Remarkable preservation of microfossils and biofilms in mesoproterozoic silicified bitumen concretions from Northern China

Prokaryotes, often generally referred to as “bacteria,” are the original and thus oldest life on Earth. They have shaped the chemical environment of the Earth, but they are difficult to find as ancient fossils due to their subtle structure. Here we report well-preserved fossilized microbial communities in silicified bitumen concretions from unit 3 of the Xiamaling Formation (1.39Ga) in northern China. The numerous silicified bitumen concretions are in a variety of forms including ellipsoidal, spindle, and pancake ones, with diameters of 1 ∼ 16cm and thicknesses of 0.5 ∼ 3 cm. The principal planes of the concretions are at low angle or directly parallel to the depositional plane level, showing obvious depositional characteristics. The concretions are silicified with abundant bitumen inside. Many different kinds of microbial fossils are found in the bitumen, including spherical forms, rods, and filaments, and some of the microbes are aggregated together in the forms of multicellular structures. These concretions preserve a delicate Mesoproterozoic biotic community.


Introduction
The Mesoproterozoic Era (1.6-1.0Ga) is intermediate between the generally well-oxygenated Earth-surface conditions of the Phanerozoic Eon and the generally anoxic Archean Eon.The Mesoproterozoic Era was also a time evolutionary transition with the emergence of eukaryotic communities [1][2][3][4], although some argue that it is an Era of geochemical stagnation, the so-called "boring billion" [5,6].
To better understand the nature and evolution of the ancient biosphere, including the ecology of paleoenvironments, we can potentially probe the ancient fossil records.There are some reports of Mesoproterozoic fossils about the discovery of eukaryotes all over the world [7][8][9][10], including the acritarchs with circular excystment, multilayered walls, or ornamentation, multicellular filaments, and algal thallus [11], string-of-beads fossils named Horodyskia moniliformis and Horodyskia williamsii from shales in the 1.48 Ga lower Appekunny Argillite of Glacier National Park [12], diverse eukaryotic fossils like Tappania plana from the Early Mesoproterozoic Roper Group in Australia, and Horodyskia moniliformis from the Mesoproterozoic Bangemall Group [13].Even the possible crown-group multicellular rhodophytes in 1.6 Ga Lower Vindhyan Supergroup in central India were reported, antedating the oldest previously accepted red alga in the fossil record by about 400 million years [14].
While it is generally shown that Mesoproterozoic microfossils are characterized by cyanobacteria, unfortunately, insights into the behavior of ancient bacteria, especially during the Proterozoic Eon, are hampered by a sparse geological record [15,16].Thus, unlike the later emerging and fossilizable animal hard parts [17], microbes in general, and prokaryotes in particular, have tiny body size and weak structures that are very difficult to fossilize and preserve [18].Therefore, there are relatively few reports of bacteria fossils in their natural settings, although the compressed, straight, circular to sinuously coiled megascopic and helical carbonaceous fossils including Grypania spiralis and Katnia singhi in the Early Mesoproterozoic Rohtas Formation in India were believed to be possible cyanobacterial origin [19].
We note, however, that early silicification offers a potential avenue for microbial fossilization, preserving some of the oldest fossils known in the geologic record.Thus, some of the earliest microfossils are in shallow-marine silicified deposits (3.2 Ga) [20], or they adhere to the detrital quartz grains of their host sediments (3.4 Ga) [21].Here we report some well-preserved bacterial communities from the unit 3 of Xiamaling Formation, northern China, in Mesoproterozoic Era.The fossilized organisms, observed in what appear to be different forms, provide direct evidence of ancient bacterial biomass records in Mesoproterozoic Era.

