Amino acids in fossil corals: racemization (epimerization) reactions and their implications for diagenetic models and geochronological studies

Thirty-eight fossil coral samples of known age from late Pleistocene uplifted reef terraces have been analyzed for amino acid composition and for the degree of racemization of selected amino acids. Particular attention has been given to the epimerization (racemization about the α-carbon) of isoleucine. The $\text{D}\text{L}$ ratios observed in many of these samples do not conform to the concept of increasing racemization being associated with increasing fossil age. It is shown that sixteen of the samples demonstrate concordance between their known age and the age estimated from racemization data. Racemization ages are based upon a kinetic model derived from the kinetics observed in foraminifera in marine sediments and published estimates of the temperature dependence of the isoleucine epimerization reaction. Lack of concordance for the remaining samples is explained by either of two separate diagenetic phenomena: extensive leaching of free amino acids from the fossil, or contamination by ‘young’ amino acids. Ambiguities observed in many of the results may be due to the fact that coralline organic matter can have a complex history because of variations in its source and in its relation to the mineral phase. Neither of these factors has been observed to exert such a significant effect on racemization kinetics observed in fossil foraminifera or molluscs. Fossil corals are of only modest value as specimens for amino acid geochronological studies.     

Amino acid racemization dating of quaternary deposits of central and Southern Italy

Results are discussed of amino acid racemization dating of numerous samples of bones, teeth, tooth enamel and fossil shells. Racemization dating proved to be a very useful tool to date non-marine and marine deposits which are a few hundred thousand years old, as well as to correlate and chronologically classify even more ancient marine deposits. Aspartic acid racemization was used to date samples aged less than 80,000–100,000 yr; for more ancient samples, isoleucine epimerization, instead, was resorted to.In this work, dates were established for some important fragments of human bones and of large-mammalian fauna weighing a few grams, which would have been impossible to date with the ¹⁴C technique, requiring a large amount of bone material.The extent of isoleucine epimerization was measured in Glycymeris genera to estimate the age of numerous marine deposits of the Tyrrhenian coast of Centra-Southern Italy and of Sardinia. In the Tarquinia area (Latium) three marine terraces were identified, which were estimated to be approx. 120,000, 200,000 and 350,000 yr old. In Sardinia, five marine horizons were identified; the youngest deposit (Neotyrrhenian) proved to be present at Punta tramontana and Santa Reparata, while, at Riola and Stagno di Sassu, the most ancient marine deposits of Sardinia were found. In the Rome area, the Monte Mario Formation was estimated to be coeval with Monte delle Piche Formation. Finally, from the terraced coastal deposits of Capo Milaazzo (Sicily), Panarea (Eolian archipelago), Archi (Calabria) and Gallipoli (Apulia), a Tyrrhenian age range of 100,000–120,000 yr was obtained.     

Source-specific variability in post-depositional DNA preservation with potential implications for DNA based paleoecological records

Recent studies have shown that genotyping preserved plankton DNA in marine and lacustrine sediment records using ancient DNA methods is a promising approach for refining paleoenvironmental information. However, the extent to which the preservation of fossil plankton DNA differs between species is poorly understood. Using a continuous 2700 year sediment record from Watts Basin in Ellis Fjord (Antarctica), we compared the level of preservation of fossil DNA derived from important plankton members with varying cellular architecture. The amount of preserved small subunit ribosomal DNA (SSU rDNA; ca. 500 base pair fragments) of dinoflagellates (as extracellular DNA rather than as preserved cysts) that could be amplified by way of PCR declined up to five orders of magnitude with increasing sediment depth and age. In contrast, the amount of similar-sized, PCR-amplifiable, diatom SSU rDNA (predominantly from a cyst-forming Chaetoceros sp.) declined only up to tenfold over 2700 years of deposition. No obvious decline in copy numbers with increasing sediment age was observed for similar-sized SSU rDNA of past chemocline-associated photosynthetic green sulfur bacteria (GSB), which do not have a protective resting stage. In good agreement with the quantitative data, the extent of post-depositional natural degradation to fragments too small to serve as a template for the quantitative PCR assays was greatest for dinoflagellates and lowest for GSB. An increase in the ratio between GSB-derived DNA and intact carotenoids with sediment depth implies that short GSB DNA fragments were better preserved than intact carotenoids and provide a more accurate view into paleoproductivity and the sediment flux of GSB in Watts Basin. We discuss the possible causes behind the variation in the level of DNA preservation among the plankton groups investigated, as well as consequences for the use of using fossil DNA records in paleoecology studies.     

