Formation of calcite in the presence of dissolved organic matter: Partitioning, fabrics and fluorescence
Introduction
The organic matter (OM) components in soil contain more than three times as much carbon as either the Earth's atmosphere or terrestrial vegetation and are sensitive to climatic and environmental changes (Schmidt et al., 2011). Soil organic matter (SOM) is a heterogenous assortment of organic compounds ranging from intact plant materials to highly oxidised carbon in carboxylic acids at different degradation stages (Lehmann and Kleber, 2015), and also includes microbial biomass. Soil organic matter can adhere to and be strongly mixed with soil minerals, and therefore the number of compounds that may constitute soil organic matter is effectively limitless, and no single chemical description can be given (Evans et al., 2005). A fraction of soil organic matter is soluble and can be transported in dissolved or colloidal form into groundwater (Hartland et al., 2012). Dissolved organic matter is ubiquitous in natural environments and is arbitrarily defined as organic matter with particle sizes below 0.45 μm. “Dissolved” organic matter is therefore a misnomer, as colloidal particles can exist down to 1 nm (Lead and Wilkinson, 2006). However, since it is the conventional term for this class of organic matter, we will be using it throughout this paper.
DOM is highly complex and includes a diverse range of aromatic and aliphatic hydrocarbon structures that may have attached functional groups (Leenheer and Croué, 2003). In terrestrial waterbodies, DOM can affect biodiversity and ecological processes (Rae et al., 2001), contribute to global climate change via degassing as CO2 and CH4 (following degradation reactions (Cole et al., 1994; Cole et al., 2007; Mayorga et al., 2005)), and act as a vector for trace metal transport (Hartland et al., 2012; Sauve et al., 2000). DOM can precipitate out of waterbodies in mineral phases (e.g. in biogenic or abiogenic carbonate precipitates) or be deposited in sediments. Herein, [DOM]aq and [DOM]s refer to the aqueous (i.e. in solution) and solid phase (i.e. incorporated in calcite, the rhombohedral phase of CaCO3) dissolved organic matter concentration, respectively. Little is known about DOM trends prior to the onset of widespread dissolved organic carbon (DOC) monitoring, which became routine in several countries the mid-late 20th century (e.g. the Acid Monitoring Network, UK (Monteith et al., 2014)). An ongoing debate surrounds the causes of recent (late 20th century to present) DOM increases in terrestrial waterbodies in mid/high-latitudes of the Northern Hemisphere (Evans et al., 2006; Monteith et al., 2007) (the Southern Hemisphere is comparatively understudied). Proposed contributing factors include increasing temperatures (Freeman et al., 2001), changes in soil water acidity due to declining atmospheric sulphur deposition (Evans et al., 2006; Monteith et al., 2007) elevated atmospheric CO2 concentrations (causing stimulation of primary productivity) (Freeman et al., 2004), and changes in land-use (Stanley et al., 2012). This debate may be resolved using long-term (centennial to millennial-scale) records of DOM variability encoded in natural sedimentary or mineralogical archives, which may allow the isolation and assessment of individual potential contributing factors.
One of the most promising environmental archives is that of speleothems, secondary calcium carbonate deposits typically found in caves (e.g. flowstones and stalagmites) (Hill et al., 1997). Inorganic geochemical properties (isotopic and trace element data) (Affolter et al., 2019; Nagra et al., 2017; Scroxton et al., 2018; Williams et al., 1999) and physical properties (e.g. nano-crystal aggregation, open vs. compact columnar fabrics, defect-ridden fabrics) of natural calcium carbonate minerals have been routinely used to determine environmental parameters at their time of formation (Frisia et al., 2000; Nielsen et al., 2014). Speleothems can preserve organic molecules from overlying allochtonous vegetation, soil and microbial communities within the cave (Blyth et al., 2016). The precision and reliability of speleothem dating means that palaeo-environmental records containing seasonal/monthly resolutions can be produced, extending to hundreds of thousands of years (Borsato et al., 2007). Speleothems thus have the potential to record DOM trends prior to anthropogenic land-use impacts and anthropogenically induced fluctuations in atmospheric S deposition, two factors that have been proposed as contributing drivers of recent increases in DOM export from soil.