Geological Setting
The Xiamaling Formation is deposited on the North China Platform and immediately overlying the Tieling dolomite.The age of the Xiamaling Formation has been constrained to 1392.2 ± 1.0 Ma for the bentonite layer at the top of unit 3 and 1384.4 ± 1.4 Ma for the tuff layer 52 m above the bentonite [22].Sediments of the Xiamaling Formation began their deposition at ∼1,400 Ma at paleolatitude between 10 ∘ N and 30 ∘ N (with an uncertainty of some 10 ∘ latitude) [23].
We previously divided the Xiamaling Formation informally into 6 units [24].Units 5 and 6 have yet to fully described, whereas unit 4 comprises alternating iron oxiderich and iron oxide-poor sediments or repeating bundles of alternating sediment type, grading upwards into alternating layers of black shale and chert of unit 3 and further upwards into unit 2 comprised predominantly of black shale alternating with grey and black silty mudstones [22,24].Uppermost unit 1 is composed of alternating layers of black and green shales.Black shales are very common in all of the Xiamaling Formation, except for the lowermost 2 units.The total organic carbon (TOC) of the Xiamaling Formation ranges from less than 1 wt% in the green and red sandy mudstones to over 10 wt% in the black shales [22].Our previous work suggests that the sediment geochemical fluctuations reflect the orbital forced changes, known as Milankovitch cycles, controlled the wind patterns, rainfall, and ocean circulation, and then translated into sediment geochemistry [22].
In addition to the highly fluctuating sedimentation, we also found concretions and bitumen in unit 3 of the Xiamaling Formation (Figure 1).Most of the concretions occurred at low angle or parallel to the depositional plane, embedded in the surrounding black shales or green chert (Figures 1(b) and 1(c)).The concretions were ellipsoidal or pie-like in form, with diameters in the range of 1 to 16 cm and thicknesses in the range of 0.5 to 5 cm (Figures 1(d) and 1(e)).Spherical or granular soft materials could be seen with black gloss and a smell of bitumen after the ellipsoidal concretions were broken.After a few minutes of exposure, visible color variation could be observed on the fresh surface of the internal bitumen, due to the possible oxidization of reactive iron.These observations suggest that the concretions are well closed within an internal reducing environment.Nonconcretionary bitumen layers or small round bitumen granules were also found sandwiched in the black and green shales, but no bacterial fossils were found in these bitumen types (Figures 1(f) and 1(g)).

Materials and Methods
Well-preserved bitumen concretions were carefully separated from the surrounding rocks and were then progressively cleaned with diluted hydrochloric acid (10%), distilled water, and high purity chloroform to remove exterior contaminations.Whole concretions, external shell, and internal bitumen were imaged in three dimensions (3D) through Xray layer mapping.
Because of the fragility of the bitumen, it was impossible to cut through them with a saw.Instead, the bitumen was opened by breaking.Small bitumen samples were ground to powders and analyzed for elemental and biomarker composition.For comparison, the fresh surrounding rocks, including the black shales and green cherts, were also sampled, crushed, and analyzed.We attempted to make petrological thin sections to detect the structure of bitumen and the relationship of fossils and bitumen but failed due to the high fragility of the bitumen.Instead, we use scanning electron microscope (SEM; VEGA 3, TESCAN) to observe the bitumen for internal biological structures.
3.1.Morphological Imaging.3D morphological imaging was performed by X-ray tomographic microscopy (XTM; XM-Tracer-225, Institute of High Energy Physics, China) at the Institute of High Energy Physics (IHEP), Chinese Academy of Sciences (CAS), China.A set of grey-level images were obtained.Then, the 3D structures of the concretions and their internal bitumen were rendered with high resolution (<27 m) through image denoising, image enhancement, contour extraction, and triangular surface reconstruction with Amira5 software.
Microscopic observations of the external shell and internal bitumen using scanning electron microscope were performed at the Key Laboratory of Petroleum Geochemistry (KLPG), China National Petroleum Corporation (CNPC).Fresh surfaces were gold-coated and photographed with the enlargement factor not lower than 10,000.Semiquantitative data of the major elements (C, O, Ca, Al, Fe, Mg, and Si) were gained with a coupled energy dispersive spectrometer [EDS].

