Microbial community dynamics in a chemolithotrophic denitrification reactor inoculated with methanogenic granular sludge

Denitrification is applied in the tertiary treatment of wastewater to reduce nitrogen pollution. Fluorescence in situ hybridization (FISH), catalyzed reporter deposition (CARD)-FISH, cloning, and scanning electron microscopy (SEM) were applied to follow the evolution of the microbial composition and structure of granular sludge in chemolithotrophic denitrifying bioreactors fed with nitrate and thiosulfate. FISH oligonucleotide probes for the chemolitoautotrophic denitrifiers Thiobacillus denitrificans and Thiomicrospira denitrificans were designed and their utility tested. CARD-FISH and cloning data showed that bacterial diversity in the biofilms changed during the reactor operation. Chemoorganotrophic fermentative Gram-positive strains in the phyla, Actinobacteria and Firmicutes, were dominant in the methanogenic inoculum, both in terms of biodiversity and in number. Other significant phyla were Bacteroidetes and Chloroflexi. After 6 months of operation, Proteobacteria became dominant (83% of the clones). The diversity of Gram-positive bacteria was partially maintained although their abundance decreased notably. After 110 d of operation, the abundance of Tb. denitrificans cells increased considerably, from 1% to 35% of total DAPI-stained cells and from no isolated clones to 15% of the total clones. Tm. denitrificans only represented a minor fraction of the microorganisms in the sludge (1-4% of the DAPI-stained cells). These findings confirm that Tb. denitrificans was the dominant chemolitoautotrophic denitrifying microorganism in the bioreactors. The Archaeal diversity remained almost unchanged and it was represented mostly by Methanosaeta soehngenii. SEM results indicated a considerable loss in the integrity of the sludge granules during the operation, with risk of sludge buoyancy.