Amino acid racemization in mammalian bones and teeth from La Chaise-de-Vouthon (Charente), France

A controlled test of the amino acid dating method as it is currently being applied to bones and teeth was attempted for the time range 100-250 ka, beyond that of ¹⁴C, at the archeological site of La Chaise-de-Vouthon (Charente, France). In Bourgeois-Delaunay, mammal fossils associated with Paleolithic artifacts were collected from layers dated at 101 ± 12 to 114 ± 7 ka by ²³⁰Th/²³⁰ dating of the over- and underlying stalagmitic floors. Racemization ratios for most amino acids were significantly lower than for comparably aged materials from other European sites. Regardless of the rate constants used, most amino acid dates were incorrect. Large associated errors spanned the late Pleistocene, making the dates useless for discriminating archaeological or geological events. Stratigraphic correlations using any tissue were also problematic. Relative interacid ratios varied with age, indicating that diagenetic alteration had affected racemization. Therefore, amino acid relative and absolute dating cannot be accurately applied to mid-Pleistocene bones or teeth.     

The racemization rate constant for protein-bound aspartic acid in woodrat middens

The racemization rate constant for aspartic acid has been determined from the d/l isomeric ratio in four strata of radiocarbon dated woodrat midden in Arizona. Two different methods of stereospecifically deaminating l-aspartic acid prior to the assay are compared. It is found that pure l-amino acid oxidase pretreatment of the dl aspartic acid mixture requires one less step than treatment with crude, dialyzed venom (Crotalus viridis) but that the two methods give the same results. Application of the theory of amino acid racemization dating is discussed in the context of the steric properties ofthe protein environment in which the racemization actually occurs.     

Aspartic acid racemization in Late Wisconsin Lake Ontario sediments

We have determined aspartic acid racemization and [¹⁴C] ages in sediment from a 17-m piston core recovered from Lake Ontario. This core represents a depositional record extending back into the Late Wisconsin. Total organic radiocarbon ages of the glaciolacustrine lower section of the core are older than the true depositional age. Hence we suggest that these ages do not represent time elapsed since deposition but rather may be up to several thousand years too old due to mixing with ¹⁴C-depleted organic matter and possibly also d-amino acids contained by the glacier and deposited as the glacier receded. Further studies are suggested that might test this hypothesis as well as establish the general applicability of racemization dating to clay sediments.     

Aspartic acid racemization in teeth from Ketef Hinnom,a late Holocene burial cave in Jerusalem: Evidence for reuse

The Ketef Hinnom tombs, lying just outside the walls of the old city of Jerusalem, were carved out of bedrock during the 7th–5th century B.C. Several artefacts dating to the Late Hellenistic Period (ca. 100 B.C.) have also been found within the tombs. Aspartic acid (Asp) racemization in 31 samples of human tooth dentine from these tombs was analyzed in order to evaluate the possible reuse of the tombs during this later period. A range of D/L Asp values was found: a group with values averaging 0.062 and another group averaging 0.043. These D/L values are close to those expected for the two archeological age groups as calculated from (1) the kinetics of Asp racemization as established from experimental studies at higher temperatures and in vivo racemization rates, and (2) the effective annual temperature in the tombs, as measured using the Pallman method. These results thus support the later reuse of the tombs for burials. Several factors contribute to the accuracy of Asp racemization dating, including the age of the individual at death, uncertainties concerning Asp racemization kinetics, and effects of temperature history. © 1999 John Wiley & Sons, Inc.     

