Introduction

Cyanobacteria are a morphologically heterogeneous division of the domain Bacteria representing the oldest life forms on earth. They have a prokaryotic cell structure and a photosynthetic apparatus similar to that of eukaryotic plants with which the cyanobacteria carry out an oxygenic photosynthesis. The cells may contain the pigments phycocyanine (blue) or phycoerythrin (red). Most cyanobacteria use CO2 in photosynthesis but some are able to use organic compounds as carbon sources and reduce inorganic compounds (Büdel 2011; Gaysina et al. 2019). The majority of calcifying cyanobacteria occur in alkaline environments with low pCO2 and mainly take up HCO3− (Obenlüneschloss 1991).

The cell size of cyanobacteria is 5–10 times larger than that of bacteria. The cells are organized in different physiological entities (Fig. 1a): (1) single-cell cyanobacteria with binary cell division, (2) single-cell cyanobacteria with multiple cell division, (3) cell rows (trichomes).

Fig. 1
figure 1

a Organization, construction, branching and growth of cyanobacteria. Modified after Esser (2000). b Red Sike River in Upper Teesdale (UK). Pebble sampled from a shallow water area of the Red Sike with brownish, hemispherical colonies of Rivularia sp. (arrows). The river water is oligotroph favoring cyanobacteria with nitrogen fixing hetero-cysts. Rivularia sp. colonies show incrustation of CaCO3. c Extant Rivularia biasolettiana from Red Sike in light microscopy. False-branching (fb), hetero-polar trichomes show basal hetero-cysts (bh) and vegetative cells (vc). Sheaths (sh) are multi-layered and show frayed openings (fo). Photos courtesy of Martyn Kelly

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The thalli of cyanobacteria show an increasing degree of organization from the unicellular organism via the cell group (coenobium) to the trichoma forming hemispherical colonies (Fig. 1b) or mats. Cell division in the capsale coenobia can be coordinated (cells arranged regularly) or uncoordinated (cells arranged randomly). Cyanobacteria organized in trichomes usually have intercalar growth by cell division in the meristematic zone or growth by cell division of the apical crest cells. Specialized cells include hetero-cysts (Fig. 1a, c) for fixation of atmospheric N2 and akinetes (spores, permanent cells).

Cyanobacteria inhabit a wide variety of environments, e.g., marine, lotic (Fig. 1b, c) and lentic freshwater, soil, biological soil crusts, snow and cryoconites (Büdel 2011; Gaysina et al. 2019).

We present a study of Middle Miocene freshwater limestones from the Alpine Foreland Basin (Mörsingen, SW Germany) based on an analysis of hand specimens, petrographic thin sections and SEM images. This is followed by a literature review of related examples of arborescent carbonate precipitates. We establish and describe two calcification patterns of shape-retentive and shape-obscuring mineralization that dominate in the studied material.

Locality and geological background

The studied locality Mörsingen is located on the northern part of the North Alpine Foreland Basin (Fig. 2). The deposits studied herein are part of the Obere Süßwassermolasse (OSM, “Upper Freshwater Molasse”) unit that was deposited in an extensive lake district area south of the Swabian Alb — which corresponds with the northern margin of the Molasse basin (Kuhlemann and Kempf 2002). Several non-marine sands, marls and limestones are cropping out there, but no modern geological and sedimentological studies exist. According to Haag (1960), OSM sediments of this area are lying discordantly above tilted Late Jurassic, Oligocene and Early Miocene deposits, respectively (Fig. 2).

Fig. 2
figure 2

Geographic position of Mörsingen (above, red dot), and geological setting and location of the Silvana Limestone, including two other fossil sites known from literature. Sediments of the Obere Süßwassermolasse (OSM) overly older sediments from the Jurassic, the Oligocene Untere Süßwassermolasse (USM), and the Süßbrackwassermolasse (SBM), (from Haag 1960)

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The sediments are well known for a highly diverse fossil land snail fauna that is currently under study. These non-marine limestones are named Silvana limestones, after the common land snail Palaeotachea silvana (Klein). The deposits are of Badenian age (Middle Miocene) and most probably lie within the European land mammal zone MN 5 (after Esu 1999).

North of the village Mörsingen, at 48°12′50″N 9°26′55″E, the forest floor is densely covered with sub-autochthonous blocks of Silvana limestone. They are more or less in place and not re-worked, but a measurable sedimentary succession does not exist. These carbonates were sampled and studied for this paper.

Materials and methods

Several petrographic thin sections were cut in vertical and horizontal planes. Transmitted and reflected light microscopy was used to investigate the thin sections and rock samples (Leica DM750 P petrographic microscope). Digital photography was used for imaging the thin sections. For the SEM examination (Zeiss Evo LS 15), several samples of the microbialite were spattered with gold–palladium at 7 nm thickness due to the porous nature of the carbonates. Samples were fixed in 2 K-epoxy to reduce movements of the samples during the scanning process. Approximately 100 filaments and cross sections were examined under SEM and transmitted light microscope.

