Microbially-mediated fossil-bearing carbonate concretions and their significance for palaeoenvironmental reconstructions: A multi-proxy organic and inorganic geochemical appraisal

Highlights

• Detailed geochemical, mineralogical and biomarker comparison of two carbonate concretions with their surrounding host shale.

• Minor organic matter degradation within the concretions bodies, highlighting exceptional organic mater preservation in the carbonate concretions.

• Sulphate-reducing bacteria activity localised to the nucleus of concretions.

• Potential use of carbonate concretion as palaeoenvironmental recorder due to the preservation of the host-sediment signal.

Abstract

Carbonate concretions are widespread within the geological record. However, the lack of recent known analogues creates a need for novel approaches to unravel the major microbial players involved in concretion formation and establish their suitability as palaeoenvironmental recorders. Here, we used a combination of geochemical and geological techniques to study two pyritiferous calcite concretions and compared the results with their host sediment (Toarcian “Posidonia Shale”, 183 Ma, SW-Germany).

The ¹³C-depleted nature of the concretion bodies, with average values of δ¹³C_carb (− 14.8‰), δ¹³C_org (− 32.4‰), and δ¹³C_n-alkanes (− 34.9‰), indicates that sulphate-reducing bacteria (SRB), played a major role in the concretion growth and preservation of the nucleus via the rapid decomposition of organic matter (OM). However, Rock-Eval analyses from both concretions revealed elevated hydrogen indices (HI) in the body and low HI values at the rim. These values suggest that most of the microbial activity did not occur in the concretion body but rather at the rim and at the surface of the nuclei, which generally supports the exceptional preservation of OM in carbonate concretions. Furthermore, enrichment in euhedral pyrite in the concretion rims suggests they were formed through increased activities of iron reducing (FeR) bacteria coupled to a decrease of SRB activity leading towards conditions more favourable to the direct precipitation of pyrite. Despite low δ¹³C values, the known lipid biomarkers such as acyclic extended isoprenoids or 3β-methyl-hopanes did not reveal evidence of an active methane cycling. The present study emphasises the crucial role of carbonate concretion in OM preservation and highlights their great potential as palaeoenvironmental recorders.

Introduction

Subsurface microbial communities decompose organic matter (OM) and trigger carbonate concretion formation in marine and lacustrine environments (Dale et al., 2014, Das and Tripathi, 2009, Marshall and Pirrie, 2013, Martill, 1988, Martill, 1989, Raiswell and Fisher, 2000). Carbonate concretions are ubiquitous in the geological record, and often associated with petroleum source rocks (Kiriakoulakis et al., 2000, Lash and Blood, 2004, Zatoń and Marynowski, 2004). They often encapsulate exceptionally-well preserved fossils of different ages and origins (Arua, 1991, Geraghty and Westermann, 1994, Martill, 1989, Wilson and Brett, 2013). Moreover, carbonate concretions can also contain exceptionally well-preserved molecular fossils (Kiriakoulakis et al., 2000, Marynowski et al., 2007a, Marynowski et al., 2007b, Melendez et al., 2013a, Melendez et al., 2013b, Pearson and Nelson, 2005, Pearson et al., 2005, Zatoń and Marynowski, 2004).

Contemporary analogues are rare and, over the last few decades, several studies have attempted to unravel details about when, where, and how carbonate concretions were formed by analysing their mineral and inorganic geochemical composition (Coleman and Raiswell, 1995, Coleman, 1993, Curtis et al., 1987, Marshall and Pirrie, 2013, Woo and Khim, 2006). Field observations of in-situ carbonate concretions, as well as macroscopic observations of internal structures, assisted in characterising the environment of formation. Most calcium carbonate concretions are suggested to form at a very early stage of diagenesis, within the top metres of sediment accumulation (Marshall and Pirrie, 2013, Raiswell and White, 1978, Seilacher, 2001, Sellés-Martínez, 1996). Furthermore, the presence of intact three-dimensional fossils and “card house” clay fabric in many calcium carbonate concretions is concordant with their early formation and highlights the ability of carbonate concretions to resist compaction (Das and Tripathi, 2009, Geraghty and Westermann, 1994, Lash and Blood, 2004, Martill, 1988, Zatoń and Marynowski, 2004).

The association of carbonate concretions with OM-rich pelitic shales reveals a formation under anoxic environmental conditions. In such conditions, OM decays at the sediment/water interface and is controlled by anaerobic micro-organisms. Berner (1968) and Allison (1988) established that microbial OM degradation was responsible for local changes in porewater chemistry. These changes can lead to the formation of a Ca-rich adipocere film playing a pivotal role in the formation of carbonate concretions. Sulphate reducing bacteria (SRB) obtain energy by oxidising organic compounds while reducing sulphate (SO₄^2 −) to hydrogen sulphide (H₂S). They are believed to play major role in the formation of calcium carbonate concretions (Coleman and Raiswell, 1980, Coleman and Raiswell, 1995, Coleman, 1993, Kiriakoulakis et al., 2000, Melendez et al., 2013b) based on the following general reaction:

$$2{\mathrm{CH}}_2\mathrm{O}+{\mathrm{SO}}_4^{2-}\to 2{\mathrm{HCO}}_3^{-}+{\mathrm{H}}_2\mathrm{S}.$$

The role of an active cycling of methane via the involvement, in the microbial consortium, of methanogenic archaea, anoxic methane oxidizers (see reaction below) is still poorly understood (Coleman and Raiswell, 1995, Coleman, 1993, Curtis et al., 1987, Kiriakoulakis et al., 2000, Woo and Khim, 2006). Such a consortium has been found in anoxic marine environments, notably gas hydrates (Boetius et al., 2000, Hinrichs and Boetius, 2002), but is yet to be associated with concretions.

$${\mathrm{CH}}_4+{\mathrm{SO}}_4^{2-}\to {\mathrm{HCO}}_3^{-}+{\mathrm{H}}_2\mathrm{S}+{\mathrm{OH}}^{-}.$$

Most studies of carbonate concretions have relied on inorganic geochemistry and petrological observations. However, relatively little attention was given to organic geochemical parameters to better understand concretion growth processes (Kiriakoulakis et al., 2000, Melendez et al., 2013b, Pearson et al., 2005, Wolff et al., 1991, Zatoń and Marynowski, 2004, Zatoń et al., 2011) or to establish a thorough comparison with their host rock (Marynowski et al., 2007a, Marynowski et al., 2007b, Melendez et al., 2013b).

The limited occurrence of known modern analogues for carbonate concretions (Reitner et al., 2005) complicates the use of DNA in the identification of microbial communities. However, work on modern microbialites supports a more complex ecosystem than originally expected (Burns et al., 2009, Edgcomb et al., 2014, Pagès et al., 2014a, Pagès et al., 2014b).

In order to obtain further insights into the complex ecosystems involved in subsurface diagenetic environments, multidisciplinary techniques need to be applied. Here we report the first integrative approach, using geological, organic and inorganic geochemistry, to gain a better understanding of concretion growth processes and identify the microbial communities involved in the formation of two carbonate concretions. Furthermore, a systematic comparison of the concretions with their surrounding shale was undertaken to identify geochemical variations between the concretion and the host sediment showing the concretions' potential to be used as a palaeoenvironmental recorder.

More specifically, we aim to i) characterise the timing of formation of the two concretions; ii) identify marker and footprints of microbial activity, iii) establish their significance for palaeoenvironmental reconstruction and iv) investigate the preservation properties of carbonate concretion using bulk OM proxies.