Major Elements and Rare Earth
Elements.The contents of major elements (Al, Ca, Si, and Fe) and rare earth elements (REEs) for the concretions and rock samples were obtained by X-ray fluorescence spectrometry (XRF; PW2404, Philips Electronics) and high-resolution inductively coupled plasma mass spectrometry (ICP-MS; Element I, Finnigan MAT) at the Key Laboratory of Petroleum Geochemistry (KLPG) at the China National Petroleum Corporation.Detailed analytical procedures can be found in Zhang et al. [26].Shale standard material (GBW 03014) was used to evaluate analytical accuracies, with the relative standard deviations (SD) of less than 1.0% for the major elements and less than 1.5% for the REEs.

The Components of Concretions and Surrounding
Rocks.XTM studies reveal an egg-like morphology for the concretions, with internal spherical cores and external dense shells (Figure 2).Rapid X-ray signal intensity changes between the shell and core imply large material density differences between the internal materials and external shell (Figure 3).XRF data show that the major component of the shell was silica (>90 wt%), at higher concentration than in the surrounding rocks (<60 wt% in the black shales and <90 wt% in the green chert) (Table 1).Correspondingly, the iron and aluminum contents in the concretion shells were 5 ＧＧ 50125 200   Green chert SC-BS-2 SC-GC-2 Figure 4: Chondrite-normalized REE patterns of the concretions and surrounding rocks in the Xiamaling Formation.SC-BS and SC-GC mean the silicified concretions in the black shales and green cherts, respectively.The contents of REEs of chondrite were referenced from [25].much lower than those in the surrounding black shales or green cherts (Table 1).
EDS data showed high contents of carbon (∼80 wt%) in the core, proving its organic origin.These internal core materials were soluble in chloroform, with a proportions of asphaltenes (∼90 wt%), as is typical of bitumen (Table 2).

The Bacterial Fossils in the Concretions
. Some of fossillike biological structures were found scattering or embedding in the bitumen.Most of them had a smooth surface, but some were winkled, with a size range of 0.5∼5 m, a characteristic of prokaryotes [27,28].Energy Dispersive Spectra (EDS) analysis shows that the carbon content of biological structures could be up to >30%, much higher than the carbon content in regular carbonate minerals, suggesting these fossil-like substances might be bacterial fossils rather than mineral crystals [29,30].The contents of Si and O were 15%∼27% and 0.5%∼4%, respectively, indicating silicification of these possible microbial fossils.Of course there is possibility that Si and C could be from the bitumen substrates, so the EDS results for the biological structure just work as a reference value.
General parameters used to identify microbial fossils include their size, shape, and the chemical composition [29].And comparison of modern and Precambrian living forms confirms the inference that cyanobacterial communities are very conservative and have changed insignificantly both morphologically and physiologically during the past two billion years [31].So modern prokaryotes growing with a wide range of recognizable morphologies provide a general reference for fossil identification.We classify the fossil-like and biofilm-like structures scattered on or embedded in the surface of the bitumen into three major categories: spheres, rods, and vibrios, based on their shapes from SEM.Each of these is present with unique colonial organization.

Category 1:
Sphere Shaped Structures.Most spheres are deflated, with a smooth and regular surface.The average diameter is about 1 m.They scatter on the surface of the bitumen and surrounding silicolites.They are found dispersed, in couples, or clustered together (Figure 5).All of these shapes are similar to modern coccus bacteria, where modern cocci sometimes maintain a distinct arrangement after they divide, giving an important reference role in classification.Figures 5(a) and 5(b) are like modern monococcus, split on two dimensions.In Figures 5(c) and 5(d), every four cells formed together, like modern tetracoccus or staphylococcus.Figure 5(e) shows clusters of various size.Overall, whether found singly, in small groups or in biofilms, these forms show great similarity to modern coccoid bacteria.These fossils also display evidence for cell shrinkage and cell wall collapse into a vacated cytoplasmic space during fossilization (Figure 5).The spherical fossils also display regular stripes on the cell surface (Figures 5(b), 5(c), and 5(e)).Some fossils were also found closely packed in a possible extracellular polysaccharide matrix (EPS) (Figures 5(e) and 5(f)).The specific morphology of these structures, combined with their high carbon content, strongly suggest a biogenic origin (Figure 5).
We also find that many of these preserved structures coexisted in a small closed concretion.The subpolygonal honeycomb coccoid structures in the Xiamaling Formation show some wall-to-wall contact, with four or even more coccoids as neighbors (Figures 5(c)-5(e)).Also, some of the fossil forms, as shown in Figures 5(e) and 5(f), are reminiscent of microbial mats or biofilms.Nearly all of the observed forms including spherical, rod, and vibrioid forms display aggregated modes including sheets, chains, and biofilms.

