Microbial communities in full-scale woodchip bioreactors treating aquaculture effluents

Sanni L Aalto,Suvi Suurnäkki,Mathis Von Ahnen,Marja Tiirola,Per Bovbjerg Pedersen

doi:10.1016/j.jenvman.2021.113852

Abstract

Woodchip bioreactors are being successfully applied to remove nitrate from commercial land-based recirculating aquaculture system (RAS) effluents. In order to understand and optimize the overall function of these bioreactors, knowledge on the microbial communities, especially on the microbes with potential for production or mitigation of harmful substances (e.g. hydrogen sulfide; H2S) is needed. In this study, we quantified and characterized bacterial and fungal communities, including potential H2S producers and consumers, using qPCR and high throughput sequencing of 16S rRNA gene. We took water samples from bioreactors and their inlet and outlet, and sampled biofilms growing on woodchips and on the outlet of the three full-scale woodchip bioreactors treating effluents of three individual RAS. We found that bioreactors hosted a high biomass of both bacteria and fungi. Although the composition of microbial communities of the inlet varied between the bioreactors, the conditions in the bioreactors selected for the same core microbial taxa. The H2S producing sulfate reducing bacteria (SRB) were mainly found in the nitrate-limited outlets of the bioreactors, the main groups being deltaproteobacterial Desulfobulbus and Desulfovibrio. The abundance of H2S consuming sulfate oxidizing bacteria (SOB) was 5–10 times higher than that of SRB, and SOB communities were dominated by Arcobacter and other genera from phylum Epsilonbacteraeota, which are also capable of autotrophic denitrification. Indeed, the relative abundance of potential autotrophic denitrifiers of all denitrifier sequences was even 54% in outlet water samples and 56% in the outlet biofilm samples. Altogether, our results show that the highly abundant bacterial and fungal communities in woodchip bioreactors are shaped through the conditions prevailing within the bioreactor, indicating that the bioreactors with similar design and operational settings should provide similar function even when conditions in the preceding RAS would differ. Furthermore, autotrophic denitrifiers can have a significant role in woodchip biofilters, consuming potentially produced H2S and removing nitrate, lengthening the operational age and thus further improving the overall environmental benefit of these bioreactors.

Highlights

Land-based recirculating aquaculture systems (RAS) are a current state-of-art technology for environmentally sustainable aquaculture production
The high abundance of fungi and bacterial in wood chip biofilm and water samples collected within the bioreactors in dicates that fungi are important members of the woodchip microbiome, being neglected in the previous studies
Fungi inhabiting woodchip bioreactors have found to possess denitrifi cation capacity (Aldossari and Ishii, 2020), but in our recent paper, we found no evidence for that in these bioreactors (Aalto et al, 2020). This suggests that the role of fungi is probably more on degrading lignocel lulose or complex organic substances into more bioavailable forms, as has been recently suggested to happen during the woodchip composting process, where fungi were abundant on the woodchip surface (Kouanda and Hua, 2021)

Summary

Introduction

Land-based recirculating aquaculture systems (RAS) are a current state-of-art technology for environmentally sustainable aquaculture production. Several studies have suggested optimal and cost-efficient design parameters for construction and operation of woodchip bioreactors treating RAS effluents (e.g. hydraulic retention time, manifold design, woodchip replacement rate; Lepine et al, 2020, 2018, 2016; von Ahnen et al, 2016). Woodchip bioreactors are currently applied for nitrate removal in commercial RAS, but in order to optimize their performance in both fresh and marine water, and to avoid potential unwanted microbial processes, it is important to gain knowledge on the overall microbial community, including currently fully neglected fungi, as well as on the microbial groups that can produce or consume H2S. We examined the microbial communities in three full-scale woodchip re actors treating the effluents of three commercial RAS, where the rates and microbiology of nitrate removal has already been examined (Aalto et al, 2020). RRNA gene, focusing especially on the microbial groups with known functions of sulfate reduction and sulfide oxidation as well as on the relative importance of heterotrophic and autotrophic denitrifiers

Study sites

Sampling

Microbial community composition

Statistical analysis

Results & discussion