You could determine the biomass of denitrifiers by the kinetic method:

O. V. Menyailo. The influence of tree species on the biomass of denitrifying bacteria in gray forest soils. Eurasian Soil Science 01/2007; 40(3):302-307.

You could determine the gene abundance of denitrifiers by Q-PCR, targeting either DNA or RNA. You can get information about Q-PCR of denitrifiers from estuarine sediments in this article:

Smith et al, (2007), Diversity and abundance of nitrate reductase genes (narG and napA), nitrite reductase genes (nirS and nrfA), and their transcripts in estuarine sediments. Applied and Environmental Microbiology, 73(11), 3612-3622.

Hi Jabir,

I'm aware of a couple other possibilities in addition to the two listed above. If you don't need precise measurements of absolute denitrifying populations, but need to make comparisons between different sediments, the Denitrifying Enzyme Activity (DEA) technique and Most Probable Number (MPN) method may both be of use. DEA focuses on the prevalence and activity of denitrifying enzymes, while MPN focuses on biomass.

Tiedje, et al. discuss both in the following paper, with more focus on DEA.

Tiedje, J. M., Simkins, S., & Groffman, P. M. (1989). Perspectives on measurement of denitrification in the field including recommended protocols for acetylene based methods. Plant and Soil, 115(2), 261-284

Although they describe it for soils, it has been successfully used for aquatic sediments as well:

McCrackin, M. L., & Elser, J. J. (2012). Denitrification kinetics and denitrifier abundances in sediments of lakes receiving atmospheric nitrogen deposition (colorado, USA). Biogeochemistry, 108(1-3), 39-54.

Davidson, et al. discuss using MPN:

Davidson, E. A., Strand, M. K., & Galloway, L. F. (1985). Evaluation of the Most Probable Number Method for Enumerating Denitrifying Bacteria1. Soil Sci. Soc. Am. J., 49(3), 642-645.

Hope these help. All the best,

David