraz et al., 2009; Della Porta, 2015). As proposed by Ginsburg (1991), the environment shapes the morphology, but the micro-organisms involved determine the microstructures. In the fossil record, it remains difficult to disentangle the role of both biotic and abiotic processes as they are closely coupled and carbonate precipitation results from a balance between both processes.

In this manuscript, we focus on the diversity of modern and fossil (Oligo-Miocene) microbial sediments and structures emplaced in the Limagne Basin. As part of the two-day excursion organized during the 2019 M-Fed meeting, the focus was on the central part of the basin, while observations from the northern and southern parts will be summarized from the literature. Based on the analysis of the different outcrops and/or quarries, we will discuss: (1) the geometry and composition of the microbial-rich deposits and their association with other biotic components (algae, insects, mollusks); (2) the main depositional environments of the lacustrine sediments in the central Limagne Basin; (3) the factors controlling the development of microbial and metazoan-rich buildups as well as their spatial and temporal evolution; and finally, (4) the mineralization processes associated with the formation of buildups and microbial mats through a modern system.

The Limagne Basin corresponds to a north-south oriented half-graben, the largest of the Massif Central Rift (35 km large, Fig. 1A). This basin formed during the Tertiary (Bergerat, 1987) and belongs to the European Cenozoic Rift System (Merle et al., 1998; Michon and Merle, 2001; Sissingh 2001; Dèzes et al., 2004). The basin is divided into the “Limagne Bourbonnaise” in the north, the “Limagne de Clermont” in the central part and the “Limagne d’Issoire” in the south (Fig. 1B). The Limagne half-graben is bounded to the west by a major north-south normal fault: the Limagne fault (Figs. 1B and 2; Michon, 2000). This basin is subdivided by secondary transverse strike-slip faults (i.e. the Aigueperse fault; Fig. 1B), responsible for the formation of several sub-basins of varying sizes, such as the Moulins, Vichy, Riom, Lembron and Brioude grabens (Donsimoni, 1975; Riveline et al., 1988; Merle et al., 1998; Sissingh, 2001). Due to its half-graben architecture (Fig. 1C), the Limagne Basin is asymmetric with a thick sedimentary succession (reaching 2500 m) in the western part, in the Riom Trough, while thinner deposits are recorded in the eastern part (Grolier and Tchimichkian, 1963; Morange et al., 1971; Pelletier, 1972). During the last 45 years, several geophysical and structural geologic studies on the deep structure of the crust and upper mantle of the Massif Central and the Chaîne des Puys have been undertaken. Following Perrier and Ruegg (1973), who revealed thinning in the Limagne Basin, the ECORS profiles (Sobolev et al., 1997; Zeyen et al., 1997) have shown that the warm mantle components beneath the Auvergne volcanoes have risen from a depth of at least 250 km. Merle and Michon (2001) and Dèzes et al. (2004) proposed a two-stage model: lithospheric thinning caused by alpine Eocene-Oligocene subduction (passive tearing), followed by thermal erosion (Miocene higher-current) of the Alps (active rifting).

The filling of the Limagne Basin extends from the lower Eocene to the lower Miocene. It is characterized by five sedimentary cycles delimited by erosional surfaces for which the amplitude and intensity vary from the margins to the center of the basin (Genter et al., 2003). Each of these cycles begins with the deposition of detrital sediments (conglomerates and sandstones), which then transition to marls and/or limestones before ending with evaporitic deposits or carbonate buildups.

As part of the fieldtrip, special attention was paid to the Oligocene-Miocene deposits (Chattian to Aquitanian) of the central Limagne Basin. The Oligo-Miocene lacustrine buildups contain prokaryotes (microbes) as well as the discussed eukaryotic algae (Cladophorites) or metazoans (mainly insects, especially caddisflies, and mollusks). Caddisfly larvae (Trichoptera) live in aquatic environments and make a protective (pupal) case that can be stacked in clusters (Mackay and Wiggins, 1979; Hugueney et al., 1990). The distribution of the buildups is non-random and is determined by the dynamics of the shoreline, as well as to the tectonic framework as they are distributed along fault corridors (Fig. 2; Wattinne et al., 2003; Roche et al., 2018).

During the Chattian, the salinity of the lake decreased as deduced from the absence of evaporitic sediments (Wattinne et al., 2018). A (weak) volcanic activity was recorded during this period which was manifested by injections of magma into wet and non-indurated sediments, resulting in the formation of volcaniclastic, phreatomagmatic rocks called “peperites” (Skilling et al., 2002; site of Grand Gandaillat). The Upper Chattian was characterized by the deposition of marls and concreted (“concretionned” sensu Dangeard, 1931) limestones in freshwater lacustrine environments (Bertrand-Sarfati et al., 1966; Rey, 1971; Donsimoni, 1975; Gorin, 1975; Donsimoni and Giot, 1977; Sissingh, 2001), recording a widespread cooling and arid climatic episode (Gorin, 1975; Giot et al., 1976; Hugueney, 1984).

The lacustrine environments associated with weak volcanic activity (with the deposition of “peperites”) recorded during the Chattian persisted during the Miocene. During the Aquitanian, warm and relatively wet conditions supported the formation of concreted limestones (Chateauneuf, 1972; Hugueney, 1984; Utescher et al., 2000; Wattinne et al., 2003; Scherler et al., 2013). During the remainder of the Miocene, the sedimentation, which was still lacustrine, became more detrital and consisted of siliciclastic sands called “Bourbonnais sands” (Rey, 1971; Donsimoni, 1975; Donsimoni and Giot, 1977; Hugueney et al., 1990, 1999, 2003; Sissingh, 2001; Wattinne et al., 2003).

The maximum extension of the lake was reached during the Oligocene where the three Limagne sub-basins were flooded (100’s kilometers; Hugueney et al., 1999). During the early Miocene, a volcano-tectonic uplift was responsible for the lowering of the subsidence rate (Sissingh, 2001; Dèzes et al., 2004) resulting in the northward migration of the depocenter toward the Limagne Bourbonnaise Basin; the central and southern parts of the basin (the central Limagne Basin) only consisted of a narrow channel along the western Limagne main fault (Hugueney et al., 1999). The lacustrine domain remained confined to the northern part of the Limagne Bourbonnaise Basin during the upper Aquitanian (Fig. 1B), before disappearing completely in the Burdigalian and giving way to a fluvial system (Wattinne et al., 2003).

Five outcrops were visited during the fieldtrip organized in the Limagne Basin during the 2019 M-Fed meeting: (i) Chadrat, (ii) Jussat, (iii) Grand Gandaillat, (iv) Puy de la Poix and (v) Sainte-Marguerite.

(i) The Chadrat outcrop (commune of Saint-Saturnin; 45°40’06.51”N, 003°05’15.85”E) is located 12 km to the south of Clermont-Ferrand, along the Montagne de la Serre (Figs. 3A and 3B). This outcrop is rich in carbonate buildups, commonly called “stromatolites”. They were used as building material for numerous houses in the villages of Chadrat and Saint-Saturnin. This outcrop is maintained and protected by the Arkose Association ( to increase the value of the heritage sites located in Chadrat. The carbonate buildups form a continuous layer up to 5 m thick, with an unique biostromal morphology at the scale of the Limagne Basin (Figs. 4A, 5 and 6). They consist of planar, globular and hemispherical structures (Donsimoni, 1975). These buildups comprise molds of microbial filaments that are included in micritic to sparitic matrices and which are described by Freytet (1998, 2000) as being different species of algae associated with bacteria. Although estimated as Oligo-Miocene in age, no precise ages have been defined in the literature for these carbonate deposits. However, a similar sedimentary succession has been observed capping the Jussat deposits.

(ii) The Jussat outcrop (45°42’13.29”N, 3°6’30.93”E) belongs to the commune of Chanonat. It is located approximately 8 km south of Clermont-Ferrand and 4 km north of the Chadrat outcrop (Figs. 3A, 3C, 4B, 5 and 7). The Jussat outcrop constitutes a prime, albeit poorly described, outcrop for investigating the lacustrine sedimentation of the Limagne Basin. This outcrop, roughly 55 m high, is an old quarry that is now abandoned and can be freely accessed. No precise dating has been carried out for the deposits in this quarry. Donsimoni (1975) placed these deposits at the Oligocene-Miocene boundary, while Freytet (2000) and the geological map of Clermont-Ferrand (1:80 000 scale) indicated an Oligocene age (Rupelian and Lower Chattian). A nearby outcrop, La Roche-Blanche, 2 km east of Jussat and at almost the same altitude, is dated based on the analysis of mammal fossils as early Miocene (Hugueney et al., 1999).

