Functional marker genes for identification of sulfate-reducing prokaryotes

Area of Science:

• Microbiology
• Environmental Science
• Biogeochemistry

Background:

• Sulfate-reducing prokaryotes (SRPs) are vital for the global sulfur cycle, utilizing sulfate for anaerobic respiration.
• Traditional 16S rRNA gene sequencing struggles to differentiate SRPs from related non-SRPs, hindering the discovery of novel lineages.
• Functional marker genes, such as dissimilatory (bi)sulfite reductase (dsrAB) and adenosine-5'-phosphosulfate reductase (apsA), offer a more targeted approach.

Purpose of the Study:

• To provide detailed protocols for using dsrAB and apsA genes to survey SRP diversity in environmental samples.
• To address the limitations of 16S rRNA gene-based identification of novel SRP lineages.
• To introduce a novel gel retardation technique for efficient dsrAB fingerprinting.

Main Methods:

• Comparative sequence analysis of environmental dsrAB and apsA gene fragments.
• Application of functional marker genes for cultivation-independent SRP diversity surveys.
• Development and application of a gel retardation technique for dsrAB PCR product fingerprinting.

Main Results:

• Demonstrated protocols for applying dsrAB and apsA genes in SRP diversity studies.
• Presented dsrAB sequence diversity data from Mariager Fjord water samples.
• Showcased the effectiveness of the novel gel retardation technique in identifying rare dsrAB sequence types.

Conclusions:

• dsrAB and apsA gene sequence analysis provides a robust method for identifying novel SRP lineages.
• The developed gel retardation technique enhances the recovery of rare and novel dsrAB sequences from environmental samples.
• These methods significantly advance the cultivation-independent study of SRP diversity and their role in biogeochemical cycles.