Results

The studied hand specimens are of light brown color and show undulating and laminated layers as well as oncoids, micritic carbonate sediment and plant debris like leaves and stalks of vascular plants with diameters up to 20 mm (Fig. 3a). Most stalks show a brown micritic incrustation on the outer surface, whereas inner surfaces remain free of incrustations. Fine-grained sediment infills in casts of former plant stems are present. Signs of reworking and compaction of the sediment like cracked laminated crusts and stalks are common. Due to high porosity, hand specimens are remarkably light in weight. Lamination is two-fold with light-colored laminae and laminae of a darker khaki color, respectively (Fig. 3b, c). The analysis with a magnifying glass reveals that the dark colored laminae are solid bands of micrite. The whitish laminae show parallel filaments oriented perpendicular to the substrate and primary porosity without cements (Fig. 3b, c). Trapping and binding of sediment particles in the mucilage of cyanobacterial biofilms is a common feature of microbial mats (Pentecost and Franke 2010; Schneider and Le Campion-Alsumard 1999). However, within the microbialites of Mörsingen, bound particles are missing (see also Koban 1993; Koban and Schweigert, 1993; Schweigert, 1996).

Fig. 3
figure 3

a Specimen showing oncoids (onc) and re-worked microbial crust fragments (rmc) with off-white and tan-colored laminations. Plant debris (pd) like stems and leaves encrusted with micritic microbial crusts with a flame-like appearance are enriched in a layer at the top of this specimen. b, c Enlarged sections revealing a two-fold zonation comprising of unbranched, parallel filaments (ubf) of a whitish color and branched filaments (fbf) of a tan color. (Polished slab, SMNS108000)

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Systematic paleontology

Kingdom Eubacteria Cavalier–Smith.

Phylum Cyanobacteria Stanier ex Cavalier–Smith (2002).

Class Cyanophyceae Schaffner (1909).

Family Rivulariaceae Bornet and Flahault (1886).

Genus Rivularia Agardh ex Bornet and Flahault (1886).

Rivularia cf. periodica Obenlüneschloss (1991)

1991 Rivularia periodica n. sp. – Oberlüneschloss, p. 28, Fig. 12

Material

The studied material has the field sample number Mö13-3 and the museum registration number SMNS108000 with the following sub-numbers: SMNS108000-1 to -10 for the SEM samples and SMNS108000-11 to -13 for the thin sections. The material is stored in the collection of Staatliches Museum für Naturkunde Stuttgart, Germany.

Description

Laminated portions of the studied freshwater limestones from Mörsingen comprise microstructures similar of modern cyanobacteria. Their lamination can be attributed to two alternating microstructures of an unbranched filament zone made of parallel and erect filaments and a branched filament zone forming a shrub fabric.

Zone of branching filaments—This zone contains, in addition to the existing filaments from the previously formed zone in the micobialite, newly formed filaments. The filaments of this zone resemble well-developed shrubs of calcified filaments (Figs. 4a–d, 5a). The shrubs show a pronounced upward, diverging and fasciculate growth habit (Fig. 5a–d). Calcified filaments with a hollow or with limpid microspar cemented inner tubule are a common feature of the shrubs (Figs. 4a, 5e, f, 6a, b). The tubules have diameters ranging from approx. 5–8 µm. They are enveloped by a variety of carbonate precipitates like khaki-colored micrite, microspar, clotted micrite and microspar associated with acicular CaCO3 crystals (Fig. 4a, b). In shrub layers associated with clotted micrite and peloidal crusts tubule, diameters range from approx. 2 to 3 µm (Figs. 4b, 6c–f). Here the tubules have black organic walls creating an opaque microstructure as described by Golubic and Seong-Joo (1999) and Javaux and Lepot (2018). Changes in the calcification pattern along the filaments are a common feature seen in the samples, e.g., a transition from micritic to micro-sparitic and acicular calcification (Fig. 4a).