(iii) The Grand Gandaillat quarry is located in the town of Clermont-Ferrand (45°46’20.34”N, 3°9’15.10”E; Figs. 3A, 3D, 4C, 5 and 8). It is part of the Cournon-Lempdes Plateau, which is estimated to date back to the late Oligocene, based on mammalian and malacological biozones (Rey, 1971; Aubert et al., 1973). Between 1985 and 1987, the company Forezienne extracted approximately one million m3 of marl-limestone for the construction of the Clermont-Ferrand A71 highway. This quarry was almost completely filled in and served a rest area for a service station. In 2014, under pressure from numerous geologists, it was taken over by the town of Clermont-Ferrand. Since then, it has been managed by the Auvergne Conservatory of Natural Spaces and it is signposted for visitors. For security reasons, the quarry is closed to the public but can be visited upon request at the Clermont-Ferrand town hall (mairie). Each year, this geosite is visited by more than 6000 middle school students and high school students ( Located in the Limagne half-graben, on the western edge of the Cournon horst (Michon, 2000), this quarry provides access to a sedimentary series that is roughly thirty meters thick and visible on several successive fronts (Roche et al., 2018). Although it is difficult to precisely date, the estimated age of these deposits is late Oligocene (Chattian, Rey, 1971). The sedimentary succession is impacted by numerous faults, reflecting both the Oligocene extension and the post-Oligocene uplift of the basin (Michon, 2000).

(iv) The Puy de la Poix (altitude 345 m) is located 5 km east of Clermont-Ferrand and only 1.2 km north of the Grand Gandaillat quarry (Figs. 3A, 3E and 4D). This is one of the major curiosities of Lower Auvergne because of the bitumen lifts, formerly used to caulk boats and mark sheep. After decades of neglect, the site has been restored and is maintained by the Auvergne Conservatory of Natural Spaces. The Puy de la Poix mound, less than ten meters high, is a severely eroded Miocene volcanic chimney that crosses the Limagne marls. A ditch is filled with blackish bitumen and highly saline mineral water that oozes through the peperites. The salt concentration, which can exceed 80 g/l, varies greatly as a result of evaporation or dilution with rainwater. This water contains a distinct, non-mineralizing, microbial ecosystem.

(v) The Sainte Marguerite site is located 15 km southeast of Clermont-Ferrand (Figs. 3A, 3F, 4E and 4F). It corresponds to an abandoned thermal spa that is now only used to produce and bottle mineral water. There are many thermal springs in this region where water and gas, rich in hypogean (volcanic) CO2 and Ca2+ ions, ascend. According to a local legend, this was the location where the Roman soldiers tended their horses during the siege of Gergovie in 52 BC, which preceded the final victory of Julius Cesar at Alésia (near Dijon) over the Gallic armies. The therapeutic virtues of these springs are currently still used and many people come to swim in Grand Saladis or drink the mineral water in Petit Saladis. The site is positioned on the southern part of the Limagne Basin along the Allier riverside (Fig. 3A). The presence of thermal springs is due to the close proximity to the volcanic “Chaîne des Puys” area, the underlying Oligocene limestone beds and the alteration of granitoids, causing the precipitation of travertine (Teboul et al., 2016) with aragonite, calcite, Fe-rich gels and oxides. The springs in the Sainte-Marguerite area, such as the Saladis spring, were primarily studied to characterize the fluids merging from a fractured basement (water and gas composition, e.g.Gal et al., 2012). Only petrographic and geochemical studies on the travertines associated with these hydrothermal vents have been published (Casanova et al., 1999; Rihs et al., 2000; Teboul et al., 2016). Travertine precipitation occurs with a significant biological influence in gradually more distal or lower energy environments, as stated by Chafetz and Folk (1984) and Chafetz and Guidry (1999).

Composition of the buildups

Buildup architectures were described according to the three commonly used scales (macro/meso/micro-fabric) according to Shapiro (2000). The macrofabric (or growth morphology) corresponds to the external shape of a single buildup. Five different macrofabrics of the buildups could be identified in the central and Bourbonnaise Limagnes basins (Roche et al., 2018), and can be found in the Chadrat and Jussat area: (1) flats, (2) cauliflowers, (3) domes, (4) cones and (5) coalescent columns. Their main characteristics are summarized in Figure 9 and illustrated in Figure 10. The mesofabric is the internal organization of the buildups as can be observed with the naked eye. All of the morphologies present at these sites display a flat to columnar laminated mesofabric (i.e. none are clotted, …). Finally, the microfabric refers to the smallest scale that can be distinguished with an optical microscope. Four microfabrics were defined by Roche et al. (2018). The three first are microbial-dominated: laminated (l), columnar (co), filamentous (f) and the fourth is a “coated-caddiflies” (cc) microfabric. All these microfabrics have been recognized in the different outcrops and used in this manuscript (see Figs. 11A11H for illustrations). This classification has been extended in including the textural features (e.g. micrite, cement, hybrid, biofeature, agglutinated; Fig. 9). However, in Chadrat and Jussat outcrops, the coated-caddiflies can be replaced in some microfabrics by Cladophorites (cl). In addition, the microfabrics are either micritic, cemented, composed of biofeatures or agglutinated and are characterized as hybrid when different microfabrics are associated (Fig. 11).

The Jussat and Chadrat buildups, are two neighboring outcrops and display similar morphologies and compositions as the ones observed in Créchy (Figs. 11A11H), while they differ to those Grand Gandaillat (Roche et al., 2018). The Grand Gandaillat buildups are mainly flat and cauliflower macrofabrics composed of laminated and columnar microfabrics (Figs. 5 and 8). The caddisfly pupal cases are entrapped in the microbial successive growth phases but remain rare (Figs. 11A and 11B).

The Chadrat outcrop mainly hosts flat macrofabrics. Individual layers are stacked to form flat to columnar laminated mesofabric organized in biostromes up to 5 m high and which extend laterally over several meters (Figs. 5 and 6). The microfabrics of the flat Chadrat buildups are mainly filamentous although they display a wide variety of morphologies (Figs. 5, 6I6N, 11G and 11H). Using a morphogeneric approach, Freytet (2000) interpreted most of the microfabrics in the Limagne Basin, filamentous or not, as resulting from the activity of algae. However, their taxonomic affiliation remains questionable, especially for the structures referred to as Broutinella arvernensis. The molds of filament preserved in the carbonate buildups instead resemble modern cyanobacteria, thereby suggesting a microbial origin. However, there is still doubt regarding of the exact genetic attribution. The association with early sparitic precipitation indicates a possible combination of biotic and abiotic carbonate precipitation processes (Roche et al., 2018). The coexistence of molds and spiritic precipitation makes it difficult to determine if the microbes were involved in the formation of the microfabric or if they were only permineralized. In this case, the term “hybrid” is particularly useful for referring to these structures, which combine both biotic and abiotic processes, especially when they are diagenetically overprinted (Riding, 2011; Vennin et al., 2019; Riding and Virgogne, 2020). Hybrid microfabric corresponds to successive micritic and cement layers (Figs. 9 and 11E).

The Jussat outcrop displays the highest diversity in terms of carbonate buildups since five different macrofabrics and four microfabrics can be distinguished (Figs. 5 and 7) and can be compared with the fabrics observed in Créchy (Roche et al., 2018). The macrofabrics are identical along a same horizon (lateral) and change only vertically. The core of the buildups corresponds either to an accumulation of caddisfly pupal cases (Figs. 11A and 11B) or Cladophorites; these two facies are never observed as being associated. The green algal (or cyanobacterial) genus Cladophorites is common in the central Limagne Basin (i.e. Chadrat and Jussat) and display filamentous microfabrics, encrusted by laminated planar cemented microfabrics (Fig. 11E). In the Limagne Bourbonnaise Basin, the occurrence of Cladophorites depends on the locality: this genus was observed in several quarries (Montaigu-le-Blin; Gondailly; Chavroches; Poncenat; Donsimoni, 1975; Wattinne, 2004) but was absent in Créchy.

