Nitrate removal and environmental side-effects controlled by hydraulic residence time in woodchip bioreactors treating cold agricultural drainage water

Bacterial bioaugmentation of woodchip bioreactors to increase nitrate removal in cold agricultural drainage water

Woodchip bioreactors (WBRs) are biological systems designed to prevent excess nitrate (NO3-) leaching from agricultural fields to aquatic ecosystems. Nitrate is removed by microbial denitrification, but the enzyme-mediated process slows down at cold temperatures (<10°C), where NO3- removal in WBRs can be less than 20%. We studied the use of bacterial bioaugmentation in replicated test-scale WBRs (∼0.1 m3) as an environmental technology to increase NO3- removal at cold temperatures. Nitrate removal rates increased following injection of a nitrate-reducing inoculum (Pseudomonas proteolytica and Klebsiella sp.), but the effect disappeared within a week and was reproduced in control WBRs by injection of sterile medium (phosphate buffer saline). Metagenome analyses showed a shift in the bacterial community composition after bioaugmentation in the planktonic phase of the woodchip reactors, but not in the solid phase (woodchip matrix). Only in the planktonic phase, Pseudomonas and Klebsiella increased their relative abundance as monitored by 16S rRNA gene sequences. In addition, an increased abundance of genes related to NO3- transformation after bacterial inoculation was observed in the metagenomic sequences. After one week, bacterial community composition became similar to its initial state, indicating resilience of the WBR microbial communities. We conclude that improved inoculation methods are needed to unlock the potential of bioaugmentation to increase NO3- removal at cold temperatures and make it a relevant technology for practical use at field-scale.

Microbial consortia driving (ligno)cellulose transformation in agricultural woodchip bioreactors

Freshwater ecosystems can be largely affected by neighboring agriculture fields where potential fertilizer nitrate run-off may leach into surrounding water bodies. To counteract this eutrophic driver, farmers in certain areas are utilizing denitrifying woodchip bioreactors (WBRs) in which a consortium of microorganisms convert the nitrate into nitrogen gases in anoxia, fueled by the degradation of lignocellulose. Polysaccharide-degrading strategies have been well described for various aerobic and anaerobic systems, including the use of carbohydrate-active enzymes, utilization of lytic polysaccharide monooxygenases (LPMOs) and other redox enzymes, as well as the use of cellulosomes and polysaccharide utilization loci (PULs). However, for denitrifying microorganisms, the lignocellulose-degrading strategies remain largely unknown. Here, we have applied a combination of enrichment techniques, gas measurements, multi-omics approaches, and amplicon sequencing of fungal ITS and procaryotic 16S rRNA genes to identify microbial drivers for lignocellulose transformation in woodchip bioreactors and their active enzymes. Our findings highlight a microbial community enriched for (ligno)cellulose-degrading denitrifiers with key players from the taxa Giesbergeria, Cellulomonas, Azonexus, and UBA5070 (Fibrobacterota). A wide substrate specificity is observed among the many expressed carbohydrate-active enzymes (CAZymes) including PULs from Bacteroidetes. This suggests a broad degradation of lignocellulose subfractions, including enzymes with auxiliary activities whose functionality is still puzzling under strict anaerobic conditions.

IMPORTANCE

Freshwater ecosystems face significant threats from agricultural runoff, which can lead to eutrophication and subsequent degradation of water quality. One solution to mitigate this issue is using denitrifying woodchip bioreactors (WBRs), where microorganisms convert nitrate into nitrogen gases utilizing lignocellulose as a carbon source. Despite the well-documented polysaccharide-degrading strategies in various systems, the mechanisms employed by denitrifying microorganisms in WBRs remain largely unexplored. This study fills a critical knowledge gap by revealing the degrading strategies of denitrifying microbial communities in WBRs. By integrating state-of-the-art techniques, we have identified key microbial drivers including Giesbergeria, Cellulomonas, Azonexus, and UBA5070 (Fibrobacterota) playing significant roles in lignocellulose transformation and showcasing a broad substrate specificity and complex metabolic capability. Our findings advance the understanding of microbial ecology in WBRs and by revealing the enzymatic activities, this research may inform efforts to improve water quality, protect aquatic ecosystems, and reduce greenhouse gas emissions from WBRs.

Extreme low-flow conditions in a dual-chamber denitrification bioreactor contribute to pollution swapping with low landscape-scale impact

Denitrification bioreactors are an effective edge-of-field conservation practice for nitrate (NO₃) reduction from subsurface drainage. However, these systems may produce other pollutants and greenhouse gases during NO₃ removal. Here a dual-chamber woodchip bioreactor system experiencing extreme low-flow conditions was monitored for its spatiotemporal NO₃ and total organic carbon dynamics in the drainage water. Near complete removal of NO₃ was observed in both bioreactor chambers in the first two years of monitoring (2019-2020) and in the third year of monitoring in chamber A, with significant (p < 0.01) reduction of the NO₃-N each year in both chambers with 8.6-11.4 mg NO₃-N L^-1 removed on average. Based on the NO₃ removal observed, spatial monitoring of sulfate (SO₄), dissolved methane (CH₄), and dissolved nitrous oxide (N₂O) gases was added in the third year of monitoring (2021). In 2021, chambers A and B had median hydraulic residence times (HRTs) of 64 h and 39 h, respectively, due to varying elevations of the chambers, with drought conditions making the differences more pronounced. In 2021, significant production of dissolved CH₄ was observed at rates of 0.54 g CH₄-C m^-3 d^-1 and 0.07 g CH₄-C m^-3 d^-1 in chambers A and B, respectively. In chamber A, significant removal (p < 0.01) of SO₄ (0.23 g SO₄ m^-3 d^-1) and dissolved N₂O (0.21 mg N₂O-N m^-2 d^-1) were observed, whereas chamber B produced N₂O (0.36 mg N₂O-N m^-2 d^-1). Considering the carbon dioxide equivalents (CO₂e) on an annual basis, chamber A had loads (~12,000 kg CO₂e ha^-1 y^-1) greater than comparable poorly drained agricultural soils; however, the landscape-scale impact was small (<1 % change in CO₂e) when expressed over the drainage area treated by the bioreactor. Under low-flow conditions, pollution swapping in woodchip bioreactors can be reduced at HRTs <50 h and NO₃ concentrations >2 mg N L^-1.