Enrichment of Polycyclic Aromatic Hydrocarbon (PAH)–Degrading Strictly Anaerobic Sulfate-Reducing Cultures from Contaminated Soil and Sediment

Abstract

Sulfate-reducing bacteria (SRB) are crucial players in global biogeochemical cycling and some have been implicated in the anaerobic biodegradation of organic pollutants, including recalcitrant and hazardous polycyclic aromatic hydrocarbons (PAHs). Obtaining PAH-degrading SRB cultures for laboratories is of paramount importance in the development of the young field of anaerobic biodegradation of PAHs. SRB grow exceptionally slowly on PAH substrates and are highly sensitive to oxygen. Consequently, enrichment and maintenance of PAH-degrading SRB cultures and characterization of the biodegradation process remain a tedious and formidable task, especially for new researchers. To address these technical constraints, we have developed robust and effective protocols for obtaining and characterizing PAH-degrading SRB cultures. In this set of protocols, we describe step-by-step procedures for preparing inocula from contaminated soil or sediment, preparing anoxic medium, establishing enrichment cultures with PAHs as substrates under completely anaerobic sulfate-reducing conditions, successive culture transfers to obtain highly enriched cultures, rapid verification of the viability of SRB in slow-growing cultures, assessment of PAH degradation by extracting residuals using organic solvent and subsequent analysis by gas chromatography–mass spectrometry, and spectrophotometric determination of sulfate and sulfide in miniaturized, medium-throughput format. These protocols are expected to serve as a comprehensive manual for obtaining and characterizing PAH-degrading sulfate-reducing cultures. © 2024 The Author(s). Current Protocols published by Wiley Periodicals LLC.

Basic Protocol 1: Obtaining PAH-degrading strictly anaerobic sulfate-reducing enrichment cultures from contaminated soil and sediment

Support Protocol 1: Operation and maintenance of an anaerobic workstation

Support Protocol 2: Setup of gas purging systems for preparing anoxic solutions

Support Protocol 3: Verification of viability in slow-growing SRB enrichment cultures

Support Protocol 4: Extraction of genomic DNA from low-biomass cultures

Basic Protocol 2: Extraction of residual PAH from liquid culture and analysis by GC-MS

Basic Protocol 3: Spectrophotometric determination of sulfate concentration in SRB cultures

Basic Protocol 4: Spectrophotometric determination of sulfide concentrations in SRB cultures by the methylene blue method

Alternate Protocol: Spectrophotometric determination of sulfide concentrations in SRB cultures by the colloidal copper sulfide method