Mud description

The massive subsurface mobile mud of RP (Figure 2e) is characterized by silt and clay grain size, high alkalinity (pH 10.38 –10.65), high volumetric water content (> 200 % WV), high conductivity (23.29– 51.4 mS/cm), organic-rich (> 6 %), and strong H2S smell. For the brine the dominant anion is Cl- and the dominant cation is Na + (Table 1). Low concentration of cations such as Ca+ 2 and Mg+2 identified in the samples is key to the chemical composition of the site because due to the shortage of these cations, anions such as Cl- and CO32- favor high alkalinity of the medium (e.g., Jones et al., 1998). Massive mud also has a high content of total organic matter of 6.77 %, which is evidenced by a characteristic black color, and might be related not only to the accumulation of plant- and animal-remains during a long depositional period but also to the biologic activity of the microbial community. SEM (Figures 5a and 5b) and DRX (Figures 5e and 5f) analyses of the mud show a highly porous structure with the presence of carbonates (aragonite: Ar; and hydromagnesite: Hy), salts (halite: Ha), minor amounts of clay minerals (montmorillonite), and detrital quartz and feldspars. At higher magnification, the mud contains subhedral crystals of halite (Figure 5c and 5d). SEM images in cryo-fixed samples of the mud revealed evidence of microorganisms (Figure 6) embedded mostly in a porous, muddy network, which acts as a substrate for their growth.

 

Microbial community composition observed in the mud brine

Sedimentary environmental DNA (Ellegard et al., 2020) from three mud samples (Sed 1, Sed 2, and Sed 3) collected below the surface were analyzed for Bacteria and Archaea domains. The results include the DNA from the actual living organisms and the preserved DNA from the past when the original mud layer was deposited at the surface. For the Bacteria domain the three samples could be characterized, but for the Archaea domain only the samples Sediment 2 and Sediment 3 had sequences that could be identified. Table 2 shows the concentrations obtained for each sample and their degree of purity (ratio 260/280). The highest yield was observed for Sediment 2 from which 32.41 ng of DNA was obtained per 30 g of sample processed; the lowest yield was obtained for Sediment 3 with 16.67 ng of DNA per 30 g.

The number of filtered DNA sequences obtained for each of the samples is shown in Table 3. The minimum number of sequences obtained for a sample was about 5500, but most samples had at least 6000 sequences. The rarefaction curves were asymptotic, indicating that analyzing more sequences would yield only a limited number of more ASVs. The number of bacterial and archaeal ASVs ranged from 99 to 182. The 16S rRNA phylogenetic analysis revealed a diverse microbial component. The bacterial assemblage was dominated by Cyanobacteria (20.2–69.1 %), Firmicutes (4.4–48.4 %), Proteobacteria (15–30.6 %), Bacteroidota (9.2–15.7 %) and, to a lesser extent, Actinobacteriota, Verrucomicrobiota, and Chloroflexi (Figure 7a). For samples Sediment 2 and Sediment 3, all the bacterial phyla were recognized but for sample Sediment 1, 0.54 % of the sequences could not be classified. At order level, Synechococcales (11.1–48.5 %), Cyanobacteriales (8.5–46.5 %), Lachnospirales (1.3–38.3 %), Bacteroidales (9.2–15.7 %), Rhodobacterales (9.1–13.4 %), Phormidesmiales (1.9–11.4 %) were the better represented orders (Figure 7b). Alpha diversity metrics for the bacterial communities included observed richness (class level), Shannon-Weiner, and Simpson indices (Table 4 and Figure 8a).

For the Archaea domain, the most abundant microorganisms are related to Crenarchaeota (50–75.7 %), Halobacterota (13.6–27.2 %), Hadarchaeota (8.5–8.6 %), Thermoplasmatota (1.1–7.2 %), Euryarchaeota (0.5–1.3 %), and as minor components Nanoarchaeota and Asgardarchaeota. A small number of sequences were not classified (0.18–0.69 %; Figure 7c). At order level (Figure 7d), Nitrososphaerales (38.6–45.8 %), Halobacterales (10.9–26.4 %), and Hadarchaeia_or (8.5–8.6 %) sequences were obtained in high percentages. Additionally, Woesearchaeales, Thermoplasmatota_or, Methanomicrobiales, Methanomassiliicoccales, Methanobacteriales, and ANME-1b were identified in minor abundance. Observed richness, Shannon-Weiner, and Simpson indices values from archaeal communities recovered at subsurface in the RP lacustrine system are reported in Table 4 and Figure 8b.