Depositional environments of the central part of the Limagne Basin

Nine facies (F1 to F9) are described in detail in Table S1 and illustrated in Figure 12. They gather the microbial and metazoan buildups and the surrounding sediments of all of the visited outcrops. Three profiles of the palustrine and lacustrine ramp margin were identified in the central Limagne area (Fig. 13): two were published by Roche et al. (2018): Grand Gandaillat and Créchy, while a third, new, profile has been identified following the description of the Jussat outcrop. The different facies are organized into three or four depositional domains depending on the setting (Fig. 13): (1) palustrine, (2) deltaic (specific to the Jussat area), (3) shallow lacustrine and (4) deep lacustrine. The Chadrat deposits, which are only shallow lacustrine deposits, are very similar to the F3 to F5 facies of Créchy (Roche et al., 2018). Therefore, the Chadrat outcrop can be considered as equivalent to the proximal part of the Créchy ramp margin model.

Palustrine domain

This domain is mainly composed of palustrine marls (F1) and mudstones with roots traces (F2). These facies have been interpreted as palustrine deposits undergoing emersion and plant colonization (Roche et al., 2018). In Chadrat and Jussat, emersion episodes are well expressed in form of desiccation cracks and orange-red colored mottled marks, glaebules and circumgranular cracks. The clay fraction is composed of iron-rich illite and kaolinite.

Deltaic domain

This domain, organized from proximal to distal deltaic environments, is only observed in the Jussat area (Figure Jussat Log). The proximal deltaic domain is characterized by a transition from the fluvial channel to the fan delta. The channels present basal erosion surfaces and are filled by microconglomerates to sandstones (F3a), passing laterally and vertically to palustrine marls (F1; Fig. 12A). The sandstones correspond to cm- to dm-thick lenticular beds with planar and oblique laminations. These deposits include quartzwackes (Pettijohn et al., 2012) composed of moderately-sorted angular to sub-angular quartz grains (100 μm to several cm), extraclasts (angular quartzite fragments and rounded volcanic grains; mm to cm), feldspars, peloids and gastropods. Lakeward, the intermediate deltaic lacustrine domain is characterized by cortoid-rich sandstones (F3b) organized in m-thick prograding lenticular beddings (Figs. 12B and 12C). They present a lobate to cuspate morphology and comprise planar to oblique laminations. The sandstones embed cauliflower and domal buildups from the shallow lacustrine domain. The cortoid grains are angular to subangular poorly-sorted quartz grains (100 μm to several cm), and are associated with feldspars, peloids, gastropods, ostracods, microbial-rich fragments and extraclasts (angular quartzite fragments and rounded volcanic grains; mm to cm). Locally, dm-thick layers composed of conglomerates, wood fragments and gastropods Cepaea Moroguesi (Rey, 1971; Hugueney et al., 2003) are preserved at the base of the sandstones. In the distal part, the deltaic domain (or prodelta) is made up of ooid-rich sandstones (F3c). This facies is organized in cm- to dm-thick planar beddings and mainly formed by an accumulation of ooid (quartz nuclei) and quartz grains. It is associated with oncoids (50–500 μm), cortoid grains, peloids, gastropods, ostracods and rare extraclasts. The grains are embedded in a micritic matrix. Bioturbation that resembles the Late Miocene ghost shrimp Egbellichnus jordidegiberti igen. and isp. nov. has also been evidenced (Fig. 12D; Hyžný et al., 2015).

In lakes, the geometry and sedimentary characteristics of deltas are controlled by the tributaries (rivers) and waves/currents dynamics of the waterbody (Galloway, 1975). The angular shape and moderate sorting of the quartz and feldspar grains in F3a suggest a low transportation distance from the source area. The lenticular beddings, oblique laminations, the coarse sandstones and conglomerates are interpreted as fluvial deposits deposited under high energy flow (e.g.Yemane et al., 1989; Platt and Wright, 1991; Olariu and Bhattacharya, 2006; Mtelela et al., 2016; Zhu et al., 2017). Similar deposits have been observed in the lacustrine margin (Yemane et al., 1989; Platt and Wright, 1991) and ephemeral fluvial channels (Scherer et al., 2007). The lacustrine part of the deltaic environment presents a lobate to cuspate morphology and is frequently shaped by waves as observed in Lake Turkana (Kenya; Schuster and Nutz, 2018). In marine environments, cortical grains are attributed to light-dependent, perforating microorganisms and usually form below the fair-weather wave base (Flügel, 2004). In contrast, cortical grains are poorly described in lakes, and in these environments interpreted as deposited under high-energy conditions (Fedorchuk et al., 2016; Platt and Wright, 1991). The presence of fragmented clasts, isolated ostracod valves and cross-bedding observed in the Jussat deltaic sediments in association with cortical grains support high-energy conditions (e.g.Yemane et al., 1989; Olariu and Bhattacharya, 2006; Zhu et al., 2017). In addition, the layers composed of conglomerates, wood fragments and gastropods Cepaea Moroguesi (Rey, 1971; Hugueney et al., 2003) indicate flooding events which have reworked material from the continental settings. Ooids are also associated with high-energy, shallow, lake environments (Eardley 1938; Swirydczuk et al., 1979; Tucker and Wright 1990; Bouton et al., 2016); the presence of ripples and reworked grains in ooid deposits argues for wind-generated resedimentation (Blair and McPherson 2008). The transition to fine material and increasing bioturbation is interpreted as a prodelta area where fine material settles out of suspension (Middleton et al., 2005). The ichnotaxon identified in the sublittoral deposits of Lake Pannon (Slovakia; Hyžný et al., 2015) can be used to confirm the subaquatic interpretation.

Shallow lacustrine domain

The shallow lacustrine domain is composed of six facies: sandstones (F3d), bioclastic-rich grainstones (F4), peloid/ooid-oncoid pack-grainstones (F5), microbialites associated with caddisfly pupal cases (F6a) and Cladophorites (F6b) and microbial-rich facies (F7). Most of these facies have been described in Roche et al. (2018) and are summarized in Table S1 and illustrated in Figure 12. The Jussat and Chadrat sedimentary records differ from that of Grand Gandaillat by the presence of gastropod and/or ostracod accumulations that are slightly encrusted by microbialites (F4: Fig. 12E; F5 a and b: Fig. 12F). The caddisfly and microbialite facies (F6a) correspond to clusters of caddisfly pupal cases. The caddisflies were attributed to Phryganeidae or Limnephilidae by Hugueney et al. (1990). Cladophorites were identified for the first time by Bertrand-Sarfati et al. (1966). They contributed to the development of cylindrical, bushy masses, 30 to 50 cm in diameter and 10 to 50 cm in height, with internal centimetric laminations (F6b). The algae are encrusted by Broutinella arvernensis (Freytet, 1998, 2000), which favors the preservation of these fragile structures. Most of the microbial-rich facies (F7: Fig. 12G) include the same morphologies as those described in Créchy and Grand Gandaillat (flat, cauliflower, dome and cone macrofabrics; Roche et al., 2018). The microbialites are frequently affected by penetrative dissolution, with cavities infilled by gastropod and ostracod grainstones (facies F4). In Chadrat, the built facies are frequently crosscut by root traces and fissure cracks.

The shallow water environments of the lake can be identified from a characteristic presence of caddisfly pupal cases, indicative of shallow conditions (Mackay and Wiggins, 1979; Leggitt and Cushman, 2001; Leggitt et al., 2007). Cladophorites, considered to be the equivalent of the current green algae Cladophora (Freytet, 2000) or cyanobacteria, are also associated with shallow lake environments, developing in fresh to brackish waters (Riding, 1979; Arp, 1995). Similar environmental conditions have been proposed in the northern part of the Limagne Basin (Wattinne et al., 2003) and the Reis impact crater (Germany; e.g.Reis, 1921; Riding, 1979; Christ et al., 2018). The maximum water level elevation is estimated from the maximum vertical development of the microbialites without interruption during their growth, until the formation of an erosion or emersion surface, i.e. when the buildups reach the lake surface (Bouton et al., 2016; Roche et al., 2018; Vennin et al., 2019). These observations reinforce the hypothesis that the water column has probably never exceeded the height of the bioconstructions (in Jussat: 3 to 4 m and in Chadrat: < 1 m) and attest to rapid water level fluctuations. Features such as highly fragmented biotic content, shell accumulation, the composite nature of the components, oblique laminations, ripples and erosional surfaces, as well as the truncation of some microbial deposits suggest a wave-influenced high-energy depositional environment (Schuster and Nutz, 2018).

