Abstract
Woodchip bioreactors are increasingly used to remove nitrate (NO3–) from agricultural drainage water in order to protect aquatic ecosystems from excess nitrogen. Nitrate removal in woodchip bioreactors is based on microbial processes, but the microbiomes and their role in bioreactor efficiency are generally poorly characterized. Using metagenomic analyses, we characterized the microbiomes from 3 full-scale bioreactors in Denmark, which had been operating for 4–7 years. The microbiomes were dominated by Proteobacteria and especially the genus Pseudomonas, which is consistent with heterotrophic denitrification as the main pathway of NO3– reduction. This was supported by functional gene analyses, showing the presence of the full suite of denitrification genes from NO3– reductases to nitrous oxide reductases. Genes encoding for dissimilatory NO3– reduction to ammonium were found only in minor proportions. In addition to NO3– reducers, the bioreactors harbored distinct functional groups, such as lignocellulose degrading fungi and bacteria, dissimilatory sulfate reducers and methanogens. Further, all bioreactors harbored genera of heterotrophic iron reducers and anaerobic iron oxidizers (Acidovorax) indicating a potential for iron-mediated denitrification. Ecological indices of species diversity showed high similarity between the bioreactors and between the different positions along the flow path, indicating that the woodchip resource niche was important in shaping the microbiome. This trait may be favorable for the development of common microbiological strategies to increase the NO3– removal from agricultural drainage water.
Highlights
Leaching of nitrate (NO3−) from agricultural soils to aquatic ecosystems is a growing environmental concern due to the globally increasing use of nitrogen (N) fertilizers in agriculture (Howarth et al, 2002)
We report the microbiome composition at a given time point in three stable operating fullscale woodchip bioreactors (BR1-BR3), where NO3− removal efficiencies were previously monitored (Bruun et al, 2016; Carstensen et al, 2019; Audet et al, 2021) and where concurrent metadata on water chemistry were available
The microbiomes of the woodchip bioreactors were dominated by the phylum Proteobacteria (70–91%) with Pseudomonas as the most abundant genus, ranging from a relative abundance of 26% at the middle of BR1 to 61% at the outlet of BR3 (Supplementary Figure 1)
Summary
Leaching of nitrate (NO3−) from agricultural soils to aquatic ecosystems is a growing environmental concern due to the globally increasing use of nitrogen (N) fertilizers in agriculture (Howarth et al, 2002). Management of the bioreactor microbiomes to increase the NO3− removal efficiency is an option that needs to be further explored and implemented (Grießmeier et al, 2017; Jang et al, 2019; Anderson et al, 2020) This necessitates a better understanding of the complex microbial populations and functional capacity of operating woodchip bioreactors that treat agricultural drainage water. A number of studies have addressed the microbial composition of woodchip bioreactors under various conditions and at various scales using 16s rRNA and microbial cultivation methods (Grießmeier et al, 2017; Jang et al, 2019; Abdi et al, 2020; Hellman et al, 2021; Nordström et al, 2021) These studies allowed to link a number of factors, such as wood type, NO3− concentration, and pesticide contamination with the presence and activity of specific microbes. The previous studies generally highlighted the importance of the phylum Proteobacteria in the bioreactor ecosystems, but provided limited insight on the entire woodchip microbiome
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