Fig. 4
figure 4

a Vertical section through well-developed tufts. Lower portions of filaments show micritic and acicular/polyhedron carbonate (AC) covering the tubules (T). Upper portions of filaments show a transition to micritic (M) preservation. (Thin section, SMNS108000-12) b Dark micritic accumulations of carbonate (arrows) at the presumed location of basal hetero-cysts. (Thin section, SMNS108000-11) c Clotted microbial mat encrusting shrub layers. The microbial crust shows an alternating lamination of dark, dense, micritic clotted and peloidal layers (1, 3) and layers with peloids suspended in a limpid sparite matrix (2, 4). Layer 3 shows a partially columnar growth behavior (C), Filaments underneath the microbial crust are preserved as dark colored black organic walled tubules. (Thin section, SMNS108000-11) d Layers of shrubs (S) and of unbranched filaments (UF). Right: spongy mircobial biscuit (MC) overgrown by curled and entangled filaments (CF). Center section shows shrinkage cracks (arrows) (Thin section, SMNS108000-12)

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Fig. 5
figure 5

a Formation of shrubs through branching. Filaments F1 to F6 forming a tuft and F1b to F3b forming a smaller tuft of filaments. At the base of the tufts lie the areas where the assumed basal hetero-cysts are located (white dotted outlines). (SEM image, SMNS108000-3) b Calcified filaments (F1, F2, F3) showing dense carbonate “nodules” (black arrows) at the presumed locations of basal hetero-cysts. F2 is a branching of F1. (SEM image, SMNS108000-1) c Calcified filaments (F4, F5, F6) showing basal “nodules” (black arrows) arranged in a horizontal zone comparable to the branching zone of Rivularia periodica. (SEM image, SMNS108000-1) d Close-up view of micro-crystalline carbonate “nodules”. Note probably extant fungal hypha (fh). (SEM image, SMNS108000-1) e First precipitation of carbonate as nanocrystals (nc) forming a tubular structure of approx. 2.4 μm in diameter. To the periphery of the calcified tubule nanocrystals coalesce to form meso-crystals (mc). (SEM image, SMNS108000-5) f Filament enclosing 3 tubules (t). Center of calcified filament is formed by nanocrystals (nc) which coalesce to meso-crystals (mc). Polyhedrons (ph) and facetted polyhedrons (fph) form toward the outer periphery of the calcified filament. (SEM image, SMNS108000-5)

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Fig. 6
figure 6

a Enlarged view from Fig. 8b. Broken-up, curled filaments show hollow inner tubules (t) enveloped with nano- and meso-crystals (nc/mc) of carbonate. They coalesce to form polyhedrons (ph) toward the outer periphery of the filaments. Carbonate fibers (fc) are suspended between the filaments. (SEM image, SMNS108000-3) b Overview showing curled, entangled filaments. Diameter (arrows) of tubule approx. 3.3 μm (SEM image, SMNS108000-8). c Fasciculate colonies of Dichothrix morphotype (layer 1 in Fig. 7) directly underlying the peloidal crust (layer 2 in Fig. 7). The diffuse shrubs are interfused by dark clotted micrite (CM). Black organic walled tubules (T) of 2–3 μm diameter are common. (Thin section, SMNS108000-12) d Detail of calcified filaments underneath the clotted, peloidal microbial crust. Black organic walled tubules (arrows) are enveloped in dark clotted micrite. Interstices between filaments are partially filled with limpid microspar. (Thin section, SMNS108000-11) e Black organic walled tubule with a possible intercalary akinete or heterocyst. (Thin section, SMNS108000-11) f Well-preserved tubules (T) of 6 μm diameter with micritic envelope (M). (Thin section, SMNS108000-12)

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Zone of unbranched filaments—This zone is characterized by a subparallel and erect filament growth (Fig. 7a) of calcified filaments with a hollow or with limpid microspar cemented inner tubule (Fig. 7b–e). The filaments run through the entire zone without existing filaments ending or new filaments being formed. Trichome tubules are arranged vertically to the underlying substratum (e.g., shrub layers, fragments of plant debris, intra-clasts, oncoliths; Fig. 7c, f) and form layers of relative constant thickness once the colony finished the phase of initial formation (Fig. 7e, f).

Fig. 7
figure 7

a Elongated and erect tubules (T). Filaments colonize (black arrows) on a peloidal layer (P) of the coccoidal algae morphotype. Sheaths show a uniform, micritic preservation. Interstices between filaments are filled with limpid micro-sparitic cement. (Thin section, SMNS108000-12) b Oblique section through several filaments showing micro-sparitic tubules (T) with micritic envelope and acicular/polyhedral crystals (AC). (Thin section, SMNS108000-12) c Spar crystals (SD) between two layers (SL). Some tubules (T) are continuous within both layers. (Thin section, SMNS108000-12) d Horizontal section through the false-branching zone. Micro-sparitic tubules (t) covered with micrite made up of nano- and meso-crystals (nc/mc) followed by polyhedrons and acicular crystals (ph/ac). (Thin section, SMNS108000-13) e Micro-sparitic tubules (T) covered with peloidal, clotted micrite (P). (Thin section, SMNS108000-12) f Vertical section through microbialite showing alternating layers of the unbranched filaments (A) and branched filaments (B). Growth of the thalli commences at the base with a layer of curled and untangled filaments (ci) including an oncoid (onc). Initial layering can be disturbed by protuberances (arrows). Toward the upper surface layering gets more regular but slight variants in thickness are recognizable. (SEM image, SMNS108000-8)