The different macrofabrics of the bioconstructions may evidence local differences in the hydrodynamic regime. In Chadrat, the flat macrofabrics and the preservation of the micritic matrix suggest low-energy conditions. The presence of dissolution surfaces, karstification and/or pedogenic features affecting the bioconstructions seem to indicate a fluctuating water level up to their exposure following emersion. Cauliflowers, domes and columns form under moderate to high-energy conditions as they are associated with packstones, grainstones and sandstones in the Jussat area. The development of microbial-rich carbonate deposits, lacking of a fine clastic component, may result from (i) a rapid increase in the water level, (ii) a fast growth of the bioconstruction supported by a high calcium carbonate precipitation rate, (iii) permanent hydrodynamics preventing the deposition of fine particles in shallow domains and/or (iv) the presence of vegetation in the littoral zone which traps fine sediments and protects them from removal (Koinig et al., 2003). In the fan delta of Jussat, an environment which usually carries consequent loads of clastic particles, the absence of clastic components entrapped in the microbialites during their growth suggests changes in the inputs, and thus to the terrestrial run-off conditions.

Deep lacustrine domain

The deep lacustrine sedimentation is characterized by coalescent columnar microbialites (F8) and lacustrine marls (F9: Fig. 12H). In the central Limagne Basin, lacustrine marls were only observed in Grand Gandaillat, and in association with the highest domes and columns in Jussat. They were absent from the Chadrat outcrop, only representing a shallow lacustrine domain. The lacustrine marls are interpreted as low-energy, organic matter-rich marls deposited in the deep parts of a shallow lake (Roche et al., 2018). In Jussat, the synoptic relief of the coalescent columns is limited to 3–4 m when they reached the lake surface (emersion surfaces have been observed on top of each individual dome).

During the Aquitanian, the Jussat and Chadrat area corresponds to shallow environments close to the shoreline. By contrast, Créchy quarry records deeper and more distal conditions as evidenced by the higher synoptic relief of the coalescent columns and the widespread lacustrine marls. In addition, the deltaic environment characterized in Jussat argues for its proximity to the mouth of a perennial river.

Modern microbial mats can be found in different locations in the Limagne Basin (e.g. Sainte-Marguerite, Source de l’Ours, Serra et al., 2003). Contrary to the Cenozoic bioconstructions, which were lacustrine, the most spectacular modern examples are associated with thermal spring environments. Although modern microbial deposits do not represent exact equivalents of the Limagne fossil systems, they offer an opportunity to understand the role microbial communities play in the precipitation of carbonates. The Sainte Marguerite thermal spring is one of the 22 springs referred to on the edge of the Limagne Basin (Serra et al., 2003). A fan-shaped flat mound forms at the outflow of the spring. This mound extends over 100 hundred square meters and constitutes a synoptic relief of a few centimeters to decimeters (Fig. 4E). The water flows downslope where iron oxides and carbonate shrubs precipitate close to the source and calcite and aragonite-rich layered deposits are present in the distal part of the fan (Fig. 14A). Benthic microbial communities (biofilms of cyanobacteria, and diverse population of other bacteria and archaea) and eukaryotes (diatoms and chlorophytes) colonize the shallow pools of the fan-shaped mound (Figs. 14A14C) and can be linked to carbonate deposition (Figs. 14C14G; Casanova et al., 1999). The diverse cyanobacterial populations can be observed by differential interference contrast microscopy (Olympus FluoView FV1000) and confocal laser scanning microscopy with an oil immersion objective (Olympus UPSLAPO 60 × 0). The prototrophs in the mat are composed of species resembling Lyngbya sp. (Figs. 15A and 15B), Spirulina sp. (Figs. 15B and 15C) and undetermined 5–8 mm long filamentous cyanobacteria, similar to Phormidium incrustatum as well as several diatom species (Fig. 15B). The main mineralized structures display stacked porous spongy laminae with erect fibrous micritic threads (15–20 μm) separated by micritic films (Casanova et al., 1999). Between the filaments and the diatoms (Fig. 15D), the fabric observed in scanning electron microscopy (SEM; JSM-IT100, JEOL Ltd, Tokyo, Japan) is composed of micro-peloids (Fig. 15E), triangular masses (Fig. 15F) and nanospheres (Fig. 15G). The micritic laminae are wavy to crenulated, locally with mm-high domal forms. These mini-domes are intercalated with wackestone to grainstone and include coated bubbles (Figs. 14C14E and 14G). The coated bubbles are spherical structures measuring several μm to 1 cm in diameter have a hollow core and a very thin micritic coating covering the surface (Figs. 14D and 14E). Coated bubble accumulations occasionally are associated and are either included within a micritic matrix or, alternatively cemented by fibrous crystals (Figure S1). The mineralogy of the coated bubbles was determined by FTIR spectroscopy and revealed a main composition of aragonite and calcite (Figure S2). The coated bubbles were cast in LR-white resin then cut and polished for micro-characterization using SEM. Secondary electron images showed that the walls of the coated bubbles are composed of several micrometer-thin layers with various morphologies (Fig. 15H and Figures S1A–S1G). Outer layers are made of needle-like (Figure S1B) and rosette-shaped crystals (Figure S1C). The inner layer part of the bubble surface is composed of hemispherical radial needle crystals (Figures S1D–S1F). Locally, carbonate paper-thin carbonate rafts, a few μm thick and up to several centimeters wide (Fig. 14F), accumulated in close proximity to the coated bubbles.

Coated gas bubbles form preferentially in travertine ponds, on shallow channel sides, and also in spring mounds (Ries Crater, Pache et al., 2001; Big Soda Lake, Rosen et al., 2004). The paper-thin rafts are submillimeter-thick carbonate films precipitating on the surface of stagnant pools. Both coated gas bubbles and rafts are common facies of hydrothermal travertines (Jones et al., 1989; Taylor et al., 2004; Della Porta, 2015) and form in low-energy depositional environments. The laminated micritic facies is related to the microbially-induced precipitation of microbial mats (Visscher et al., 1998; Dupraz et al., 2009; Bouton et al., 2016; Pace et al., 2018). The development of this travertine facies is thought to result from alternating humid periods with high energy flow and an evaporative period leading to low-energy flow (Rodríguez-Berriguete and Alonso-Zarza, 2019). It remains difficult to distinguish between biotic and abiotic processes of mineralization in microbial mats, especially in a travertine system, and is the focus of ongoing work in the Limagne Basin. Cyanobacteria present at the surface of the microbial mats and degassing of CO2 may both trigger mineralization, biotically in the first case (Dupraz et al., 2009) and abiotically in the second. If so, microbial mats may be site of the nucleation and encrustation and considered as a biologically-influenced mineralization process (Merz-Preiß and Riding, 1999; Dupraz et al., 2011).

The Puy de la Poix mound contains a very particular microbial ecosystem, a so-called “sulfuretum” (Baas-Becking, 1925), which is based on sulfur cycling (Fig. 4D). In this bitumen and saline, sulfate-rich water system, two main microbial populations dominate: (1) sulfate-reducing bacteria, which respire sulfate instead of oxygen and couple this to the oxidation of long chain hydrocarbons present in the bitumen to gain energy (Rosenfeld, 1947). In this process, hydrogen sulfide (visible as gas bubbles) is produced; (2) sulfide- (and/or reduced sulfur-) oxidizing bacteria convert the hydrogen sulfide to sulfate, with an intermediate accumulation of zero-valent sulfur (Megonigal et al., 2003; Hines et al., 2007). This zero-valent sulfur forms the whitish precipitate at the water-air interface. No specific mineralization processes have been observed linked to the metabolism of the microbial communities, although sulfur cycling can result in carbonate precipitation (Visscher et al., 1998).

This discussion summarizes the main controlling factors that were involved in the formation, development and transformation of the microbial deposits in fossil and modern examples of the Limagne Basin. Some of the controlling factors have been extensively discussed in Roche et al. (2018); however, new outcrops of Jussat and Chadrat provide additional information to better constrain the depositional environments. In addition, the modern microbial-rich systems visited during the 2019 meeting emphasized the importance of microbially-mediated carbonate precipitation. This information can be used to better approach the mineralization processes involved in the fossil deposits.