Stromatolites in the Late Ordovician Eureka Quartzite: implications for microbial growth and preservation in siliciclastic settings

Well-preserved siliciclastic domal stromatolites, up to 2 m wide and 1·5 m high, are found in a 10 to 15 m thick interval within the Late Ordovician Eureka Quartzite of Southern Nevada and Eastern California, USA. These stromatolites appear as either isolated features or patchy clusters that contain more than 70% by volume quartz grains; their association with planar, trough and herringbone cross-bedding suggests that they were formed in an upper shoreface environment with high hydraulic energy. In this environment, sand bars or dunes may have provided localized shelter for initial microbial mat colonization. Biostabilization and early lithification of microbial mats effectively prevented erosion during tidal flushing and storm surges, and the prevalence of translucent quartz sand grains permitted light penetration into the sediment, leading to thick microbial mat accretion and the formation of domal stromatolites. Decimetre-scale to metre-scale stromatolite domes may have served as localized shelter and nucleation sites for further microbial mat colonization, forming patchy stromatolite clusters. Enrichment of iron minerals, including pyrite and hematite, within dark internal laminae of the stromatolites indicates anaerobic mineralization of microbial mats. The occurrence of stromatolites in the Eureka Quartzite provides an example of microbial growth in highly stressed, siliciclastic sedimentary environments, in which microbial communities may have been able to create microenvironments promoting early cementation/lithification essential for the growth and preservation of siliciclastic stromatolites.     

Grain susceptibility to the effects of microboring: implications for the preservation of skeletal carbonates

The boring activity of microendolithic organisms such as cyanobacteria, chlorophytes, rhodophytes and fungi, represents a major destructive process affecting sediment preservation within reef environments. This study demonstrates the presence of two distinct assemblages of microborers within sediments collected from the fringing reefs of north Jamaica, correlating to the upper (<18 m depth) and lower (>18 m depth) photic zones. The upper photic zone assemblage is dominated by cyanobacteria and chlorophytes, whilst rhodophytes and fungi become more abundant with increasing water depth. Most significant from a grain preservation perspective is the variable nature of grain infestation observed between different reef sites and different carbonate grain types. The highest degree of grain infestation occurs within shallow, low-energy back-reef environments and the most susceptible grains (at all sites) are corals, molluscs and foraminifera. Coralline algae, Halimeda and echinoid fragments are rarely heavily infested. High rates of infestation at back-reef sites result in rapid diminution of the most susceptible grains, especially coral, which are either underrepresented, or contribute only to the finer sediment fractions, in the subsurface. Fore-reef grain assemblages undergo relatively little alteration. Microboring therefore has potential to bias the fossil record by removing the most susceptible skeletal grains. The impact of microboring upon back-reef grain assemblages must be considered when attempting to model depositional processes within both modern and ancient reef environments.     

Geothermal and other effects on amino acid racemization in selected Deep-Sea Drilling Project cores

Kinetic parameters for the epimerization of isoleucine in multispecific foraminiferal asemblages were used to establish the effects of burial depth and the geothermal gradient on the extent of reaction. It was observed that with a little as thirty meters of burial in a normal thermal regime there were differences between the extent of epimerization measured and that which would have been predicted for thermal equilibrium with bottom water temperatures. As would be expected, these differences are greatest when the heat flow (the geothermal gradient) and/or the sedimentation rates are highest. These effects were observed in most of the DSDP samples studied, and have been used to estimate the average heat flux since the time of sample deposition. Occasional anomalous effects were observed which could not be related to past or present heat flux. These were determined to be due to such geologic occurrences as slumping and reworking or to recent sample contamination. Other problems emerged related to bottom water temperatures including changes over geologic time which are unknown and could not be deduced. Thus, the presence of epimerization anomalies in DSDP cores as noted above limits the effectiveness of amino acid geochronology in such cores, unless these anomalies can be recognized as ab initio.     

Speleothem preservation and diagenesis in South African hominin sites implications for paleoenvironments and geochronology

Plio‐Pleistocene speleothems from australopithecine‐bearing caves of South Africa have the potential to yield paleoenvironmental and geochronological information using isotope geochemistry. Prior to such studies it is important to assess the preservation of geochemical signals within the calcitic and aragonitic speleothems, given the tendency of aragonitic speleothems to recrystallize to calcite. This study documents the geochemical suitability of speleothems from the principal hominin‐bearing deposits of South Africa. We use petrography, together with stable isotope and trace element analysis, to identify the occurrence of primary aragonite, primary calcite, and secondary calcite. This study highlights the presence of diagenetic alteration at many of the sites, often observed as interbedded primary and secondary fabrics. Trace element and stable isotopic values distinguish primary calcite from secondary calcite and offer insights into geochemical aspects of the past cave environment. δ¹³C values of the primary and secondary calcites range from +6 to −9‰ and δ¹⁸O values range from −4 to −6‰. The data are thus typical of meteoric calcites with highly variable δ¹³C and relatively invariant δ¹⁸O. High carbon isotope values in these deposits are associated with the effects of recrystallization and rapid outgassing of CO₂ during precipitation. Mg/Ca and Sr/Ca ratios differ between primary and secondary calcite speleothems, aiding their identification. Carbon and oxygen isotope values in primary calcite reflect the proportion of C₃ and C₄ vegetation in the local environment and the oxygen isotope composition of rainfall. Primary calcite speleothems preserve the pristine geochemical signals vital for ongoing paleoenvironmental and geochronological research. © 2009 Wiley Periodicals, Inc.     

