Abiotic Racemization Kinetics of Amino Acids in Marine Sediments

<div><p>The ratios of d- versus l-amino acids can be used to infer the sources and composition of sedimentary organic matter. Such inferences, however, rely on knowing the rates at which amino acids in sedimentary organic matter racemize abiotically between the d- and the l-forms. Based on a heating experiment, we report kinetic parameters for racemization of aspartic acid, glutamic acid, serine, and alanine in bulk sediment from Aarhus Bay, Denmark, taken from the surface, 30 cm, and 340 cm depth below seafloor. Extrapolation to a typical cold deep sea sediment temperature of 3°C suggests racemization rate constants of 0.50×10⁻⁵–11×10⁻⁵ yr⁻¹. These results can be used in conjunction with measurements of sediment age to predict the ratio of d:l amino acids due solely to abiotic racemization of the source material, deviations from which can indicate the abundance and turnover of active microbial populations.</p></div

Observed racemization rate constants, yr⁻¹.

<p>Observed racemization rate constants, yr⁻¹.</p

Activation energies, E_a, kJ mol⁻¹; frequency factors (ln A), yr⁻¹; and consensus Arrhenius equations for racemization rate constants (in which temperature T is in K and <i>k</i> is yr⁻¹).

<p>Values in bold are the median of bootstrap-simulated values and values in parentheses indicate +/−1 standard deviation. Consensus values are based on observed rate constants at all sediment depth for each amino acid.</p

Simulated rate constants at −4–105°C.

<p>The solid line and shaded areas indicate predicted rate constant and error as a function of temperature (see Methods section for details).</p

Arrhenius plot of measured racemization rate constants for each amino acid.

<p>Lines for each depth indicate the median rate constant predicted using the bootstrap-Monte Carlo approach (see Methods section for details).</p

Estimating the Abundance of Endospores of Sulfate-Reducing Bacteria in Environmental Samples by Inducing Germination and Exponential Growth

<p>It is a challenge to quantitatively distinguish active from dormant microbial populations in environmental samples. Here we present an approach for estimating the abundance of dormant sulfate-reducing bacteria (SRB), present as viable endospores in environmental samples. This is achieved by inducing endospores to germinate and grow exponentially. We demonstrate this approach for thermophilic SRB in temperate sediment from Aarhus Bay, Denmark. The approach is based on measuring bulk sulfate reduction rates (SRRs) in pasteurized sediment and calculating associated cell-specific SRRs based on average values for SRB growth yield and cell size known from exponentially growing pure cultures. The method presented is a faster bioassay than most probable number enumerations and has the potential to distinguish between slow- and fast-growing SRB populations in the same sample. This bioassay is attractive given the challenges posed by endospores with respect to cell permeabilization and lysis, which are prerequisite in quantitative microscopy- and nucleic acid extraction-based strategies. These molecular approaches additionally rely on designing target-appropriate oligonucleotide probes, whereas the method presented here considers the trait of interest more broadly. This strategy thus presents a useful complement to other methods in ecological investigations of microbial biogeography and for specific industrial applications such as reservoir souring and corrosion risk assessments in the oil and gas sector.</p