Depositional environment models

The lateral and vertical distributions of the facies in Jussat and Chadrat can be used to propose a 3D depositional model that gathers the sedimentation zones of the two areas. This model is proposed considering that both outcrops are contemporary (Aquitanian). However, to validate this hypothesis, palynological, mammalogical data or stratigraphic correlations should be refined. A synthesis of the 2D deposition models illustrating all of the visited outcrops (Chadrat, Jussat and Grand Gandaillat) and the northern Limagne Basin is proposed in Figure 13. All three of these Oligo-Miocene outcrops depict the same general cycle pattern evolving from palustrine to lacustrine domains. However, the three settings differ from each other in terms of the composition and size of the buildups, the respective thicknesses of the palustrine- and lacustrine-related sediments and the clastic inputs.

The 2D depositional model is based on the Grand Gandaillat outcrop and illustrates the Chattian sedimentary dynamics (Fig. 13B). During this period, the lake presented a flat margin profile which leads to the formation of microbial buildups with a low synoptic relief. Cauliflowers are the main microbial macrofabric encountered in the restored quarry and do not exceed 1 m in height. They pass vertically and laterally to lacustrine marls enriched in organic matter (Roche et al., 2018). The two other 2D models illustrate the Aquitanian sedimentation in Créchy and Jussat and they display the same succession of carbonate facies (Fig. 13A). The Jussat area differs mainly by higher clastic sediments consecutive to the development of a lacustrine fan delta in association with the development of microbial and metazoan buildups (Fig. 13A). The flat and cauliflower macrofabrics form in the shallowest part of the lacustrine domain and record a high-frequency water level fluctuation as indicated by the presence of successive emersion surfaces and pedogenesis overprints. Lateral or vertical variations of the macrofabrics illustrate changes in the hydrodynamics: flat macrofabrics thrived under low-energy conditions whereas cauliflower macrofabrics developed under stronger energy conditions. In addition, the morphology and size of the cauliflowers result from the evolution of the sedimentation rate, accommodation (Wattinne et al., 2003) and the nature of the substrate on which they developed (Vennin et al., 2019). The Chadrat outcrop only presents the very shallow marginal settings of the lake, protected from clastic inputs. The stacking of flat macrofabrics, ultimately forming a biostrome, attests to a shallow lake environment (water depth less than 1 m). The presence of many root traces and karstified surfaces within the biostrome suggests that the area was regularly subjected to exposure and colonization by vegetation. By contrast, the lacustrine facies filling the dissolution cavities provide evidence for the re-submersion of the buildups and greater hydrodynamics. Donsimoni (1975) proposed that this tabular structure was induced by the formation of a natural dam and compares them to the travertines of Afghanistan described by Lang (1984). However, the Chadrat facies do not show any evidence of hydrothermal activity frequently described for the travertines (Della Porta, 2015). In Jussat, the shallow domain is colonized by abundant caddisfly pupal cases and Cladophorites that constitute the nucleation point for carbonate buildups. They preferentially developed in the wave-dominated littoral area (Hugueney et al., 1990; Freytet, 1998; Leggitt et al., 2007). The dome, cone and coalescent columns, the macrofabrics displaying an important synoptic relief, result from an increasing accommodation. In the Jussat area, the maximum height of the buildups (ca. 4 m) suggests that the water depth was usually lower than 5 m. The buildups from the central Limagne Basin are systematically smaller than those observed in the northern Limagne Basin, which can reach 10 m in height (Wattinne et al., 2003; Roche et al., 2018). The palustrine facies, mainly represented by marly and muddy facies with subaerial exposures, desiccation cracks, chip levels and karstification, indicate a low-energy platform along a gentle lake margin (Alonso-Zarza and Wright, 2010).

Sedimentary cycles

As proposed in Roche et al. (2018), the different outcrops show a high frequency, repetitive succession (cycle) of lacustrine to palustrine facies. Figure 16 summarizes the main characteristics of the cycles with a comparison to the one proposed for the northern Limagne Basin (Créchy). The base of the cycles corresponds to a lacustrine unit comprising well-developed microbial deposits. This unit is poorly developed in the Grand Gandaillat and Chadrat outcrops while it is thicker in the Jussat and Créchy outcrops. A palustrine unit overlies the lacustrine one. These littoral to continental facies were relatively thick during the Chattian and the palustrine part of the cycle became thinner during the Aquitanian, or was even absent or not preserved at all in Jussat and Chadrat outcrops. Each cycle is characterized by a first deepening trend followed by a shallowing-upward one, which indicates environmental changes related to high-frequency fluctuations in the lake level and high-to-low hydrodynamic conditions. In Grand Gandaillat, the cycles are symmetrical with a relative equal thickness of the lacustrine and palustrine deposits (Fig. 16). The same pattern has already been described in the literature for the Chattian deposits of the Créchy quarry (Wattinne 2004; Wattinne et al., 2018). On the contrary, the cycles evidenced in Jussat and Créchy are asymmetrical, with thicker lacustrine deposits (and thus shoreline expansion) than the palustrine ones (Fig. 16). Both symmetrical and asymmetrical cycles follow a five-step model that has already been discussed in Roche et al. (2018). However, the thickness of the Aquitanian cycles differs between the northern and southern part of the Limagne Basin. In the central Limagne Basin (Jussat), the cycles are thinner than the ones described in the northern Limagne Basin (1 to 3 m vs. 2 to 10 m) and, locally, present medium to coarse clastic deposits (Fig. 16). Steps 1 to 3 develop within a context of increasing accommodation while steps 4 and 5 record a decreasing accommodation. Step 1 initiates over either a basal erosion surface or an emersion one. The facies are made of sands, floatstones rich in wood fragments or peloid/ooid-oncoid grainstones and are interpreted as the shoreline domain. Step 2a is characterized by the initiation and development of the first buildups, with a low synoptic relief in shallow water. They are mainly composed of caddisfly pupal case accumulations or Cladophorites bushes. These first-built structures can be encrusted by microbial-rich layers forming macrostructures with variable morphologies (Step 2b) and embedded by carbonate sands (F4; Step 3) or sandstones (F3; Step 3). When located in the fan delta environment, the structures formed by caddisfly pupal case accumulations or Cladophorites bushes were poorly encrusted by microbialites. Steps 2 and 3 depict the maximum lake level, and thus lake expansion. In the central Limagne Basin, the absence of deep lacustrine marls, the progradation of the fan delta and the thinner cycles provide evidence for shallow conditions with low accommodation. The cycle ends with the installation of the palustrine facies (Steps 4 and 5). The palustrine deposits represent episodes of reduced accommodation (Alonso-Zarza and Wright, 2010). Each cycle is limited by widely traceable surfaces that are marked by desiccation cracks, dissolution cavities and root traces. Throughout the Chattian and Aquitanian successions, the restoration of full lacustrine conditions requires a positive water budget. Lake-level fluctuations could have been induced by various mechanisms, such as climate and tectonics (Madsen et al., 2001).

Factors controlling the development of fossil buildups

Each visited outcrop offers an opportunity to discuss the main controlling factor involved in the formation and development of the metazoan and microbial-rich buildups during the Chattian and Aquitanian. Even though each of these outcrops was involved in the global understanding of sedimentation in the Limagne Basin, the specificities of each outcrop are highlighted in the following section.

The carbonate factory and the biotic/abiotic influence on microbial-rich deposits

The dominant carbonate factory of the lacustrine Limagne deposits is driven by both (1) abiotic and (2) biotically-induced processes. These processes are two of the dominant carbonate factories proposed by Schlager (2000) in aquatic realms (the third is the biotically-controlled factory). It corresponds to the M-factory characterized by the microbial-mediated (e.g. bacteria including cyanobacteria) precipitation of mud (Schlager, 2000, 2003). The most prominent features of this factory are microbial mats, which usually contain several microbial genera and species from various key metabolic groups (e.g. cyanobacteria, anoxygenic phototrophs, sulfate reducers; Visscher and Stolz, 2005; Baumgartner et al., 2009), and their organic EPS (extracellular polymeric substances) matrix steering the different organo-mineralization processes (Dupraz et al., 2009). These different organo-mineralization processes may produce diverse microbialites through a variety of in situ carbonate precipitating and lithification processes potentially present in various aquatic environments (Dupraz et al., 2009; Della Porta, 2015).