Slightly acidic groundwater dissolves limestone bedrock and thus transport both soil organic matter and calcium (Ca2+) and carbonate (CO32−) ions into cave systems. There, ions are reprecipitated as solid calcium carbonate, forming speleothems. During this process, soil-derived organic matter (including DOM) may be incorporated into the speleothem CaCO3 (Baker et al., 1999; Genty et al., 2001). Organic matter has long been known to alter speleothem colour (Caldwell et al., 1982): dark coloured speleothems are known to contain greater amounts of particulate organic matter (POM), fulvic acid (FA) and humic acid (HA) compared to light-coloured speleothems (Van Beynen et al., 2001). Several studies (Chalmin et al., 2012; Quiers et al., 2015) have observed that humic acid fluoresces more strongly after incorporation into calcite, which suggests an interaction between humic acid molecules and the crystal lattice (fluorescence yields increase when molecules adopt more rigid conformations) (Sulatskaya et al., 2010), such as surface adsorption of organic molecules, and bonding between organic functional groups (e.g. carboxyl (COO−) and cations (Ca2+) (Fairchild and Baker, 2012; Hartland et al., 2014). It has also been suggested that organic matter may be incorporated into speleothems as fluid inclusions (Ramseyer et al., 1997). Blyth et al. (2016) reviewed the origin, transport and transformation of OM in speleothems and suggested that speleothem OM is primarily derived from vegetation or soil overlying the cave. An important consideration is that dripwater OM can be altered during transport, prior to being preserved in a speleothem. For example, speleothems fed by water with a long-residence time are likely to contain OM that has been heavily altered (e.g. by microbial activity) along the flow-path. It has been proposed that DOM may interfere with the calcium carbonate precipitation process by chelating calcium ions in solution (Falini et al., 2009). However, this is unlikely to be significant because of the limited number of cation exchange sites in DOM compared to the large number of Ca2+(aq) ions, as well as competition from transition metals which preferentially occupy binding sites in DOM (Hartland and Zitoun, 2018). Frisia et al. (2018) investigated the role of DOM in CaCO3 precipitation using transmission electron microscopy of both marine, non-bio-precipitated carbonates and natural precipitates from cave waters and fossil speleothems. They found that organic substances can act as either catalysts or inhibitors of crystal nucleation and growth and diagenesis, strongly influencing the preservation of original structures (Frisia et al., 2018). They proposed that, regardless of origin, the simple presence of organic molecules catalyses the precipitation of a carbonate from aqueous solution and allows its preservation. Thus, the interaction between [DOM]aq and the process of calcium carbonate precipitation may complicate the picture of DOMs as a faithful recorder of [DOM]aq and requires further investigation. Further, the presence of DOM in growth-solution has also been shown to alter crystal structure in experimental studies (Hoch et al., 2000). Yet, in cave environments, speleothem crystal habit has typically been related to dripwater supersaturation and flowrate (Frisia et al., 2000; Gonzalez et al., 1992).
