Journal
ENVIRONMENTAL MICROBIOLOGY
Volume 25, Issue 9, Pages 1696-1712Publisher
WILEY
DOI: 10.1111/1462-2920.16387
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Denitrifying woodchip bioreactors (WBRs) are used to manage non-point source nitrogen release by stimulating microbial denitrification. Oxic-anoxic cycling increases organic carbon mobilization, nitrate removal rates, and attenuates nitrous oxide production. Fungal ligninolytic enzymes and denitrification genes play a crucial role in this process.
Denitrifying woodchip bioreactors (WBRs) are increasingly used to manage the release of non-point source nitrogen (N) by stimulating microbial denitrification. Woodchips serve as a renewable organic carbon (C) source, yet the recalcitrance of organic C in lignocellulosic biomass causes many WBRs to be C-limited. Prior studies have observed that oxic-anoxic cycling increased the mobilization of organic C, increased nitrate (NO3-) removal rates, and attenuated production of nitrous oxide (N2O). Here, we use multi-omics approaches and amplicon sequencing of fungal 5.8S-ITS2 and prokaryotic 16S rRNA genes to elucidate the microbial drivers for enhanced NO3- removal and attenuated N2O production under redox-dynamic conditions. Transient oxic periods stimulated the expression of fungal ligninolytic enzymes, increasing the bioavailability of woodchip-derived C and stimulating the expression of denitrification genes. Nitrous oxide reductase (nosZ) genes were primarily clade II, and the ratio of clade II/clade I nosZ transcripts during the oxic-anoxic transition was strongly correlated with the N2O yield. Analysis of metagenome-assembled genomes revealed that many of the denitrifying microorganisms also have a genotypic ability to degrade complex polysaccharides like cellulose and hemicellulose, highlighting the adaptation of the WBR microbiome to the ecophysiological niche of the woodchip matrix.
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