 

DISCUSSION

Fluid mobility

Layers of lacustrine, organic rich, high porosity, massive clayey sediments in the crater of RP host mud mobilization and disrupt the original stratification of the ancient lake. This results in a highly dynamic geological environment. Disruption of the original stratification by the mud mobility has profound implications to the stability of the sedimentary record of RP that needs to be considered in other environmental studies that require a stable sedimentary layering. The high volumetric water content of these sediments (> 200 % WV) and deformation of the lakebed causes slow pore fluid dissipation and mud overpressure (e.g., Revil, 2002). Eventually, mud ascends and is ejected locally in mud domes. More than 76 domes or small mud intrusions were found distributed mainly on the surface at the western portion of the subsiding bottom of the former lake at RP. Their size and ubiquitous presence indicates forced mud ascent to the surface from a shallow underground source. Differences observed in shapes of the structures can be attributed to mud viscosity, differences in the brine and gas content and pore pressure of the mobile mud, and fracturing patterns in the unsaturated cap layer. When mud ascends to the surface it dries in a short period of time and the structures are preserved in the driest zone of the crater. Upward movement of mud is currently active as it has been observed the growth of larger domes and the emergence of new, smaller structures. Two main mechanisms responsible for the creation of fluid overpressure in RP mud are considered: a) disequilibrium compaction and b) gas input/generation (e.g., Wangen, 2001).

 

Disequilibrium compaction

Disequilibrium compaction results when mud is unable to drain fluids in response to loading or compressive stresses. Disequilibrium compaction forces mud to flow upwards. Structures that formed in close relation to mud displacement can be seen at the margins of the former lake including ductile deformation structures such as folds and the mud injections. The main geometrical and kinematic aspects of this deformation for the margin of the crater were explored and described in detail by Aranda-Gómez et al. (2017). In the case of RP, the injection domes formed by disequilibrium compaction show three different associations regarding their origin (Aranda-Gómez et al., 2017; Figure 3): a) Domes associated with compressive stresses generated by volume loss during fault displacement, these structures are generated by gravitational gliding/spreading and are between the largest domes in RP. The likely mechanism for the formation of these domes is overpressure formed at the diffuse detachment level that is associated with the gliding structures near the margin of the crater (Figure 4). b) Domes caused by local overpressure triggered by load associated with small landslides; these structures are formed in areas partially surrounded by megabreccias associated with landslides in areas where the calcareous platform is nearly absent. The weight of the landslide deposit can produce overpressure in the underlying wet mud triggering

mud injection (Figures 3 and 4); c) Domes and mud extrusion in portions of extensional faults/fractures. Massive mud concentrations with a characteristic "popcorn" weathering texture in relatively small, nearly circular areas suggest the presence of domes and/or "central vents" in areas at the carbonate platform scarp or in the pelagic zone. In cross-section wet mud appears to be injected in tensional fractures/faults. These structures were interpreted in the GPR profiles as domes and mud uplifting associated with gas seeps (Figure 4e).

 

Mud mobility possibly related to groundwater input and degassing in RP

Fluid mobility and mud extrusion can also be associated with the volumetric expansion accompanying the phase change associated with gas generation in the pore system or from groundwater input (e.g., Revil, 2002). RP has previously been shown to emit fluids and gases. The present-day manifestations include soil degassing and pipe-like structures (Paz et al., 2020). Bubbling can be observed in remnant brine ponds. A recent study by Paz et al. (2020) has verified the emanation of gases such as CO2 with an estimated total flow of 10.6 ton.d-1 and 6.3 ton.d-1 of CH4 in RP. These authors suggest a strong biogenic contribution in the origin of methane, while CO2 is probably a mixing among volcanic and biologic sources mainly within sediments. Gas production may be a consequence of a prolonged phase of low volcanic activity (e.g., Loher et al., 2018) and/or result of underground biological activity. Small amounts of methane can produce expansion and drive extrusion (e.g., Brown, 1990).

A close spatial association of large domical biohermal thrombolites and the annular fault (i.e., the diatreme - country rock boundary; Lorenz, 1986) suggest that this structure might have controlled groundwater flow into the paleolake before desiccation (Aranda-Gómez et al., 2017; Sánchez-Sánchez et al., 2019). Further evidence of this channelized, preferential groundwater flow includes the presence of chimney-like structures and the thrombolytic texture of most microbialites (Sánchez-Sánchez et al., 2019), which also suggests an upward groundwater flow during the lake period that might have helped to maintain a stable water level in the lake. The presence of springs associated with groundwater inflow was observed during the lake period in the past century (Escolero-Fuentes and Alcocer-Durán, 2004). We interpret this evidence as an indication of active input of fluids into the mud layer.