The filamentous microfabrics of the bioconstructions of the Limagne Basin are particularly well preserved in Chadrat, where they show diverse and clearly identifiable morphologies despite the overprint of diagenesis, pedogenesis and karstification (Figs. 5 and 6). Freytet (2000) attributes their origin to green algae, however, he specifies that other frequent microorganisms have similar morphologies such as cyanobacteria, chlorophyceae, xanthophyceae (unicellular algae), phaeophyceae (brown algae) and rhodophyceae. Since the work of Freytet (2000), similar filamentous structures have been reported from many continental environments: in lakes (e.g. Great Salt lake, USA, Vennin et al., 2019; Mono Lake, USA, Guo and Chafetz, 2012; Brasier et al., 2018; Pyramid Lake, USA, Arp et al., 1999), hydrothermal vents (e.g. Italy, Della Porta, 2015; Bolivia, Bougeault et al., 2019), and in rivers (e.g. Japan, Kano et al., 2003; Slovakia and Poland, Gradziński, 2010; Spain, Arenas et al., 2014; Roche et al., 2019). The filamentous structures are identified as either molds or the remains of cyanobacteria (e.g.Freytet and Verrecchia, 1998; Arp et al., 1999; Brasier et al., 2018; Vennin et al., 2019). These structures present some similarities with the “shrub”, formed by in-situ upward growth from a lake substrate, descripted in the Aptian lacustrine deposits of Brazil. Many authors (e.g.Wright and Barnett, 2015; Herlinger et al., 2017; Souza et al., 2018; Lima and De Ros, 2019; Farias et al., 2019; Gomes et al., 2020) have considered these deposits as abiotic carbonate since they recognize some morphometric similarities with travertine deposits. Wright and Barnett (2015), Lima and De Ros (2019) and Wright (2021) assumed that the formation of shrubs is the combined result of changes in the lake water chemistry related to climate, abiotic precipitation resulting from CO2 loss by evaporation, magmatic CO2 input and hydrothermal activity. Although these authors admit that microbial mats were present in the lakes, they consider that the extreme alkalinity conditions reduced the level of metabolic activity to a point where biotic processes were minimized and thus the abiotic precipitation of carbonates predominated. It should be noted that microbial metabolisms notably alter the alkalinity and highly alkaline environments may support microbial mat development (Boomer et al., 2009; Dupraz et al., 2013). Indeed, alternative hypotheses suggest that biological factors triggered the initiation of the shrubs (Chafetz and Folk, 1984; Chafetz et al., 2018; Ceraldi and Green, 2017). The association with early sparitic precipitation indicates a possible combination of biotic and abiotic carbonate precipitation processes. More specifically, early diagenetic imprints are easy to recognize in microfabrics if the microbial activity is partly preserved as mold or filament. A secondary diagenetic mineralization superimposed on the primary lamination makes it difficult to determine the biotic vs. abiotic origin for the development of the cemented structures in the buildups. De Boever et al. (2017) proposed an overview and a short, non-exhaustive list of petrographic characters towards the recognition of primary textures in non-marine carbonates, but additional geochemical and microbiological analyses are necessary. They concluded that the presence and activity of microorganisms and organic matter seems to have a profound impact, not only on the precipitation of carbonates, but also on the micro-scale localization of early diagenetic processes (replacement) that rapidly transform the primary microfabrics. Broutinella arvernensis described in the Limagne Basin is considered as a combined association of biotic (filamentous bacterial development) and abiotic (cements) processes, but could also result from early diagenesis. The lateral variation from filamentous to cements, the presence of cements mainly toward the edges of the buildups and the repetitive succession of filamentous-rich and cement-rich layers point to high-frequency alternating dry and wet episodes associated with change in physico-chemical conditions (Bougeault et al., 2019). Carbonate precipitation depends on multiple factors (intrinsic, extrinsic and environmental) and results from a continuum of physico-chemical and microbial processes that are biologically induced or influenced (Dupraz et al., 2009). Consequently, the analysis and identification of the contribution of each of these factors to precipitation are difficult, even more so in the fossil record (e.g.Brasier et al., 2018).

The buildup diversity and composition seemed to have been modified between the Chattian and Aquitanian, and usually evidenced environmental changes (Fig. 2). The low diversity and predominance of Broutinella arvernensis in the Chattian buildups of Grand Gandaillat is considered as resulting from peculiar chemical conditions and a thermal stratification of the lake, favoring shallow anoxic conditions (Wright and Barnett, 2015; Bouton et al., 2016; Roche et al., 2018). In addition, the small size and scarcity of the buildups formed at the Oligo-Miocene transition may be related to brackish conditions, as suggested by the faunal association (i.e. gastropods and ostracods; Hugueney et al., 2003). In contrast, the Aquitanian buildups became dominated by larger and more diversified structures, mainly composed of microbialites and caddisflies. In Jussat, the buildups differ from those of Créchy (described in Roche et al., 2018) by the presence of Cladophorites, another contributor to the initial development of buildups. Cladophorites were never found in association with caddisfly pupal case accumulations, as they were probably removed by grazing organisms (Garrett, 1970; Javor and Castenholz, 1984; Tinsley et al., 2016). Consequently, the massive presence of caddisfly pupal cases may have prevented the development and/or preservation of Cladophorites. The local preservation of Cladophorites may also indicate a change in the physico-chemical conditions of the lake, as they tolerate variations in salinity (fresh to brackish water; Riding, 1979; Arp, 1995).

Contrasting buildup composition, size and distribution through time

During the Chattian and Aquitanian ages, the central Limagne Basin hosted a perennial lake system. However, climatic, tectonic, volcanic and other local controls affected its sedimentary dynamics (Figs. 17 and 18), resulting in spatial and temporal differences in the (i) cycle organization, (ii) composition of the sediments, (iii) distribution and (iv) development (in the case of buildups).

(i) The sedimentary record of the Jussat, Chadrat and Grand Gandaillat outcrops, and more generally the whole Limagne Basin, is organized in cycles (see Sect. 6.2), a feature commonly encountered in palustrine-lacustrine environments. While the interpretation of the cycles is frequently related to climatic fluctuations in open lake areas (e.g.Bohacs et al., 2000), short-term subsidence episodes cannot be ruled out, reflecting the influence of tectonic factors (Alonso-Zarza and Wright, 2010). In the Limagne Basin, the Oligo-Miocene sedimentary cycles usually comprise a lacustrine part and a palustrine part. However, a difference between the Aquitanian and Chattian cycles has been evidenced by Roche et al. (2018): the Aquitanian cycles are thicker and considered as asymmetrical (the lacustrine parts are more developed than the palustrine ones); on the contrary, the Chattian cycles are thinner and symmetrical. The composition and size of the buildups also differ between the two time intervals: the Chattian buildups are exclusively microbial and only a few centimeters high, whereas the Aquitanian ones may reach several meters in height and are composed of both microbes and metazoans (caddisfly pupal cases and Cladophorites, mainly). Climatic, tectonic, volcanic and local parameters were proposed as the main control on the deposition of buildups and their organization in each different cycle (Wattinne et al., 2003; Roche et al., 2018). However, the change in the cycle symmetry observed at the Oligo-Miocene transition can instead be attributed to a long-term climatic control, with thin and symmetrical cycles during the drier Chattian and thick and asymmetrical ones during the wetter Aquitanian.

(ii) The Jussat outcrop differs from the other studied sites by the presence of significant siliciclastic deposits (Fig. 17). These clastic accumulations, and thus inputs, may have both a climatic and tectonic origin (Platt, 1989; Platt and Wright, 1991; Kreuser, 1995). An increase in precipitation will induce an increase in surface runoff which, by promoting weathering and transport, will allow the deposition of siliciclastic sediments (Platt, 1989; Carroll and Bohacs, 1999; Bohacs et al., 2000; De Wet et al., 2015). The significant clastic accumulations recorded in Jussat are then consistent with the humid climate proposed for the Aquitanian (Chateauneuf, 1972; Hugueney, 1984; Scherler et al., 2013). In contrast, the dry climate proposed for the Chattian (Gorin, 1975; Zachos, 2001) is consistent with the low content of clastic sediments preserved in Grand Gandaillat.