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Layers of curled, entangled filaments—Growth of colonies commenced on indurated substrates, such as intra-clasts, laminar crust fragments, plant debris, pre-existing microbial sediments and other available nuclei, e.g., peloidal microbial biscuits (Figs. 3a–c, 4c, 8a). Filaments can also colonize on a peloidal layer (Fig. 7a) that resembles the coccoidal algae morphotype (Leinfelder, 1985). Mat-like colonies are common, but completely overgrown nuclei forming oncoids are also present (Figs. 3a–c, 7f). Layers consisting of curled and entangled filaments (Figs. 6a, 8a) forming a dense network are found either at the base of a colony or intercalated (Fig. 7f) within the colony.

Fig. 8
figure 8

a Spongy microbial biscuit with broken micritic intra-clast (IC) and dislocated fragments (arrows). (Thin section, SMNS108000-12) b Overview showing a peloid (p) suspended in curled filaments (cF) and fibrous carbonate (fc). Carbonate fibers are stacked parallel to their C-axis. (SEM image, SMNS108000-3)

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Remarks on taxonomy and comparison of extant and fossil forms

The studied microbialites show morphological similarities with the genus Rivularia as proposed by the morphological classification of Riding (1991). In contrast to Rivularia genera of the Angulocellularia Group, e.g., Frutexites, form tuft-like colonies of erect or pendant growth forms constructed of thin-walled tubes. Their colonies do not show a zonation caused by horizons enriched in branched filaments. The Epiphyton Group shows dendritic filaments made of micrite forming colonies of erect or pendant growth forms. Their colonies do not show a zonation caused by horizons enriched in branched filaments, too. Examples of the Hedstroemia Group, e.g., Cayeuxia, are characterized by a radially and erect growth of calcified filaments that form branching lobes or clusters of the colony resulting in a nodular appearance of the thalli. Several adjacent tubes can share common walls in the colony. The fossil Cayeuxia resembles the extant Rivularia but lacks the zonation formed by horizons enriched in branched filaments. Examples of the Garwoodia/Mitcheldeania Group show thin-walled tubes of larger diameter than Rivularia and right-angle branching. Clusters of radiating tubes create nodular colonies.

Branch-points: The fossil material does not allow for a distinction of the branch points in true- and false-branching (Golubić et al. 1996) as no cellular material or structures are preserved. The presence of a zone of unbranched filaments and a zone of branching filaments indicates a morphological similarity to Rivularia periodica. Figure 9a shows a detailed view of a filament of Rivularia periodica. Figure 9b shows the colony structure of Rivularia periodica (see also Obenlüneschloss 1991: Fig. 12 on page 28). Figure 9c shows a vertical petrographic thin section of the fossil form. Both forms share the characteristic two-fold zonation of branched and unbranched filaments. Attribution of the fossil specimens to the extent Rivularia periodica can only be made once further research on the branching points has clarified the transferability of biological characteristics of the branch points to fossil structures. Therefore, we determine the fossil form as Rivularia cf. periodica.

Fig. 9
figure 9

a Details of Rivularia periodica OBENLÜNESCHLOSS. (1) Funnel-shaped opening of frayed multi-layered sheath. (2) Apical hair formed by vacuolated vegetative cells. (3) Meristematic zone of the trichome. (4), (6) Vegetative cells. (5) Basal heterocyst. (7) Sheath made of multiple layers parallel to the trichome. b, c: Comparison of extant and fossil forms: b Structure of Rivularia periodica and reconstructed fossil Rivularia cf. periodica. c Petrographic thin section of studied fossil form showing two alternating zones of unbranched and branched filaments. (8) Zone of branching filaments. (9) Zone of unbranched filaments. (10) Zone of funnel-shaped openings. a, b Modified after Obenlüneschloss (1991)

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Discussion

Carbonate precipitates attributed to cyanobacterial activities play an important role in carbonate sedimentation, but little is known about pre-Quaternary taxa and processes. Fasciculate or arborescent fabrics formed by branched filaments of a probably cyanobacterial origin have been described in several studies. Some are briefly reviewed below, followed by patterns for the mineralization of the microbialites studied herein.

Organomineralization sensu lato

Microbial mats are assemblages of diverse and interacting microbial communities that can include filamentous, unicellular and coccoidal oxygenic and sometimes anoxygenic cyanobacteria, oxygenic heterotrophic and chemo-lithotrophic bacteria, sulfate-reducing bacteria, sulfide-oxidizing bacteria, fermenters and eukaryotic microorganisms like diatoms, foraminifera, calcareous algae and coccolithophorids (Marshall 1989, Visscher et al. 2000; Paerl et al. 2001; Golubic et al. 2006, Charpy et al. 2007, Dupraz et al. 2009).