A small fraction of DOM is fluorescent and is typically described as fluorescent dissolved organic matter (FDOM). Three-dimensional excitation emission matrix (3D EEM) fluorescence can be used to quantify and characterise FDOM properties (Coble, 1996; Stedmon and Bro, 2008). When fluorescence conforms to the Beer–Lambert law (i.e. the amount of light absorbed by a solution is proportional to the solution's molar absorptivity and the concentration of solute), mathematical identification (i.e. PARAFAC- parallel factor analysis of components) can be used to quantify and characterise analytes (Murphy et al., 2013), including DOM concentration and constituent molecules, by assessing fluorophore intensity and the wavelengths at which excitation and emission occur. Fluorescence methods (but not necessarily 3D EEMs) have been applied to assess DOM quantity and quality in speleothems and cave drip-waters in a diverse range of environmental and palaeo-environmental studies. Examples include studies of DOM loss and processes in the overlying soil (Genty et al., 2001; Perrette et al., 2015), land-use change (Blyth et al., 2007) and vegetation change (Baker et al., 1996). Several studies have also focused on the relationship between trace-metal-DOM complexation in cave dripwaters and speleothems (Hartland et al., 2012; Rutlidge et al., 2014).
Here, we aim to test (a) whether secondary calcium carbonate is a faithful recorder of [DOM]aq and (b) the effect of [DOM]aq on calcium carbonate crystal morphology and lattice defects. We test this by precipitating calcium carbonate in solutions containing varying concentrations of DOM (approximately 0, 5, 10, 15 mgC/L). Our calcite crystals were synthesised using an adapted Gruzensky protocol (Gruzensky, 1967), in which NH3 and CO2 gases are sublimed from ammonium carbonate and diffuse into an aqueous solution of calcium and ammonium chloride, causing supersaturation and precipitation of CaCO3. Laboratory experiments exclude the complexities of changes in water chemistry, DOM characteristics, interactions with trace elements and potential microbial activity that may influence crystallisation pathways in the cave environment, therefore enabling us to simply test the effects of natural [DOM] on crystallisation processes and the relationship between [DOM]aq and [DOM]s.
Most laboratory studies that focus on incorporation of organic impurities in calcite have relied on laboratory grade humic acids (Chalmin et al., 2012; Falini et al., 2009) or isolation of individual organic ligands (Mavromatis et al., 2017). However, carbonate precipitation in natural environments occurs with a range of organic molecules that may be altered by natural processes (e.g. microbial degradation, decomposition). In this study, we aimed to address this issue by using natural DOM sourced from Kopuatai peat dome, a raised bog in central North Island, New Zealand. We also used the same fluorescence methods to test the reliability of three flowstones to record DOM concentrations from their parent dripwaters at three different cave sites in New Zealand.
Section snippets
Experimental design
The carbonate precipitation experiment applied a range of methods to analyse the growth-solutions and the carbonate produced under the different experimental conditions (Fig. 1a).
Flame atomic absorption spectroscopy (FAAS) was used to determine the loss of calcium ions from the growth solution through time, whilst 3D EEM spectroscopy was used to measure removal of DOM through time. Post-experiment, 3D EEM spectroscopy was used to quantify [DOM] from the dissolved crystals, the morphology of the
Determining the calcium carbonate polymorph
FTIRS (Fig. 4a) of the precipitated carbonate crystals displayed the characteristic v2 band of calcite at 874 cm−1 and the characteristic v4 band of calcite at 713 cm−1. These observations were in agreement with spectra obtained from pure calcite crystals (Ni and Ratner, 2008). XRD (Fig. 4b) analysis displayed diffraction patterns that are consistent with calcite x-ray diffraction standards (Ni and Ratner, 2008).
DOM incorporation into calcite crystals
Table 1 gives the fluorescence-inferred DOM and FAAS-inferred Ca2+ concentrations
Assessing the potential effects of [DOM] on CaCO3 polymorph
Our experiment also allows us to assess the effect of [DOM] on the CaCO3 polymorph. XRD and FTIRS analysis has determined that the synthesised crystals were calcite in each treatment. These data suggest that [DOM] up to ~15 mgC/L does not produce changes in CaCO3 polymorphs during crystal growth, but rather drives calcite crystal morphogenesis (Cölfen and Antonietti, 2005). This finding may be consistent with a previous study, in which solutions containing 40 mgC/L humic acids were shown to
Conclusions
Calcite crystals precipitated from solutions containing variable initial [DOM] showed consistent variability in organic carbon content and crystal habit, as well as less consistent variability in final crystal yield. We observed a positive, linear correlation between initial organic carbon concentration in solution and final organic carbon concentration in calcite, with log Kd values of around 0.5. Crystals produced in 0 mgC/L DOM solutions were rhombohedral, white in colour and had very low
Funding
This study was made possible by the Royal Society of New Zealand Marsden Fund Grant UOW1403 and Rutherford Discovery Fellowship award RDF-UOW1601 (AH) and the Australian Research Council (grant DP160101058) (SF).