The composition, organization and geometry of the sediments in the Jussat outcrop suggest a deltaic depositional environment, emplaced at the mouth of a river. The clastic contributions within a lake can be localized close to reliefs (Platt and Wright, 1991), and reflect a specific paleogeographical position as deltas are shore related features (Schuster and Nutz, 2018). Some local factors may also modify the input and/or distribution of clastic sediments, such as the vegetation. Stabilization of the banks by the vegetation may facilitate the trapping of siliciclatic deposits (Dunagan and Driese, 1999; Schnurrenberger et al., 2003).

(iii) Lacustrine systems can be deeply affected by climatic and tectonic changes, which modify the hydrological conditions, the basin morphography and the sedimentary dynamics. At the Chattian/Aquitanian transition, a long-term climatic change toward wetter conditions coupled to a regional uplift tilting northward in the central Limagne Basin have resulted in a modification of the distribution and thickness of the sediments (Fig. 18; Roche et al., 2018). Carbonates, especially microbial, constitute prime tools to investigate environmental and paleogeographical variations (through space and time) as they are very sensitive to changes. The spatial distribution of the buildups and sedimentary structures may constitute accurate proxies to reconstruct the water level fluctuations through time. In the Limagne Basin, most of these fluctuations can be explained by climatic variations (e.g.Chateauneuf, 1972; Hugueney, 1984; Roche et al., 2018). However the peculiar straight distribution of the buildups along the regional faults raises the question of whether tectonics may be an additional driver for the development and distribution of the buildups (Fig. 2). Faults can produce structural microtopographic highs and thus impact the development and distribution of buildups from a local to regional scale (Bouton et al., 2016; Gomes et al., 2020). Given that they allow the circulation of groundwater rich in ions (Ca2+; HCO3), fault systems also promote the mineralization of microbial buildups (Arenas et al., 2015). This last explanation is commonly proposed to justify the alignment of microbialites along faults (e.g. Lake Van in Turkey; Kempe et al., 1991; Cukur et al., 2015; Mono and Searles Lake in the USA; Rieger 1992; Guo and Chafetz, 2012; Great Salt Lake, USA; Bouton et al., 2016; Janecke and Evans, 2016, 2017; Early Cretaceous, Brazil; Gomes et al., 2020). Currently, several studies provide evidence for a significant degassing of CO2 linked to faults in the Limagne Basin (e.g.De Lary et al., 2016; Bräuer et al., 2017; Duwiquet et al., 2019). Isotopic analyses have shown that the CO2 has a mantle signature and is found in association with listric faults anchoring in the lithosphere, serving as drains for hydrothermal flows (e.g.Bräuer et al., 2017; Ars et al., 2019; Duwiquet et al., 2019). A hydrothermal activity, similar to the one recorded currently, is supposed to have occurred at the end of the Eocene, in association with the rift magmatism. Indeed, many modern rift systems (e.g. East African rifts, Coussement et al., 1994; Lee et al., 2016; Wilks et al., 2017; the New Zealand Rift, Rowland and Sibson, 2004), show that extensive magmatism is accompanied by hydrothermal activity, which can directly influence the chemistry of the lake (Renaut et al., 2017). The impact of hydrothermalism on the sedimentation of the Limagne Basin was already suggested by the distribution of gastropods (Valvatidae) only along the Aigueperse fault during the Aquitanian (Rey, 1964; Wattinne, 2004; Fig. 2).

(iv) The magmatic activity of the region also seems to have deeply affected the bio-physico-chemical conditions of the lake, and thus the development of the microbial buildups. For example, Bertrand-Sarfati et al. (1966) proposed that the development of caddisfly pupal cases was linked to hydrothermal activity. However, the effects of the magmatic framework are not limited to the hydrothermal flow; some phreato-magmatic events and associated deposits may have impacted the sedimentation. A phreato-magmatic activity that persisted from the Chattian to the Early Aquitanian has been recorded in the Grand Gandaillat area (Fig. 13; Goër de Hervé, 2000; Michon, 2000; Chazot and Mergoil-Daniel, 2012). A phreato-magmatic activity that persisted from the Chattian up to the Early Aquitanian has been recorded in the Grand Gandaillat area (Fig. 18; Goër de Hervé, 2000; Michon, 2000; Chazot and Mergoil-Daniel, 2012). The influence of volcanism on subaerial and lacustrine deposits in a rift setting has been extensively discussed (Cerling, 1994; Wright and Barnett, 2015; Szatmari and Milani, 2016) and contributes to the changes in the alkaline conditions and/or the modification of magnesium, calcium and silica concentrations in lakes (Cerling, 1994; Armienta et al., 2008) in lakes. In the Grand Gandaillat outcrop (Chattian), the peperites are clearly syn-lithication to post-lithification since dykes and peperitic sills intersect the sedimentation of the lake. In contrast, the peperites seem to be located topographically below the lacustrine deposits in Jussat (Aquitanian). However, the vegetation cover, the lack of dating and the presence of a fault (as proposed by Morange et al., 1971) in this outcrop mean that it is not possible to propose a robust correlation or chronology between the deposition of the peperites and the lacustrine sedimentation. By increasing the local heat gradient, the peperites could also support the local maturation of the organic matter present in the sediments, as observed in the Grand Gandaillat quarry and in Puy de la Poix. Since they are rich in silicium, the dissolution of these phreatomagmatic rocks may be responsible for the occurrence of late silica-rich diagenetic features (Lussatite; Mallard, 1890).

The development of the microbial buildups may have also been controlled by the substrate (Fig. 17; Della Porta, 2015; Bouton et al., 2016). Recently, Roche et al. (2019) and Vennin et al. (2019) discuss the role of substrate on the mineralization potential and distribution of continental microbial deposits and tufa. The presence of hard substrate, by its stability and the limited disturbance, enhances the development and preservation of microbial mats (by limiting the effects of erosion) and thus favors lithification (Della Porta, 2015; Bouton et al., 2016; Roche et al., 2019; Vennin et al., 2019). In the Limagne Basin, the largest microbial buildups (domes, cones, columns and coalescing macrofabrics) develop exclusively on caddisfly pupal case accumulations and Cladophorites. Therefore, biotic components appear to be favorable substrates for the development of microbialites and, in addition, to determine the distribution of the buildups. The microbialites themselves, due to their rapid mineralization and lithification, constitute a favorable substrate for further buildup formation as observed in Chadrat. As underlined by the molding imprints of plant structures at the base of the microbialites, wood fragments also represent an ideal substrate for the development of microbial deposits. Furthermore, as observed in Jussat, the buildups preferentially developed on coarse substrates; only a few rare examples of planar macrofabrics were reported on fine substrates. These observations support the hypothesis that the formation of microbialites is controlled by the presence of firm and stable substrates, including those from a biotic origin (e.g.Casanova, 1994; Dromart et al., 1994; Winsborough et al., 1994; Ginsburg and Planavsky, 2008; Saint Martin and Saint Martin, 2016).

The contribution of modern microbial deposits to understanding the mineralization and preservation processes.