In extant cyanobacteria, carbonate precipitation is associated with the extracellular polymeric substances (EPS) and the sheath (Pentecost and Franke 2010; Shiraishi et al. 2020, 2022a) and is probably boosted by heterotrophic bacteria and their metabolic activity. Abiotic CaCO3 precipitation is also of importance (Knorre and Krumbein 2000, Shiraishi et al. 2022b).

Dupraz et al. (2009) define the term Organomineralization sensu lato for all processes that lead to the precipitation of organo-minerals on an organic matrix that lacks genetic control. Organo-minerals are defined by Perry et al. (2007) as "any minerals precipitated by interaction of organo-polymers, bioorganic and/or non-biological organic compounds, without evidence of direct skeletal, intracellular or extracellular biological control". Biologically induced mineralization originates from biological activity (providing the organo-matrix and metabolites) and the interaction with the environment. Biologically influenced mineralization results from environmental changes (e.g., in pH, temperature, pCO2) that lead to the precipitation of organo-minerals on an organo-matrix. This organo-matrix does not necessarily reflect living organisms but can represent decaying or lysed organic tissues and organic matter (Dupraz et al. 2009). Organomineralization can be extrinsically caused by environmental changes, e.g., degassing of CO2, evaporation of H2O (Shiraishi et al. 2022b) or intrinsically caused by microbial metabolisms (Dupraz et al. 2009; Shiraishi et al. 2020, 2022a).

The Dichothrix-pattern

Koban (1993) describes a calcification pattern (Fig. 10a–d) of Dichothrix tufts from Quaternary travertines of Stuttgart. The nucleation of spar crystals starts along the cyanobacterial filaments and leads to their incorporation into the crystals. Subsequent microbial micritization starts at the outer rims of the spar crystals and leads to the decay of the tufts into micritic peloidal aggregates (Koban 1993; Koban and Schweigert, 1993). This pattern shows similarities to the calcification of extant Rivularia haematites with filaments crosscutting sparite crystals (Fig. 10e, f) (Obenlüneschloss, 1991). Interstices between the micritic filaments can remain void, show internal sediment or are diagenetically cemented with microspar.

Fig. 10
figure 10

Development (a–d) of the Dichothrix calcification type (Koban 1993). a branched cyanobacterial filaments with basal hetero-cysts. b Precipitated spar crystals cross-cut by filaments. c Beginning spar micritizing. d Peloidal degradation of the tufts. Examples of crystals enveloping filaments: e Two parallel filaments crosscutting a spar crystal. f Filament crosscutting a rhombohedron. a–d modified after Koban (1993). e, f modified after Freytet and Verrecchia (1998)

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Calcification in travertines of Tuscany

Guo and Riding (1994) describe arborescent, shrub-like calcite fabrics from Quaternary hot water travertines from Tuscany, Italy. Extantly formed fabrics consist of a random mixture of clotted micrite aggregates of sub-hedral to euhedral calcite rhombs (spar crystals) (Fig. 11). Their formation can be attributed to predominantly abiotic CaCO3 precipitation due to evaporation and degassing of hot spring water within a regime of medium water energy in shallow ephemeral pools.

Fig. 11
figure 11

Schematic diagram of a shrub consisting of micrite aggregates and spar rhombs. Micrites are interpreted to be of bacterial origin, spar rhombs occur together with diatoms and are interpreted to be of algal or abiotic origin. Modified after Guo and Riding (1994)

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The authors attribute calcite precipitation of the shrub fabrics to the metabolic activities of microorganisms like bacteria and diatoms and/or the nucleation of CaCO3 in microbial biofilms. Within the micrite aggregates, bacteriform bodies like spheres and rods (0.2–0.4 µm in diameter; 0.4–1.5 µm in length) are present and may represent calcified heterotrophic bacteria. Mini-micrite (approx. 0.1 µm in diameter) forms around these bacteriform bodies as a result of metabolic activities of the bacteria and within the associated biofilm resulting in a typical clotted texture of the micrite aggregates. Spar-rhomb aggregates commonly are of 20–40 µm in size and form clusters of 30–60 µm across. Associated with the spar-rhomb aggregates are microorganisms like diatoms and fungi. Euhedral calcite rhombs may form abiotically from supersaturated water. Sub-hedral spar crystals are often directly associated with diatom frustules. Abiotic nucleation of spar-rhomb aggregates is triggered by successive desiccation and flooding of the pool substrates with ion enriched water. Biogenically induced CaCO3 precipitation starts with nucleation sites located on and around heterotrophic bacteria resulting in aggregates of clotted micrite and mini-micrite. Diatoms are associated with spar rhombs and can stimulate biotic precipitation of calciumcarbonate, too. Both biotic and abiotic precipitation contributes to the arborescent growth of the shrubs.