Declaration of competing interest
The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.
Acknowledgements
We would like to acknowledge Joshua L. Ratcliffe and Associate Professor David Campbell (University of Waikato) for assistance in collecting the peat water from Kopuatai bog, Dr. John C. Hellstrom (University of Melbourne) and Travis Cross (University of Auckland) for assistance in flowstone sample collection. Thanks to the Department of Conservation for allowing us to access and sample from Dave's Cave and Hodges Creek Cave (Research and Collection Permit 37934-GEO), and Pete and Libby
References (73)
- et al.
The N-way toolbox for MATLAB
Chemometrics and Intelligent Laborary Systems
(2000) - et al.
Speleothern luminescence intensity and spectral characteristics: signal calibration and a record of palaeovegetation change
Chem. Geol.
(1996) Stalagmite luminescence and peat humification records of palaeomoisture for the last 2500 years
Earth Planet. Sci. Lett.
(1999)- et al.
Relating dissolved organic matter fluorescence and functional properties
Chemosphere
(2008) - et al.
A new approach to detecting vegetation and land-use change using high-resolution lipid biomarker records in stalagmites
Quatern. Res.
(2007) - et al.
Organic proxies in speleothems – New developments, advantages and limitations
Quat. Sci. Rev.
(2016) - et al.
Trace element distribution in annual stalagmite laminae mapped by micrometer-resolution X-ray fluorescence: implications for incorporation of environmentally significant species
Geochim. Cosmochim. Acta
(2007) Paleohydrological records from peat profiles and speleothems in Sutherland, northwest Scotland
Quat. Res.
(2001)Characterization of marine and terrestrial DOM in seawater using excitation-emission matrix spectroscopy
Mar. Chem.
(1996)- et al.
Distribution and optical properties of CDOM in the Arabian Sea during the 1995 Southwest Monsoon
Deep-Sea Res. II Top. Stud. Oceanogr.
(1998)
Long-term increases in surface water dissolved organic carbon: observations, possible causes and environmental impacts
Environ. Pollut.
High spatial resolution investigation of nucleation, growth and early diagenesis in speleothems as exemplar for sedimentary carbonates
Earth Sci. Rev.
Dead carbon in stalagmites: Carbonate bedrock paleodissolution vs. ageing of soil organic matter. Implications for 13C variations in speleothems
Geochim. Cosmochim. Acta
Fluorescent properties of organic carbon in cave dripwaters: effects of filtration, temperature and pH
Sci. Total Environ.
Size, speciation and lability of NOM–metal complexes in hyperalkaline cave dripwater
Geochim. Cosmochim. Acta
From soil to cave: transport of trace metals by natural organic matter in karst dripwaters
Chem. Geol.
Preservation of NOM-metal complexes in a modern hyperalkaline stalagmite: implications for speleothem trace element geochemistry
Geochim. Cosmochim. Acta
Calcite crystal growth inhibition by humic substances with emphasis on hydrophobic acids from the Florida Everglades
Geochim. Cosmochim. Acta
Molecular signatures of dissolved organic matter in a tropical karst system
Org. Geochem.