Aragonite preservation in late Quaternary sediment cores on the Brazilian Continental Slope: implications for intermediate water circulation

We present late Quaternary records of aragonite preservation determined for sediment cores recovered on the Brazilian Continental Slope (1790–2585 m water depth) where North Atlantic Deep Water (NADW) dominates at present. We have used various indirect dissolution proxies (carbonate content, aragonite/calcite contents, and sand percentages) as well as gastropodal abundances and fragmentation of Limacina inflata to determine the state of aragonite preservation. In addition, microscopic investigations of the dissolution susceptibility of three Limacina species yielded the Limacina Dissolution Index which correlates well with most of the other proxies. Excellent preservation of aragonite was found in the Holocene section, whereas aragonite dissolution gradually increases downcore. This general pattern is attributed to an overall increase in aragonite corrosiveness of pore waters. Overprinted on this early diagenetic trend are high-frequency fluctuations of aragonite preservation, which may be related to climatically induced variations of intermediate water masses. Received: 9 November 1998 / Accepted: 25 August 1999     

Highly depleted isotopic compositions evident in Iapetus and Rheic Ocean basalts: implications for crustal generation and preservation

Subduction of both the Iapetus and Rheic oceans began relatively soon after their opening. Vestiges of both the Iapetan and Rheic oceanic lithospheres are preserved as supra-subduction ophiolites and related mafic complexes in the Appalachian–Caledonian and Variscan orogens. However, available Sm–Nd isotopic data indicate that the mantle source of these complexes was highly depleted as a result of an earlier history of magmatism that occurred prior to initiation of the Iapetus and Rheic oceans. We propose two alternative models for this feature: either the highly depleted mantle was preserved in a long-lived oceanic plateau within the Paleopacific realm or the source for the basalt crust was been recycled from a previously depleted mantle and was brought to an ocean spreading centre during return flow, without significant re-enrichment en-route. Data from present-day oceans suggest that such return flow was more likely to have occurred in the Paleopacific than in new mid-ocean ridges produced in the opening of the Iapetus and Rheic oceans. Variation in crustal density produced by Fe partitioning rendered the lithosphere derived from previously depleted mantle more buoyant than the surrounding asthenosphere, facilitating its preservation. The buoyant oceanic lithosphere was captured from the adjacent Paleopacific, in a manner analogous to the Mesozoic–Cenozoic “capture” in the Atlantic realm of the Caribbean plate. This mechanism of “plate capture” may explain the premature closing of the oceans, and the distribution of collisional events and peri-Gondwanan terranes in the Appalachian–Caledonian and Variscan orogens.     

Age estimations based on amino acid racemization: Reply to comments of J.F. Wehmiller

Determining geologic ages of fossils by amino acid racemization techniques is often difficult because of the uncertainties in assumptions about diagenetic temperatures. Two kinetic model methods have been employed. Method 1, used by us, assumes that racemization of amino acids in the bivalve mollusk Saxidomus giganteus from Willapa Bay, Washington, follows linear kinetics. Ages are calculated by means of first-order kinetic equations. Method 2, used by Wehmiller, involves an empirical non-linear kinetic model Method 1 is simpler in concept and more easily applied. Wehmiller claims that ambiguities in paleotemperature arise when method 1 is used and that these ambiguities can be reconciled by the use of method 2. We show that application of method 1 can also provide reasonable temperature histories and leads to age estimates that are consistent with the geologic history of the sedimentary deposits at Willapa Bay.     