Influence of biofilms in fabric formation of calcareous tufa

Perri et al. (2012) investigated the influence of biofilms on mineral precipitation and fabric formation in calcareous tufa at three locations in Italy and the UK. The authors describe several depositional facies including a dendrolithic fabric attributed to calcified tufts of filamentous cyanobacteria. The microbiocenosis of the biofilm consists of prokaryotes, filamentous cyanobacteria, green algae, actinobacteria, fungi and EPS. The biofilm marks the location of the Active Depositional Zone (ADZ) where mineral precipitation occurs. Mineral precipitation nucleates in the ADZ with nanospheres (nanocrystals) replacing degrading (dead) organic matter or at the surface of living cyanobacterial sheaths. The biological activity of the biofilm is therefore a key factor in mediating the precipitation of organo-minerals.

Precipitation of organo-minerals begins with the nucleation of sub-spherical nanocrystals (Fig. 12a, b). These merge to form irregular or rod-shaped meso-crystals of 100–200 nm size (Fig. 12b, c). Meso-crystals develop further into solid polyhedrons (Figs. 5f, 12d) or into triads (long and short variants) of calcite fibers (Figs. 6a, 8b). Tetrahedrons (> 10 µm) then develop from merging of triads and polyhedrons to form the basic construction units of the micro-columns.

Fig. 12
figure 12

a Beginning calcification of filament formed by nanocrystals. Diameter of orifice approx. 8.8 μm. (SEM image, SMNS108000-4) b Dense network formed of coalescing meso-crystals (mc). Sub-spherical nanocrystals (nc), rod-shaped (rs) and irregular (ir) meso-crystals are recognizable. (SEM image, SMNS108000-1) c Filament incrusted by meso-crystals (mc) starting to coalesce to form polyhedrons (ph). (SEM image, SMNS108000-1) d Well-developed polyhedrons (ph) and facetted polyhedrons (fph). Smaller meso-crystals (mc) are shown merging to form the polyhedral (ph) crystals to the left of the SEM image. (SEM image, SMNS108000-1)

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Calcification patterns for the Mörsingen microbialites

Two patterns of mineralization can be distinguished in the samples of Mörsingen´s microbialites: (1) Shape-retentive mineralization: successive carbonate precipitation from nanocrystals, meso-crystals, polyhedrons to facetted polyhedrons along the filaments. (2) Shape-obscuring mineralization: clusters of clotted micritic precipitates along and within the vicinity of micro-sparitic tubules that probably represent remains of the former cyanobacterial sheath. Table 1 provides a comparative overview followed by a detailed description of both patterns.

Table 1 Comparison and features of mineralization patterns
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Pattern 1: shape-retentive mineralization

Carbonate precipitation on an organized organo-matrix

The micro–nano-structures of the carbonate precipitates encountered in the microbialites of Mörsingen show similarities to the mineral morphology described from calcareous tufa by Perri et al. (2012). We structure the mineralization in Mörsingen´s microbialites into the phases I to IV (Fig. 13).

Fig. 13
figure 13

Schematic pattern of shape-retentive mineralization shown in a longitudinal section of a filament. a EPS reaching saturation of Ca2+-binding capacity of functional (acidic) groups. Extrinsic alkalinity control. b Supersaturated EPS leading to nucleation of CaCO3. c Random distribution of functional/acidic groups. d Reorganized acidic groups forming an organo-matrix. Phase I: Formation of nanocrystals. Phase II: Formation of meso-crystals. Phase III: Formation of polyhedrons. Phase IV: Formation of faceted polyhedrons. a–d modified after Dupraz et al. (2009). Color code: phase I = purple, phase II = cyan, phase III = green, phase IV = red

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Phase I: SEM images (Figs. 5e, 6a, 12a, 14a) show that calcification starts with the nucleation of sub-spherical nanocrystals at the outer surface of the sheaths (Fig. 13: phase I). Crystal sizes are ≤ 0.1 µm. These well-defined boundary surfaces and biological structures form an organized organo-matrix for the nucleation of nanocrystals (Fig. 13a). In modern cyanobacteria, nucleation of CaCO3 starts on or within the mucilaginous sheath (Pentecost and Riding 1986; Riding 1991; Shiraishi et al. 2020, 2022a). In extant Rivularia periodica, calcification nucleates at the outer surface of the sheaths, too (Obenlüneschloss 1991). Judging from the diameter of the orifice of the impregnated filament sheath, diameter was approx. 10 µm (Fig. 12a). Continuing nucleation and precipitation of CaCO3 cause a progressing calcification of the sheath toward its center enclosing the trichome(s) (Fig. 5f). In living colonies of Rivularia periodica, carbonate crystals grow toward the center of the filaments with increasing sizes from micrite to micro-sparite (Obenlüneschloss 1991). In contrast to the extant Rivularia periodica, calcification of the central areas enveloping the trichome(s) shows no increase in crystal sizes and leaves hollow tubules of a minimal diameter of approx. 2.5 µm (Figs. 13: phase I, 6b, 12a, 14a, e).