Cu (II) adsorption at the calcite–water interface in the presence of natural organic matter: kinetic studies and molecular-scale characterization
Geochim. Cosmochim. Acta
Effect of organic ligands on Mg partitioning and Mg isotope fractionation during low-temperature precipitation of calcite in the absence of growth rate effects
Geochim. Cosmochim. Acta
The influence of impurities on the growth rate of calcite
J. Cryst. Growth
Trends in the hydrochemistry of acid-sensitive surface waters in the UK 1988–2008
Ecol. Indic.
Determining soil sources by organic matter EPR fingerprints in two modern speleothems
Org. Geochem.
NMR spectroscopic study of organic phosphate esters coprecipitated with calcite
Geochim. Cosmochim. Acta
Geochemical mapping of organic carbon in stalagmites using liquid-phase and solid-phase fluorescence
Chem. Geol.
Nature and origin of organic matter in carbonates from speleothems, marine cements and coral skeletons
Org. Geochem.
Water table fluctuations control CO2 exchange in wet and dry bogs through different mechanisms
Sci. Total Environ.
Dripwater organic matter and trace element geochemistry in a semi-arid karst environment: implications for speleothem paleoclimatology
Geochim. Cosmochim. Acta
Effects of impurities on crystal growth processes
Prog. Cryst. Growth Charact. Mater.
Rapid measurement of strontium in speleothems using core-scanning micro X-ray fluorescence
Chem. Geol.
Causes of colour and fluorescence in speleothems
Chem. Geol.
Sulphate partitioning into calcite: Experimental verification of pH control and application to seasonality in speleothems
Geochim. Cosmochim. Acta
Central Europe temperature constrained by speleothem fluid inclusion water isotopes over the past 14,000 years
Sci. Adv.
Bacterially induced mineralization of calcium carbonate in terrestrial environments: the role of exopolysaccharides and amino acids
J. Sediment. Res.
Colour in some Nullarbor Plain speleothems
Helictite
Cited by (30)
A mid-Holocene stalagmite multiproxy record from southern Siberia (Krasnoyarsk, Russia) linked to the Siberian High patterns
2023, Quaternary Science ReviewsExploring soluble and colloidally transported trace elements in stalagmites: The strontium-yttrium connection
2023, Geochimica et Cosmochimica ActaCitation Excerpt :Among colloidally transported elements, Y is exceptional in that it is extremely insoluble and therefore entirely dependent on organic ligands for transport (i.e., not labile; Hartland et al., 2014), unlike P, Zn and Cu (Hartland and Zitoun, 2018; Stoll et al., 2012). Furthermore, there are few if any isobaric interferences or polyatomic interferences on mass 89 when analyzing calcite by ICP-MS (Jochum et al., 2012), meaning that the signal to noise ratio is maximized for Y. Meanwhile, the choice of Sr as a counterpart to Y is governed by its relatively high concentration in the karst system, low potential for isobaric interferences by ICP-MS, and, relative to Mg, its low response to sea spray input (i.e., Sr from bedrock dissolution >> Sr from sea water) and sectoral zoning (Paquette and Reeder, 1995; Sliwinski and Stoll, 2021; Tremaine and Froelich, 2013). We begin by testing the classical notion that Sr incorporation is positively driven by growth rate (e.g., Lorens, 1981), and use covariations of this element with Y to build on a conceptual model proposed by previous authors, wherein Sr and Y represent soluble elements and colloidally transported elements (respectively).
Crystallization pathways, fabrics and the capture of climate proxies in speleothems: Examples from the tropics
2022, Quaternary Science ReviewsDifference in calcium ion precipitation between free and immobilized Halovibrio mesolongii HMY2
2022, Journal of Environmental Sciences (China)Citation Excerpt :As for the free bacteria, different organic metabolites released by bacteria would be diffused into the liquid system, not like the immobilized bacteria in a confined space. Dissolved organic substances are omnipresent in the natural environment, and usually incorporated into carbonate minerals (Pearson et al., 2020). Therefore, the better developed protein secondary structures hideen in the minerals may indicate that much more dissolved organic matter was present in the environment under the action of free bacteria.