Micro-environmental change as a trigger for granite decay in offshore Irish lighthouses: implications for the long-term preservation of operational historic buildings

Following automation of lighthouses around the coastline of Ireland, reports of accelerated deterioration of interior granite stonework have increased significantly with an associated deterioration in the historic structure and rise in related maintenance costs. Decay of granite stonework primarily occurs through granular disintegration with the effective grusification of granite surfaces. A decay gradient exists within the towers whereby the condition of granite in the lower levels is much worse than elsewhere. The lower tower levels are also regions with highest relative humidity values and greatest salt concentrations. Data indicate that post-automation decay may have been triggered by a change in micro-environmental conditions within the towers associated with increased episodes of condensation on stone surfaces. This in turn appears to have facilitated deposition and accumulation of hygroscopic salts (e.g. NaCl) giving rise to widespread evidence of deliquescence in the lower tower levels. Evidence indicates that the main factors contributing to accelerated deterioration of interior granite stonework are changes in micro-environmental conditions, salt weathering, chemical weathering through the corrosive effect of strongly alkaline conditions on alumino-silicate minerals within the granite and finally, the mica-rich characteristics of the granite itself which increases its structural and chemical susceptibility to subaerial weathering processes by creating points of weakness within the granite. This case study demonstrates how seemingly minor changes in micro-environmental conditions can unintentionally trigger the rapid and extensive deterioration of a previously stable rock type and threaten the long-term future of nationally iconic operational historic structures.     

Factors controlling the burial of organic carbon in laminated and bioturbated sediments off NW Mexico: implications for hydrocarbon preservation

Factors controlling the burial of organic carbon (OC) in Late Quaternary sediments on the NW Mexican continental margin are assessed using a suite of box and piston cores strategically located on the shelf-slope rise with respect to the intense oxygen minimum in this region. An OC concentration maximum occurs on the mid-slope, below the core of an intense water-column O₂ minimum, due to current winnowing on the outer shelf, the preferential accumulation of organic matter in fine-grained deposits, and the offshore decrease in the settling flux of organic detritus. The organic matter at all water depths is overwhelmingly marine. Hydrogen indices (HI) are higher on the slope (>300 mg HC/g TOC) than on the shelf (<300 mg HC/g TOC), where current winnowing has promoted organic matter degradation, but there is no difference in HI in slope sediments accumulating under well oxygenated and O₂-deficient conditions. The degree of winnowing appears to be the primary factor affecting the preservational quality of organic matter deposited on this margin.Rates of accumulation of OC and opal are all higher in the interglacial intervals when compared with the glacial deposits over the last 140,000 yr. However, matrix-corrected HI values in the mid- and lower-slope cores are invariant and are similar to values in the laminated intervals from the oxygen-minimum site. Thus, cyclic changes in organic carbon accumulation on this margin have been controlled by production variations rather than differential preservation. HI values in Late Quaternary sediments from several continental margins, including NW Mexico, and euxinic basins correspond to type II kerogen, irrespective of bottom water O₂ concentrations. Therefore, the preservation of oil-prone kerogen in productive margin settings does not appear to be restricted to sediments deposited under conditions of low bottom water O₂ concentrations as envisioned in models of petroleum source-rock deposition.     

Interfacial friction-induced pressure and implications for the formation and preservation of intergranular coesite in metamorphic rocks

The finding of intergranular coesite and coesite pseudomorphs has been taken as critical evidence to support that the formation of coesite was related to regional ultrahigh pressure (UHP) metamorphism rather than the pressure-vessel effect. Previous laboratory deformation experiments found that coesite occurs in practically undeformed strain-forbidden zones immediately adjacent to the piston–sample interfaces while the mean stress applied to the specimen is remarkably lower than the quartz–coesite equilibrium boundary. The formation and preservation of intergranular coesite in eclogites from UHP metamorphic terranes and the occurrence of coesite in strain-forbidden zones within experimentally deformed rocks can be more satisfactorily explained by the theory of interfacial friction-induced pressure, which is a well-known in metal forging. During certain episodes of fast tectonic deformation under high transient differential stresses, the interfacial friction can induce very significant deformation pressures in thin layers of weak materials (e.g., SiO₂) between large garnet crystals that are refractory and mechanically strong, thus act as excellent anvils. The local deformation pressure, which deviates from the lithostatic value, is likely an intrinsic property of highly constrained flows of weak materials between strong walls at least on a microstructural scale.