Aquaponics is a production system based on the dynamic equilibrium between fish, plants, and microorganisms. In order to better understand the role of microorganisms in this tripartite relationship, we studied the bacterial communities hosted in eight aquaponic and aquaculture systems. The bacterial communities were analyzed by 16S rRNA gene deep sequencing. At the phylum level, the bacterial communities from all systems were relatively similar with a predominance of Proteobacteria and Bacteroidetes. At the genus level, however, the communities present in the sampled systems were more heterogeneous. The biofilter samples harbored more diverse communities than the corresponding sump samples. The core microbiomes from the coupled and decoupled systems shared more common operational taxonomic units than with the aquaculture systems. Eventually, some of the taxa identified in the systems could have beneficial functions for plant growth and health, but a deeper analysis would be required to identify the precise functions involved in aquaponics.

In aquaponics, nutrients originate mainly from the fish feed and water inputs in the system. A substantial part of the feed is ingested by the fish and either used for growth and metabolism or excreted as soluble and solid faeces, while the rest of any uneaten feed decays in the tanks. While the soluble excretions are readily available for the plants, the solid faeces need to be mineralised by microorganisms in order for its nutrient content to be available for plant uptake. It is thus more challenging to control the available nutrient concentrations in aquaponics than in hydroponics. Furthermore, many factors, amongst others pH, temperature and light intensity, influence the nutrient availability and plant uptake. Until today, most studies have focused on the nitrogen and phosphorus cycles. However, to ensure good crop yields, it is necessary to provide the plants with sufficient levels of all key nutrients. It is therefore essential to better understand and control nutrient cycles in aquaponics.

Studies in plant-microbiome currently use diverse protocols, making their comparison difficult and biased. Research in human microbiome have faced similar challenges, but the scientific community proposed various recommendations which could also be applied to phytobiome studies. Here, we addressed the isolation of plant microbiota through apple carposphere and lettuce root microbiome. We demonstrated that the fraction of the culturable epiphytic microbiota harvested by a single wash might only represent one-third of the residing microbiota harvested after four successive washes. In addition, we observed important variability between the efficiency of washing protocols (up to 1.6-fold difference for apple and 1.9 for lettuce). QIIME2 analysis of 16S rRNA gene, showed a significant difference of the alpha and beta diversity between protocols in both cases. The abundance of 76 taxa was significantly different between protocols used for apple. In both cases, differences between protocols disappeared when sequences of the four washes were pooled. Hence, pooling the four successive washes increased the alpha diversity for apple in comparison to a single wash. These results underline the interest of repeated washing to leverage abundance of microbial cells harvested from plant epiphytic microbiota whatever the washing protocols, thus minimizing bias.

The study of microorganisms in aquaponics is an important topic which requires more research before exploiting the full potential of beneficial microorganisms. In this experiment, we focused on the evolution over time of the bacterial communities in four compartments of an aquaponic system i.e., the sump, the biofilter, the lettuce rhizoplane and lettuce root. We studied these communities over the course of a lettuce growth cycle via regular sampling and sequencing of the 16S rRNA gene of the collected bacteria. We also followed the physicochemical parameters of the aquaponic water throughout the experiment. Results show that a different community could be found in each compartment and that all four communities were stable throughout time and resilient to naturally occurring water parameter changes which characterize functioning aquaponic systems. Furthermore, the communities of the sump and biofilter also seem stable over the years as the predominant taxa (Luteolibacter, Flavobacterium, Nitrospira) observed in our study are similar to the ones previously reported for this aquaponic system. Finally, our results provide proof for similarities between aquaponic and soil borne lettuce root communities (gammaproteobacteria, Flavobacterium, Pseudomonadaceae, Sphingomonadaceae) thus showing that aquaponics can be similar to soil production in terms of microbial life.

Anaerobic soil disinfestation (ASD), as a bio-fumigation technology, has been developed to control soil-borne pests. There is increasing evidence showing that carbon sources and cover tarps play an important role in the ASD suppression of soil-borne pests, but little is known about the effect of composted chicken manure (CCM) and totally impermeable films (TIF) against soil-borne pests in the strawberry production system. In experiments, the colonies of Fusarium spp. and Phytophthora spp., which are recognized to cause strawberry soil-borne diseases, decreased significantly after ASD. The soil promoted a significant increase in ammonium nitrogen, nitrate-nitrogen and organic matter, but a decrease in oxidation-reduction potential after ASD. Besides, the strawberry plant height, stem thickness and yield were significantly higher than in the non-amended soil. Compared to the untreated control, ASD, both at 6 and 12 ton/ha of CCM, significantly (p = 0.05) increased strawberry marketable yield and income. The economic benefit could be due to the suppression of soil-borne diseases and the improvement of soil nutrition. The soil bacterial and fungal diversity and richness increased after soil fumigation. The increased presence of biological control agents led to the suppression of soil-borne pathogens. In summary, ASD with CCM amendments could be applied in pre-plant fumigation to control strawberry soil-borne pests, strengthen soil fertility, improve crop yield and increase growers’ income.

Because viruses have been mostly studied in cultivated plants, little is known about virus diversity and ecology in less-managed vegetation or about the influence of human management and agriculture on virome composition. Poaceae (grass family)-dominated communities provide invaluable opportunities to examine these ecological issues, as they are distributed worldwide across agro-ecological gradients, are essential for food security and conservation, and can be infected by numerous viruses. Here, we used multiple levels of analysis that considered plant communities, individual plants, virus species, and haplotypes to broaden understanding of the Poaceae virome and to evaluate host-parasite richness relationships within agro-ecological landscapes in our study area.

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Aquaponics is a developing, soilless production technique combining hydroponics and recirculating aquaculture and is now spreading worldwide. Nevertheless, several aspects of aquaponics still need research. Indeed, despite being key-players in the dynamic equilibrium of aquaponic systems, microorganisms and their roles in aquaponics are still scarcely known. The aim of this study is thus to explore the microorganisms communities thriving in the root compartments of lettuce in the closed-loop aquaponic system of Gembloux Agro-Bio Tech and to focus on the differences between the microbial communities of lettuce of varying age. Therefore, root samples were collected from lettuces of five different age groups and microorganisms from the rhizoplane and from the endosphere were harvested. DNA was then extracted and sequenced on an Illumina MiSeq platform, targeting the V1-V3 region of the 16S rRNA gene. Results show that no significant difference could be noted between the different age groups despite a visible trend on the Bray-Curtis PCoA. However, significant differences in alpha-and beta-diversity could be observed between the rhizoplane and endosphere compartments. In terms of taxonomy, the composition of the root community is similar to what can be found in the literature and coherent with the previous experiments conducted in the same aquaponic system.