Fig. 14
figure 14

a Enlarged view from Fig. 6b. Filaments incrusted by meso-crystals (mc) starting to coalesce to form polyhedrons (ph). Cross-section of filament shows inner nucleation layer of nanocrystals (nc). (SEM image, SMNS108000-8) b Peloid between filaments covered with facetted polyhedrons (fph). (SEM image, SMNS108000-5) c Enlarged view from Fig. 16b. Peloid is made up from sub-spherical nanocrystals (nc) which merge to form irregular (ir) or rod-shaped (rs) meso-crystals. (SEM image, SMNS108000-5) d Facetted polyhedrons (fph) develop crystallographic surfaces of calcite crystals, e.g., rhomb-scalenohedrons (s = scalenohedron surfaces; q = rhombohedron surfaces). Modern fungal hypha (fh) impregnated with neo-formed carbonate (nfc). (SEM image, SMNS108000-1) e Shell-like structuring (arrows) of calcified filament suggesting a multi-layered sheath. Composite of two images. (SEM image, SMNS108000-4)

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Phase II: After nucleation (Fig. 13b) and formation of sub-spherical nanocrystals (Figs. 5e, 12a, 13: phase I) ongoing precipitation leads to the formation of irregular to rod-shaped meso-crystals (Figs. 12a, b, 13: phase II) through agglutination of nanocrystals (Figs. 5e, f, 12d, 13: phase II, 14a). Crystal sizes range from 0.1 to 0.2 µm. Peloids suspended between calcified filaments are build up from nanocrystals and meso-crystals (Figs. 8b, 14b, c).

Phase III: Polyhedrons form through clustering of meso-crystals (Fig. 13: phase III). These mineral aggregates are characterized by the formation of rhombohedral/trigonal trapezohedral outer contours (Figs. 5f, 12c, d, 14a). Cluster sizes range from 1 to 10 µm.

Phase IV: Facetted polyhedrons (Figs. 5f, 12d, 13 phase IV, 14b, d) evolve from polyhedrons by developing crystallographic surfaces of calcite crystals, e. g. rhomb-scalenohedrons (Fig. 14d). The sizes of these aggregates range from 2 to 10 µm.

Pattern 2: shape-obscuring mineralization

Carbonate precipitation on an irregular, randomly organized organo-matrix

Heterotrophic bacteria are common and abundant epibionts on cyanobacteria and within the EPS (Fig. 15a) (Marshall 1989; Obenlüneschloss 1991; Arp et al. 1999; Golubic et al. 2006; Charpy et. al. 2007, Perri et al. 2012). Metabolically active cyanobacteria and heterotrophic bacteria, degradation of EPS leads to the release of Ca2+ cations into the micro-environment (Paerl et al. 2001; Dupraz et al. 2009; Shiraishi et al. 2020, 2022a). The oxidation of acidic groups results in the formation of CO32—ions (Dupraz et al. 2009; Shiraishi et al. 2020, 2022a). The subsequent binding of Ca2+ cations to the CO32− ions leads to the nucleation of CaCO3 on the organo-matrix (Fig. 15b).

Fig. 15
figure 15

Schematic pattern of shape-obscuring mineralization. a Cyanobacterial filament with epibiontic and associated bacteria. b Degradation of EPS leads to the release of Ca2+. Oxidation of acidic groups results in carbonate formation. Binding of Ca.2+ to carbonate ions leads to the nucleation of CaCO3. c Metabolically active and partially lysed or decaying microbes and EPS inducing CaCO3 precipitation. d Randomly organized acidic groups forming an organo-matrix. e Photomicrograph of fossil microbialite. (Thin section, SMNS108000-12)

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Fresh and degrading EPS material, living microbes and partially decaying and disintegrated cyanobacterial trichomes, sheaths and heterotrophic bacteria form an irregular organo-matrix for CaCO3 precipitation (Fig. 15c, d). Binding of Ca2+ cations to randomly distributed acidic and functional groups within an irregular organo-matrix (Fig. 15d) causes textures of clotted micrite including hardly recognizable filaments and branching tufts and spar-filled interspaces in the microbialite (Figs. 7e, 13e).

Diagenesis

Some areas of the specimens and samples show a micritizing of the cyanobacterial micro-fabrics in SEM images. Micritized fossil filaments are often accompanied by extant fungal hyphae impregnated with neo-formed precipitates (Figs. 5d, 7f, 16). EPS associated with the fungal hyphae can lead to dissolution and fragmentation of the fossil fabrics. Repeated fragmentation and binding of fragments by carbonate precipitates results in a micritized fabric. Repeated abiotic dissolution and precipitation of Ca-carbonates can also lead to a micritized micro-fabric (Guo and Riding, 1994).