In the GPR profiles dome-shaped geometries were observed below the desiccated crust at the center of the crater, in areas not directly associated with the disequilibrium compaction in the margins. In this zone the surface dry mud crust forms a brittle cover atop the wet mud (Figure 4d and 4e). In the central part of the crater, we measured about 1.2 m of dry brittle mud three months after the end of the rainy season of 2018. The vertical transition between dry and wet mud in RP is diffuse because pore pressure increases with depth and almost certainly has a seasonal depth variation. In this setting, particularly at the western side of the lake bottom, wet mud has formed several diapir-like mud injections whose basal diameter varies from several tens of meters to less than one meter in diameter. These structures interpreted from the GPR profiles present surface evidence of fluid leakage as well as mud extrusion, indicated by the presence of a popcorn texture in the mud that reached the surface.

 

Insights from the microbial communities DNA fingerprint documented in the mud

This is the first study of sedimentary environmental DNA for identifying the bacterial and archaeal communities in the near-surface sediments of Rincón de Parangueo maar. Our results can provide an insight into the identities of members of the bacterial and archaeal communities in the three samples obtained in the crater discharging methane. As a prospective study, our results have limitations, one is the small number of samples collected (three) that prevent a complete statistical analysis among them. Despite this limitation, the high-quality data of the Bacteria and Archaea phylotypes allow us to calculate alpha diversity indices for each sample, making it possible to differentiate diversity values from previous studies in the area. Alpha diversity and observed ASVs of the bacterial and archaeal community measured in mud samples were lower than those reported by Ibarra-Sánchez et al. (2020) in superficial sediment samples. Despite physico-chemical parameters like grain size, alkalinity and conductivity were similar in both investigations, this downward trend in diversity values is consistent with the results, since it is known that the relative abundance of 16S rRNA genes from Archaea and Bacteria generally decreases with depth of sediment (Hoshino and Inagaki, 2019). The results reveal a connection of the occurrence of specific microbes with the geological environment, can be particularly valuable for understanding community composition in future works, and give useful information on the relative importance of specific environmental drivers. Our interpretation is thus dependent not only on the DNA results but also on understanding contemporary geological and ecological controls as well as the sedimentation environment and its context.

Additionally, sedimentary environmental DNA does not distinguish from living organisms or those derived from genetic archives of past environments preserved in dead cells, resting stages, or as an extracellular fraction in the mud (Torti et al., 2015; Vuillemin et al., 2017; Giguet-Covex et al., 2019). In RP, the persistence of extracellular DNA may be influenced by adsorbing to soil minerals. Silt and clay minerals could protect extracellular DNA from nuclease mediated enzymatic hydrolysation and by adsorbing DNases and nucleases, thereby reducing the potential for enzymatic DNA restriction (Levy-Booth et al., 2007). Montmorillonite, a clay mineral identified in the mud samples (Armienta et al., 2008; Aranda-Gómez et al., 2013), has a higher DNA binding capacity than other minerals (e.g., kaolinite) (Pietramellara et al., 2001). The adsorption of DNA to clay minerals is enhanced by divalent cations like Mg2+ and Ca2+, also described for the samples, forming bridges between DNA and clay minerals above pH 5 (Levy-Booth et al., 2007). Mineral mud properties allow the conservation of extracellular DNA at high pH (> 10) in RP. Thus, the sedimentary environmental DNA provides simultaneous information on multiple taxa potentially composed of phylotypes that live or lived in the sediments, probably within the last hundreds of years.

Our results suggest that the overall DNA fingerprint obtained shares similarities with the DNA of the microbial communities identified previously on the crater surface at the phylum level (Sánchez-Sánchez et al., 2019; Ibarra-Sánchez et al., 2020). Bacteria phyla such as Cyanobacteria and Proteobacteria were abundant in two mud samples (this work, Sediment 1 and Sediment 3) as well as in the surface samples (Sánchez-Sánchez et al., 2019; Ibarra-Sánchez et al., 2020). Phyla identified in the mud such as Firmicutes, Actinobacteriota, Bacteroidota, Verrucomicrobiota, and Chloroflexi were also previously identified on the surface. These bacterial phyla dominate often in sediment samples of saline lakes (Vuillemin et al., 2018) and play an important role in biological cycles at these habitats. For instance, members of Proteobacteria, Firmicutes, Actinobacteriota, and Bacteroidota are heterotrophic organisms, so they are involved in processes of organic matter transformation (Sorokin et al., 2014; Ibarra-Sánchez et al., 2020). Phylotypes belonging to Firmicutes can fix nitrogen and members of Deltaproteobacteria and Firmicutes participate in the sulfur cycle (Sorokin et al., 2014).

