A comparison of non-hydrolytic methods for extracting amino acids and proteins from coastal marine sediments

Advances in analytical techniques now allow for the potential analysis of intact peptides and proteins isolated from marine sediments. However, there is no established technique for the extraction of macromolecular materials from marine sediments. Six different methods for extracting the amino acid component from coastal marine sediments were compared to the standard hot acid hydrolysis technique for their percent recovery and amino acid composition. The standard hot acid hydrolysis on dried, whole sediments released the greatest concentration of total amino acids (PS-THAA; 3.52 mg gdwt^− 1 ± 10% (SMD)), yet this only accounted for 22% of the total nitrogen in Puget Sound sediments (Washington, USA). Repeated hydrolysis of the same samples did not improve the recovery of nitrogen by more than an additional 10%. Base extraction (0.5 N NaOH) was the second best method for recovering amino acid nitrogen, releasing 60% of the Puget Sound total hydrolyzable amino acids (PS-THAA) (corresponding to 13% of the total sedimentary nitrogen), and has the advantage that it does not rely on peptide hydrolysis to free the nitrogenous component from the sediment matrix. The amino acid distribution of the 0.5 N NaOH extract was not significantly different than the initial THAA. Other non-hydrolyzing methods released lower yields of amino acids (Triton X-100 ≥ hot water > 50 mM NH₄HCO₃ > HF), but might prove to be of use to investigators interested in specific fractions of sedimentary organic nitrogen because these four methods had distinctly different amino acid compositions (enrichments in basic amino acids and depletions in acidic amino acids). Treatments with HF both before and after traditional hydrolysis and/or extractions with base did not release any more of the sedimentary nitrogen. Our results are consistent with the hypothesis that a large fraction of the sedimentary nitrogen (TN) is protected within an organic matrix.