Category 2:
Rod-shaped Structures.Most of the rodshaped forms are found in rods and cylinders, with blunt or sharp ends (Figure 6).The length and width are about 1.0 to 2.0 m and 0.2 to 0.5 m, respectively.These structures are presented singularly and in chains, with possible dissepiment structures within the fossil cells (Figures 6(j) and 6(k), as the arrow shows).These forms show a great deal of similarity with modern bacillus.Possible septum-like features may be the junction points for individual rod cells.For convenience of description, the rod structures are grouped into three categories.Figure 5: SEM photomicrographs of the spherical bacteria fossils and the colonial structures.EDS data of (a) and (d) were showed in Table 1.

Category 2a: Straight Rod and Round End (Figures 6(a)-6(c)).
Single or several structures cluster together, projecting from the bitumen surface.They have straight and rounded ends, 1.5 to 5 min length and ca.0.5 m width.Rods are parallelsided, with a smooth, clean appearance.The chemical composition is dominated by C, O, and Si.It is possible that the rod-shaped structures were originally bacteria that acted as a template for mineral deposition, which then replaced the organic material [32].

Category 2b: Curved Rod and Round End (Figures 6(g) and 6(h))
. These structures are scattered on the surface of the bitumen and silicolites, with a curved structure and round end, 2 to 4 m in length, 0.5 m in width, presenting a smooth, clean appearance.They have the chemical composition of C, O, Si, and Fe or C, O, Si, and Ca.

Category 2c: Curved Rod and Sharp End (Figures 6(i)-6(m)).
These structures have a good three-dimensional form.They occur in pairs or scattered on the surface of the bitumen and silicolites, with dissepiment sometimes in the middle of the structures, some evidence of cell division (Figure 6(m), as the arrow shows).These structures are usually slightly crooked with a length of ca. 2 m, a width of 0.5 m, and a smooth, clean appearance and sharp end.The chemical composition is mainly C, O, Fe, and Si.These rod-shaped structures resemble the modern bacillus bacteria in their size range and distribution.Surfaces are usually smooth, occasionally granular.Some of the cells existed in chains of two or three through end-to-end contact, with possible internal channel in each cell (Figures 6(j), 6(k), and 6(m)).

Category 3: Navicula Structure (Figures 6(n) and 6(o)).
This unusual feature is comprised of collapsed surfaces, traversed by deep grooves in the center of the structure.The structure has an overall length of ca. 2 m, a width of ca.0.4 m, and a depth of ca.0.2 m, with a smooth, clean appearance, while having no ridges.Analyses showed a narrow range of elements C, O, and Si.The elongated Figure 6: SEM photomicrographs of the rod bacteria fossils and biofilms.EDS data of (a), (b), and (c) were showed in Table 1.
grooves and wrinkles could be possibly presumably produced by dehydration.