One of the peculiarities of the Limagne Basin is that it hosts fossil (Cenozoic) microbial deposits and modern microbial mats. Although modern occurrences cannot be considered as exact analogues to the Chattian and Aquitanian buildups, understanding their development and biogeochemical cycling (including carbonate precipitation), may improve our ability to decipher the processes that lead to the formation of fossil microbialites. Modern microbial mats can be found in two spring systems: Sainte-Marguerite and the Puy de la Poix area. The first system comprises a thermal spring, and the second system is associated upwelling of bitumen- and sulfate-rich water. Since the physico-chemical conditions strongly differ between the two sites, each is unique in terms of the dominant microbial communities and associated biological mineralization. Despite the fact that the Sainte Marguerite bio-hydro-geosystem can be considered of endogenic travertine origin (Pentecost, 2005; Crossey et al., 2009), in addition to abiotic processes, biotic activity has been proposed in order to explain the formation of the carbonates. Changes in the mineralization intensities may be explained by the specific physico-chemical conditions (e.g. calcite saturation index (SIcalc) and the partial pressure of CO2 (pCO2) and close proximity of the cyanobacterial biofilm and carbonate precipitates. Preliminary observations at Sainte Marguerite suggest that the microbial mats are involved in microbially-mediated carbonate precipitation (Fig. 15). The production of O2 bubbles suggests high rates of oxygenic photosynthesis; the white sheen at the water interface is indicative of rapid sulfur cycling, similar to what has been observed in hypersaline and marine microbial mats forming microbialites (Dupraz and Visscher, 2005; Dupraz et al., 2011). It has been suggested that microbes mediate the formation of hydrous iron oxides and carbonates in modern low-temperature CO2-rich spring waters in Cézallier (Casanova et al., 1999). The microbial mats of Sainte Marguerite resemble the mats that thrive in Yellowstone National Park (USA; Fouke, 2011) or those present near the hydrothermal field associated with the Taupo Fault Zone (New Zealand; Brock and Brock 1971). The microbial coating of various surfaces by cyanobacterial mats is sometimes referred to as tufa-travertine (Freytet and Plet, 1996) and the roles of microbial mats and cyanobacteria in travertine deposits have been studied extensively in Mammoth Springs (Castenholz 1977; Fouke et al., 2000; Fouke, 2011). The preliminary results obtained from SEM investigations of microbial mats and associated carbonate precipitates have highlighted the role of the biotic components, especially microorganisms and EPS (Fig. 15) in mineral precipitation. The micro-peloids (Fig. 15E) found in the carbonate deposits of Sainte Marguerite are similar to the ones observed by Roche et al. (2019) in the Merantaise River and by Payandi-Rolland et al. (2019) in laboratory experiments. The formation of micro-peloids is likely mainly related to the activity of filamentous cyanobacteria and possibly diatoms although the entire microbial mat community ultimately determines the net precipitation result (Dupraz and Visscher, 2005; Dupraz et al., 2009. The presence of nanostructures (nanospheres, and agglutinated triangular polyhedra) argues for a biologic role on the mineralization (Folk, 1999; Manzo et al., 2012; Perri et al., 2012; Roche et al., 2019). Concerning the coated bubbles, similar microstructures were described in travertines from Yellowstone (USA; Fouke et al., 2000) and Saturnia (Italy; Ronchi and Cruciani, 2015). The complex structures of the coated bubbles and their association with EPS observed at the water-air interface along the stream may suggest a biotic influence on the observed mineralization.

In closing, it should be noted that presence of cyanobacteria does not necessarily imply that there is oxygenic photosynthesis as observed in Puy de la Poix. The metabolism of the phototrophs is very diverse and the capacity to perform anoxygenic photosynthesis has been demonstrated in cyanobacteria as well as many in anoxyphototrophs. Thus, the presence of a fossil microbial mat (microbialites) does not imply the presence of oxygen. Furthermore, it should be noted that the layering in microbial mats is not the same as the lamination in microbialites: an entire microbial mat was found to form one layer in the open marine Bahamian and Cuban stromatolites (Reid et al., 2000; Pace et al., 2018). Near the surface, cyanobacteria produce EPS and increase the alkalinity through oxygenic photosynthesis during the daytime (Dupraz and Visscher, 2005). Deeper in the mat, the rapid consumption of oxygen through aerobic respiration (using O2 as an electron acceptor) leads to the formation of an anoxic environment, in which anaerobic metabolisms are then responsible for the oxidation of the remaining organic matter using other terminal electron acceptors for respiration (e.g. SO42−, NO3, Fe3+). This general notion has evolved further when it was demonstrated that sulfate-reducing bacteria (SRB) are metabolically very active near the surface of the mat in the photosynthetically active, oxic zone (see Visscher et al., 1991; Baumgartner et al., 2006 for a review; Pace et al., 2016). In Sainte Marguerite, sulfate is abundant in the water, and then SRB could play an important role in microbialite formation as they usually increase the carbonate alkalinity and remove sulfate which inhibits carbonate precipitation (Vasconcelos and McKenzie, 1997; Visscher et al., 2000; Dupraz et al., 2009). The study of microstructures and their relation with biological components facilitate a better understanding of a biotic vs. abiotic origin of the tufa microbialites. Even if some authors proposed a purely physico-chemical role in the shape of crystals (Pedley, 1992; Reid et al., 2000), the role of microorganisms has been also recognized (Dupraz et al., 2009; Della Porta, 2015). The supersaturation of the water with respect to calcite is a fundamental condition that is required to trigger mineralization in lacustrine settings. Even if the abiotic processes govern induction of mineralization and carbonate precipitation in the fan-shape delta of Sainte Marguerite, biological factors played a critical role in the mineralization processes. These results are encouraging and may enable a better understanding of the microbially-induced or -influence carbonate precipitation in the fossil record.

This publication results from a fieldtrip organized in the Limagne Basin as part of the Microbialites: formation, evolution and diagenesis (M-Fed) meeting (October 2019). The objective of this paper is to assess the diversity of modern and fossil (Chattian to Aquitanian) microbial sediments and structures through a regional sedimentological and stratigraphic study. Investigations carried out in various Oligo-Miocene outcrops found in the central Limagne Basin demonstrate the potential impact of the climate, tectonic and volcanism in the sedimentary dynamics of the basin, especially carbonate buildups and microbialites. The microbial and metazoan buildups from the Limagne display five different macrofabrics (flats, cauliflowers, domes, cones and columns) and four main microfabrics (laminae, columns, filaments and their association with other biotic components). Three main depositional models were proposed from the different outcrops and show the spatial and temporal evolution of the Chattian and Aquitanian buildups.

All of the fossil outcrops visited record several lacustrine/palustrine cycles. While the symmetrical Chattian cycles result from long-term dry climatic conditions, the Aquitanian counterparts provide evidence for wetter conditions. The difference in the thickness and non-random distribution of the microbial and metazoan buildups along the faults are related to the tectonic framework. In Jussat, the presence of thinner cycles during the Aquitanian (in comparison to those recorded in the northern Limagne Basin) and a fan delta are consistent with the hypothesis of a regional uplift tilting northward in the central Limagne Basin. The Grand Gandaillat and Puy de la Poix outcrops are characterized by bitumen seep resulting from the transformation of the organic matter deposited in the deep lacustrine marls. The modern microbial communities of Sainte Marguerite can be compared with those developed in association with modern endogenic travertine. The microbial deposits observed in the Limagne setting show that carbonate production continues today in connection with fluid circulation within the basin. The specific mineralization processes described in relation with the microbial mats provide in-depth insights into understanding fossil microbial-induced precipitation of the Oligo-Miocene lacustrine carbonates.

This manuscript results from a fieldtrip organized as part of the “M-Fed Microbialites: formation, evolution, diagenesis” meeting held in Dijon, on October 26–27th, 2019 [Cet article est écrit suite à une excursion en Limagne lors du congrès « M-Fed Microbialites: formation, evolution, diagenesis » organisée les 26–27 octobre 2019].

The authors would like to thank Elias Samankassou and an anonymous reviewer whose work has helped to improve the manuscript. The authors would like to thank Total E&P (FR00008732) for funding the project and this study is a contribution from Total R&D (supervisor, E. Poli). This work is a contribution from the SEDS team at the Biogéosciences Laboratory (University of Bourgogne/Franche-Comté, France) and the I-site project UB18016-BGS-IS. We are very grateful to Lionel Weitz and the Vicat Society for providing access to the quarries. We are also grateful to all of the people who participated in the fieldtrip in October 2019 for their helpful discussions (Afroz Munira, Barreiros Heitor, Bielski Paul, Bougeault Cédric, Boussagol Pierre, Bouton Anthony, Brito Marlisa, Bundeleva Irina, Decraene Marie-Noëlle, Des Marais David, Durlet Christophe, Gallois Arnaud, Gaucher Eric C., Gérard Emmanuelle, Ghosh Parthasarathi, Lalonde Stefan, Martín-Pérez Andrea, Muller Elodie, Patry Laureline, Portier Eric, Ragazzo Alfonso, Ramsay Brittnay, Roche Adeline, Sansjofre Pierre, Vennin Emmanuelle, Visscher Pieter and Wilmeth Dylan). The organizers of the field trip gratefully acknowledge the Arkose Association for their support on the field. We also thank Pascal Taubaty for preparing the thin sections. Authors are thanking Emilie Steimetz (Bourgogne Franche Comté University, Platform Gismo) for SEM acquisition and Jonathan Edwards (ESRI France) for his help with GIS.

Cite this article as: Vennin E, Bouton A, Roche A, Gérard E, Bundeleva I, Boussagol P, Wattinne A, Kolodka C, Gaucher E, Virgone A, Visscher PT. 2021. The Limagne Basin: a journey through modern and fossil microbial deposits, BSGF - Earth Sciences Bulletin 192: 41.

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