Fig. 16
figure 16

Modern fungal hypha (fh) encrusted by sub-spherical, neo-formed crystals. Sub-spherical crystals can merge to form rod-shaped crystals (white arrows). (SEM image, SMNS108000-1)

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Climate control on microbial growth

Biological and chemical processes are well known to depend on a wide range of physical factors. This raises the question, whether microbialites can be used as paleoclimate indicators.

An upward and diverging growth habit of the filaments can be interpreted as a phototrophic and/or phototactic behavior of the involved organisms (Golubic and Seong-Joo, 1999). Shrubs of the Dichothrix morphotype as those described herein and in the reviewed literature, are interpreted as predominantly biogenic carbonate precipitation during the summer or early autumn season (Koban and Schweigert 1993; Schweigert 1996). Dense carbonate layers in microbial crusts formed by extant Rivularia species are interpreted as predominantly abiogenic carbonate precipitation during winter, with only little or no biogenic contribution (Pentecost and Franke 2010). However, dense carbonate layers in the studied microbialites are the result of the morphological features of the zone of densely arranged branching filaments (Fig. 9b). When calcifying, these densely packed filaments form “dense carbonate crusts” within the colonies.

According to Perri et al. (2012), seasonal temperature variations probably influence the nano-morphology of the precipitated crystals attributing polyhedral crystals to the colder seasons. The studied limestones were deposited during the Miocene Climatic Optimum (MCO), which spans the whole MN 5 zone. It was characterized by a constantly high mean annual temperature of 22 °C and a lack of seasonality according to Böhme (2003) and Böhme et al. (2011). However, both the vegetation and the varved sediments of the fossil lagerstaette Randeck Maar of the same biostratigraphic age (Rasser et al. 2013) reveal distinct seasonality with dry summers and humid winters. The MN 5 zone spans a long interval from 17 to 15 million years before present. Therefore, these results are not necessarily contradictive, because the studied sediments as well as Randeck Maar sediments could be deposited during the late stage of MCO, with a temperature decline toward the Quaternary ice age.

This is supported by the observation that Mörsingen´s microbialites show layers of curled filaments. Obenlüneschloss (1991) reports such layers from the colonies of the extant Rivularia periodica caused by a dry-fall of the colonies. Layers of curled filaments would form preferentially in the dry season of the year. Obenlüneschloss (1991) showed that in extant Rivularia periodica the zone of branching filaments forms annually in springtime (Fig. 9b). Growth of the thalli and formation of new trichomes through branching require sufficiently good environmental conditions with sufficient water coverage of the colonies. The formation of the unbranched and the branched filaments therefore can be placed within the humid season. The irregular inter-bedding of laminae of curled and branched/unbranched filaments in the studied microbialites probably represent a beginning seasonality in precipitation at the time of their formation. Further research is needed to better specify these relationships.

Conclusion

Middle Miocene freshwater carbonates from the North Alpine Foreland Basin of Mörsingen, SW Germany, comprise a number of microbialites with morphotypes that can be attributed to the Genus Rivularia. A comparison of the extant and fossil forms shows a similar zonation of the colonies caused by zones of branched and unbranched filaments. Therefore, we determine the fossil form as Rivularia cf. periodica. Based on a broad literature review and a detailed study of these microbialites, we present two patterns of mineralization.

Pattern 1 describes a shape-retentive mineralization. The mineralization is differentiated into phases 1 to 4. The outer sheath surface acts as the predominating organo-matrix for the nucleation of nanocrystals in phase 1. Further crystal growth and coalescence of precipitates in the phases 2 to 4 create well-defined calcified shrubs and filaments due to the presence of a well-defined organo-matrix of intact cyanobacterial filaments.

Pattern 2 describes a shape-obscuring mineralization. Degradation of EPS, metabolically active microbes and partially lysed and decaying cyanobacterial trichomes, sheaths and bodies of heterotrophic bacteria create a highly irregular organo-matrix for the nucleation of CaCO3. This randomly organized organo-matrix changes its chemical and morphological features and characteristics within small distances. This results in hardly recognizable mineralized filaments and branching tufts of a probable cyanobacterial origin.

The climate of the Early Badenian was characterized by a pronounced seasonality in precipitation with a dry season lasting for up to six months. The formation of the branched filament zone, which required sufficiently good environmental conditions (e.g., water coverage of the colonies), can be placed in the humid season of the year. In combination with layers of curled filaments representing a dry-fall of the colonies, which occurred most likely in the dry season, the morphological zonation of Mörsingen´s microbialites reflects a beginning seasonality in precipitation during the Badenian age of the North Alpine Foreland Basin.