Category 4: Filaments/Tubes Bacteria Fossils (Figures 6(p) and 6(r)).
The surfaces of the individual units of the structure are irregularly undulating, very similar to the modern filamentous bacteria.The diameter of this possible filamentous fossil is 0.2 m.The long units are divided into many cells by some structure like septate hyphae and the biomass could possibly assimilate nutriment by it.This kind of fossil structure shows C, Si, and traces of Al and Fe.
Anyway, some ancient bacteria-like forms have proven controversial [33][34][35], and some ancient fossil microbial forms are regarded as the result of the evaporation and precipitation of rocks or the transformation of soft sediment and the silicious solution [36,37].Thus, we appeal to general parameters used to establish microbial fossil biogenicity including the characteristics of size range, shape features, distribution abundance, and chemical compositions [29].As prokaryotes have likely undergone little morphological evolution through Earth history, morphological comparison with modern bacteria provides the general reference guiding our ancient bacterial fossil identification.Thus, in drawing conclusions as to whether these fossil microbes from the Xiamaling Formation are from the Mesoproterozoic Era, we appeal to the criteria used during similar interrogations of possible Precambrian prokaryote record [28,38].Based on above observations and discussion, we emphasize the observed structures are indigenously syngenetic microbes.
As the microbes are found within the bitumen inside the highly silicified concretions, they should occupy the bitumen before silicification or contemporaneous with the formation of concretion, not invaded later.Thus, the age of the microbes could be linked to the age of the concretions.Silicification could have resulted from either hydrothermal or digenetic processes, which can be distinguish based on REE patterns [40,41].Indeed, the concretions display exceptionally low contents of ΣREE, slight LREE enrichment, and occasional positive Eu anomalies, quite different from the patterns observed in the sedimentary chert (Figure 4).Therefore, the concretions did not form by simple digenetic remobilization of sedimentary chert, and the REE patterns themselves suggest another source for REE and possibly also for the silicon for the concretions [40].Thus, the concretion formation might be related to a hydrothermal event.
Good candidates for hydrothermal activity are found in Zhaojiashan (about 10 kilometers away), Qinyu (about 100 kilometers away), and Kuancheng area (about 200 kilometers away), where, in each locality, 3∼4 layers of intrusive diabase are found in the unit 3 of Xiamaling Formation.These have U-Pb isotope age of 1320 ± 6 Ma and 1327 ± 2.3 Ma [42,43] and postdate deposition of unit 3 by about 70 million years.Therefore, the concretions housing bitumen-associated microbes might be silicified by a local heating of diabase intrusion at about 1320∼1327 Ma, and before this, as the bitumen formed, microbes would have been attracted to the available organic matter provided by the bitumen.It is quite likely that the bitumen sustained the microbial population from the time of their colonization, some unknown time after sediment deposition at about 1390 Ma [22], continuing to the time when the bitumen silicified at about 1325 Ma.
The high contents of silicon in most of the microfossils (Table 1) demonstrate the critical role of silica-saturated water in promoting fossil preservation.Experiments of artificially silicified microorganisms have demonstrated that most microbial cells were generally silicified through the silicification of the outer cell membrane, which might have resulted in the bacterial apoptosis and left the silicified membrane intact [44].Of course, most of time, the cells will likely lose their cytoplasm through the silicification process, and their original three-dimensional shapes also might change as seen in Figures 5 and 6.Anyway, the microbes themselves were preserved in silica during this silicification process, leading to their exquisite preservation.