The archaeal DNA obtained at depth in RP was classified into seven phyla: Crenarchaeota, Halobacterota, Hadarchaeota, Thermoplasmatota, Euryarchaeota, Nanoarchaeota, and Asgardarchaeota. Crenarchaeota was the most abundant phylum found in the mud at depth, in contrast to surface samples where the dominant phylum was Euryarchaeota (Sánchez-Sánchez et al., 2019; Ibarra-Sánchez et al., 2020). Crenarchaeota are globally ubiquitous, and members of this phylum are often the most abundant Archaea in various environments including marine sediments (Kubo et al., 2012) and salt marsh sediments (Seyler et al., 2014). Candidatus_Nitrososphaera, the dominant genus identified in mud samples for the Crenarchaeota phylum, is a moderately thermophilic microorganism (46 °C) with demonstrated capacity for ammonia oxidation (Hatzenpichler et al., 2008). These archaeal genera have been found to be one of the dominant phylotype in hypersaline sediments from the saline-alkaline soils of the former lake Texcoco (Navarro-Noya et al., 2015) and, also was found by Ibarra-Sánchez et al. (2020) as the dominant genera in superficial sediments samples (0–20 cm) in RP. Halobacterota, the second archaeal phylum most represented, are obligately halophilic (Papke et al., 2011), which explains their high relative abundance in the alkaline saline sediment of RP. Some habitats for these microorganisms are widespread around the world in salt lakes, hypersaline soils, underground salt deposits, and evaporation ponds (Oren et al., 1995; Arahal et al., 1996; Wainø et al., 2000; Mesbah et al., 2007; Papke et al., 2011; Kambura et al., 2016; Han et al., 2017).

 

Methanogenic microorganisms and biogenic methane production in the sediments

Phylotypes of methanogenic Archaea identified in RP comprise high percentages (13.2–32.1 %) of the total archaeal DNA, and include four phyla: Crenarchaeota, Halobacterota, Thermoplasmatota, and Euryarchaeota (Lyu et al., 2018). Archaea methanogenic microorganisms are strictly anaerobic and convert several substrates (i.e., H2 + CO2, methyl compounds, and acetate) into methane gas in order to obtain energy. Methanogens groups occupy geothermal CO2 and H2 as the predominant substrates for methane production in places that emit gases, such as hot springs and volcanic fissures (Whitman et al., 2006), making them valuable for assessing volcanic degassing. Some of the organisms reported here have been found in deep sediments and soils elsewhere (Paul et al., 2012). The Bathyarchaeia class, member of Crenarchaeota, was previously reported in the deep sediment biosphere of lakes (Thomas et al., 2020) and subseafloor sediments (Kirkpatrick et al., 2019). Methane production by Bathyarchaeia was hypothesized by the metabolic reconstruction of its genome, the key genes associated with archaeal methane metabolism including methyl–coenzyme M reductase complex suggests their potential for diverse methyl compound utilization for gas production (Evans et al., 2015). The order Methanomicrobiales of Halobacterota, is a hydrogenotrophic methanogen exclusively restricted to CO2 as a substrate for methanogenesis with the principal electron donor being H2 (Costa and Leigh, 2014). It has been previously reported in hot springs of the Central-Eastern Tibet (Huang et al., 2011), wetland soil (Tian et al., 2010), in two alkaline Indian hot springs (Panda et al., 2016), and soda lake sediments (Antony et al., 2012). The Methanomicrobiales and Methanomassiliicoccales orders of Thermoplasmatota use an external H2 source to reduce methyl-compounds into methane (Borrel et al., 2014). They were originally recognized in digestive tracts of animals (Poulsen et al., 2013) but also have been reported in natural wetlands, rice paddy fields, subseafloor and freshwater sediment (Borrel et al., 2013). Methanobacteriales is another hydrogenotrophic methanogen order found in this study belonging to the Euryarchaeota phylum (Buan, 2018). This order has been identified in sediments of fluvial (Chaudhary et al., 2017), lake (Yang et al., 2017), and mangrove environments (Li et al., 2016).