The Ecological
Meaning.These ancient microbes are intimately associated with Xiamaling Formation bitumen and therefore likely occupied the deep biosphere at sufficient depth or temperature for bitumen formation to occur, since the bitumen of unit 3 is ranked as either immature or of early thermal maturity, indicating that the heating temperatures should be about 90 ∘ C [45].Combining the size, shape, surface features, dissepiment, and the biological association, we can get the conclusion that most of the fossils should not be crystals of the permineralizing agent or migrated through fissure and fracture, but mineralized bacterial cells.It is, unfortunately, impossible from morphological considerations alone to identify the exact physiology of any of these organisms.The microbes are not associated with pyrite so sulfate reduction seems an unlikely metabolism.In the lack of any other metabolic oxidants (iron and manganese oxides and nitrate, e.g.), it would seem likely that the microbes were involved in either fermentation or possibly also methanogenesis, but it is difficult to say much more than this.
The aggregated bacterial populations adhere to each other on the bitumen as found in typical biofilms [46,47], where microbial cells are typically embedded in EPS [48].Indeed, the cells in Figures 5(e) and 5(f) seem to be preserved in a fossilized extracellular EPS-like matrix.Anyway, all of these aggregated bacteria likely form a consortia life style, a major form of microbial life, although this life style is poorly discussed and often confused with species-specific defense mechanisms.The consortia life style benefit is a number of aspects of life and the economical utilization of critical resources [49], making microbial respond to their specific microenvironmental conditions [50].Also this life style forms some secondary structures as an attempt to benefit a population such as aiding in the search for food, resisting aggression, or striving for better life style [51,52].These kinds of bacterial aggregations might indicate some cooperative, unselfish behavior of the individual members like multicellular organisms.Some bacteria might also maintain their primary metabolism and physical characteristics, while others may be more altruistic to small size, collapsed, or wrinkled (Figures 5, 6(n), and 6(o)).Previous researches have shown that the aggregated life styles as found in biofilms represent a stable juxtaposition of cells and physiological cooperation and are much more efficient for living than mixed populations of free-living planktonic organisms [53,54].Whether these fitness advantages benefited the survival of the whole original bacteria population still needs to be confirmed.
The aggregated bacterial colonies form partially overlapping, locally recruited microcommunities.The single cells might represent noncooperating individuals, a prologue of the collapsed microcommunity [55], while the aggregated bacteria in these bitumen concretions constitute a stable microbial ecosystem.We can speculate that the aggregated bacterial species communicated via secreted molecules or through cell-cell contacts in what may have been a demonstration of social behavior [56], an essential trait of organisms.In another possible expression of communication, some of the spherical fossils have regular stripes, similar to the distinctive striations of "cable" bacteria, where the striations contain conductive materials allowing the transport of electrons over long distances of a cm or more [57].
There are fundamental distinctions between bacteria and multicellular organisms, although there are indeed similarities between biofilm bacteria, aggregated colonies in our bitumen, and multicellular organisms exhibiting some cooperative, unselfish behaviors [58].In any event, the discovery of fascinating biofilm fossils and their physical cell-to-cell contact within biofilms shows that prokaryotes might have been well adapted to their surroundings and communicated and coordinated for the benefit of the whole community, a type of microbial behavior that existed since the Mesoproterozoic Era.

Conclusions
Although Mesoproterozoic Era is widely disputed between biological evolutionary stagnation time and macroscopic multicellular eukaryotic diversified time, our research from body fossils and molecule fossils declares that the bacteria is still the dominated biomass at that time.The silicified concretions in Xiamaling Formation have exquisite three-dimensional bacteria colonies in a remarkable state of preservation.The bitumen acted as matrix for microbe life to provide food.The microbe should be indigenous bacteria according to the judging criterion.According to the biomarker comparison, the bitumen in the core of the concretion should come from the surrounding black shales, with the help of hydrothermal activity and later silicification with the bacteria by the thermal water.So the age of bacteria should be 1.32 Ga, likely contemporaneous with the age of the nearby intrusive diabase.Although some bacteria form in biofilms or aggregates, they are not multicellular organisms, just illustrating the early state of cooperative, unselfish behaviors, having great ecology meaning.Therefore, the bitumen concretions provide an ideal living space for the bacteria in Mesoproterozoic Eon.

Figure 1 :
Figure 1: Generalized stratigraphy of unit 3 of Xiamaling Formation (a), representative photographs of the bitumen concretions embedded in black shales (b) and green cherts (c), the ellipsoidal or pie-like concretions (d-e), and the bitumen layers sandwiched between the black shales (f) and green shales (g).

Figure 2 :
Figure 2: Selected ellipsoidal-type concretion (a) and the reconstructed three-dimensional imaging with resolution of 27 m (b-d).

Figure 3 :
Figure 3: Sudden X-ray signal changes in the shell and core show great material density differences between internal and external substances.The concretion sample was the same as that in Figure 2.

Table 1 :
Major and rare earth elements contents in the concretion shells and surrounding rocks.LREE: light rare earth elements, containing La, Ce, Pr, Nd, Sm, and Eu; HREE: heavy rare earth elements, containing Gd, Tb, Dy, Ho, Er, Tm, Yb, and Lu.

Table 2 :
The group components of the internal materials in the concretions.The sample numbers were same as those in Table1and Figure4.