Based on the 16S rRNA results RP mud contains microorganisms with the potential to produce methane. Methylotrophic methanogens, the most represented methanogenic microorganisms in the sediment samples, are common in hypersaline and marine sediments (Lyu et al., 2018). Obligately methylotrophic methanogens have an ecological advantage over other groups of methanogens since they utilize compounds such as methanol and methylated amines, avoid competition with sulfate-reducing Bacteria also present in this type of environments (Antony et al., 2012). Methanogenic Archaea use organic solutes for osmotic stabilization in hypersaline environments at a high energetic cost, methylotrophic methanogenesis produces more energy than methanogenesis from acetate and CO2 reduction (Oren, 2001). The greatest amount of energy generated by this type of methanogenesis may provide a possible explanation for why methanogenesis on methylated compounds is more feasible at the high salt concentrations in the RP sediments. On the other hand, hydrogenotrophic methanogenesis suggested by the identification of Methanomicrobiales and Methanobacteriales phylotypes could be explained by the presence of post eruptive gases still released in the RP crater. The huge amounts of CO2 gas verified by Paz et al. (2020) could be being reduced by methanogenic Archaea for methane formation.

Mud in RP could be considered as analogue habitats of fluidized mobile muds in submarine mud volcanoes, since they consist of a mixture of fine-grained, fluid-rich mobile sediment (i.e., Pachiadaki et al., 2011). Active fluid seepage and gas bubble release are common in other similar environments such as submarine mud volcanoes driven by overpressured subsurface sediment found at tectonically active and passive continental margins (Lazar et al., 2011). Mud volcanoes emitting biogenic methane have been characterized by previous molecular genetic analyses, detecting the three methanogenic pathways (methylotrophic, hydrogenotrophic and acetoclastic) (e.g., Lazar et al., 2011; Lazar et al., 2012). These former authors report that methylotrophic methanogenesis was the most active process in a mud volcano where hypersaline conditions persist.

 

 

CONCLUSION

We report the presence of a layer of mobile mud below the surface of the crater RP. Mud is organic rich, high porosity, with high volumetric water (> 200 % WV), massive, clayey, and has a sedimentary origin. This mud layer hosts present-day mobilization triggered by two combined processes, disequilibrium compaction and pore overpressure enhanced by an input of groundwater and gas content in the sediments. Mud mobilization disrupted the stratification of the ancient lake and produced mud tectonic structures such as injection mud domes, recorded in field and in GPR profiles. Mud ascends from a shallow underground source to the surface and results in more than 76 domes or small mud intrusions distributed mainly at the western portion of the former lake at RP.

The microbial communities’ fingerprint, or sedimentary environmental DNA, documented in the mud provide an insight into the identities of members of the bacterial and archaeal communities in three mud samples, and allow to discuss the probable role played by biogenic methane in mud mobilization observed on the surface. We emphasize that given the small number of samples available for this work, the details of the methanogenic activity in the RP sediments needs to be corroborated with further and more detailed studies. We hypothesize that pore pressure in the mud may periodically be increased as a consequence of microbe’s activity; for instance, the biogenic degradation of organic matter (i.e., methanogenesis). We identified methanogenic microorganisms in the DNA fingerprint. The phylotypes Bathyarchaeia, Methanomicrobiales, Methanomassiliicoccales, and Methanobacteriales were recognized in the mud samples, giving way to the possibility of biogenic gas production by them. Analogue habitats of fluidized or mobile muds are those observed in brine‐sediments (mud volcanoes) driven by overpressured subsurface sediment where methanogenic microorganisms have an active influence in the methane fluxes. Coupling the geological and microbiotic factors can provide a holistic view of this dynamic extreme environment.

 

ACKNOWLEDGMENTS

We thank Sara Solís Valdez, Marina Vega, Ricardo Carrizosa and María Carolina Muñoz Torres for help on the soil and water analysis, and Luis Aguilar, Alejandro de León, Carlos S. Flores and Jair García of the Laboratorio Nacional de Visualización Científica Avanzada (UNAM) for assistance in the bioinformatic analysis. Barbara Moguel is thanked for help on the DNA analysis. We thank Dante Morán-Zenteno and two anonymous reviewers for their revision that helped to improve this work. This work was supported by projects of the Laboratorio de Mecánica de Geosistemas (LAMG, UNAM). Sánchez-Sánchez received a PhD scholarship from Consejo Nacional de Ciencia y Tecnología (CONACyT).

 

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