In fed aquaculture, fishes are commonly fed with a fish-oil based diet mostly coming from captured fishes. This is one main global issue leading to overfishing of wild species (Cashion et al., 2017; Tacon & Metian, 2008). Several alternatives in lipid sources for fish diet have been tested and promising alternatives such as plants (e.g. rapeseed oil) or microalgae (e.g. Schizochytrium sp.) have been identified (Pérez-Pascual et al., 2020). Like other animals, fishes’ digestive tract is composed of a microbiota whose composition is linked to the host physiological state as well as its diet (Yukgehnaish et al., 2020). In reared fishes such as the European sea bass (Dicentrarchus labrax), replacing fish oil by other sources such as microalgae in their diet has been shown to modify the digestive microbiota composition (Pérez-Pascual et al., 2020).

Here, the aim of Katsoulis-Dimitriou et al. (2024), was to test the effect of three dietary microalgae blends on the midgut microbiota composition of the reared fishes. The authors compared the effect of a control diet (i.e. with only fish oil as lipid source, namely, FO) with that of three experimental diets with two thirds of the fish oil replaced by either a mixture of the microalgae Microchloropsis gaditana and Isochrysis sp. (now known as Tisochrysis lutea, MI), Phaeodactylum tricornutum and Isochrysis sp. (PI) or Schizochytrium sp. and P. tricornutum (SP). For each diet, 25 fishes were reared in each of the triplicated tanks and, after 80 days of experiment, a total of 10 fishes per diet were sampled. DNA was extracted from the midgut part of the intestine and a 16S rDNA-based metabarcoding approach was conducted to survey the associated bacterial community. Each diet type, FO, MI, PI and SP, was mostly characterized by a composition of specific abundant OTUs, indicating the clear influence of the oil composition on the digestive microbiota. When feeding with the MI diet, the authors also highlighted the presence of some candidate genera (e.g. Pseudoalteromonas, Pseudomonas, Bacillus and Rhodopseudomonas) as potential probiotics for fish aquaculture. Finally, in comparison to the fish oil diet, a predictive metabolic analysis of the bacterial community could suggest a differential expression of some polysaccharide metabolisms with the microalgae-based diets, highlighting a probable diet-based effect on the microbiota functioning.

The work from Katsoulis-Dimitriou et al. (2024) completes the current knowledge on using sustainable alternatives to traditional fish feed and its effect on the digestive microbiota composition of fishes. This work also opens new ways to be explored considering the enrichment of potential probiotics using microalgae-base diets. Further analyses testing specific functional approaches (e.g. transcriptomics, metabolomics) may allow completing the understanding of the gut microbiota functioning linked to diet composition. Finally, measurements on fish biometrics in a similar experiment should help understanding the contribution of a microalgal-diet to fish fitness.

References

Cashion, T., Le Manach, F., Zeller, D., & Pauly, D. (2017). Most fish destined for fishmeal production are food‐grade fish. Fish and Fisheries, 18(5), 837–844. https://doi.org/10.1111/faf.12209

Katsoulis-Dimitriou, S., Nikouli, E., Gkalogianni, E., Karapanagiotidis, I., Kormas, K. (2024) The effect of dietary fish oil replacement by microalgae on the gilthead sea bream midgut bacterial microbiota. BioRxiv, ver.3 peer-reviewed and recommended by PCI Microbiol https://doi.org/10.1101/2024.01.24.576938

Pérez-Pascual, D., Estellé, J., Dutto, G., Rodde, C., Bernardet, J.-F., Marchand, Y., Duchaud, E., Przybyla, C., & Ghigo, J.-M. (2020). Growth Performance and Adaptability of European Sea Bass (Dicentrarchus labrax) Gut Microbiota to Alternative Diets Free of Fish Products. Microorganisms, 8(9), 1346. https://doi.org/10.3390/microorganisms8091346

Tacon, A. G. J., & Metian, M. (2008). Global overview on the use of fish meal and fish oil in industrially compounded aquafeeds: Trends and future prospects. Aquaculture, 285(1–4), 146–158. https://doi.org/10.1016/j.aquaculture.2008.08.015

Yukgehnaish, K., Kumar, P., Sivachandran, P., Marimuthu, K., Arshad, A., Paray, B. A., & Arockiaraj, J. (2020). Gut microbiota metagenomics in aquaculture: Factors influencing gut microbiome and its physiological role in fish. Reviews in Aquaculture, 12(3), 1903–1927. https://doi.org/10.1111/raq.12416

In this interesting study by Bruley et al. (2024), the cyanobacterium Microcystis aeruginosa PCC7806 is taken as a model organism for intracellular CaCO3 precipitation in Cyanobacteria, i.e. in the form of intracellular amorphous calcium carbonates (iACC). This phenomenon, which was first described in 2012, is an example of genetically controlled biomineralization in bacteria. Hence, a gene coding for the protein calcyanin (ccyA) has been documented in iACC biomineralizing cyanobacteria. Nevertheless, so far, the functioning of the calcyanin protein remains unknown. As a first step to elucidate its role in iACC biomineralization the authors study the diel variations of ccyA expression. An approximately 2.5-fold variation in abundance of ccyA transcripts has been observed with the highest values of ccyA expression observed during the second half of the dark period. In addition, the authors made a thorough investigation of transcriptomics data, to detect gene-expressions with temporal patterns that positively or negatively correlate with ccyA. A particular focus was made on neighboring genes (both upstream and downstream) to detect a possible operon gathering ccyA with other genes. Very interestingly, the authors discovered that some neighboring genes coding for Ca2+/H+ antiporter systems, showed transcripts with abundances that correlate with that of ccyA. 

This study raises many interesting questions on genetically controlled biomineralization in bacteria and more particularly the function of iACC biomineralization in Cyanobacteria. As the authors write, iACC biomineralization could be involved in carbon-concentrating mechanisms (CCM), intracellular pH buffering, and create “ballast” for buoyancy and floatability regulation. Nevertheless, these roles would require mechanisms for the dissolution of iAAC in concert with its precipitation ; fine-tuning of both resulting in homeostasis or cyclic temporal patterns of iAAC increase/decrease. As a perspective, the response of Microcystis to fluctuations in calcium and/or pCO2 levels could provide valuable insights into the molecular mechanisms underlying the biomineralization of iACC, as well as comparisons with non-iACC biomineralizing strains or with a mutant of PCC 7806 with a deactivated/deleted ccyA gene.

Reference:

Bruley A, Gaëtan J, Gugger M, Pancrace C, Millet M, Gaschignard G, Dezi M, Humbert J-F, Leloup J, Skouri-Panet F, Callebaut I, Benzerara K and Duprat E (2024) Diel changes in the expression of a marker gene and candidate genes for intracellular amorphous CaCO3 biomineralization in Microcystis. bioRxiv, ver.3 peer-reviewed and recommended by PCI Microbiol. https://doi.org/10.1101/2024.07.07.602159

Nitrogen fixation and elimination are two key microbial processes that significantly impact the release (and removal) of reactive nitrogen into natural ecosystems. Unlike global change, caused by the emission of greenhouse gasses into our atmosphere, the release of reactive nitrogen into our biosphere only recently (in the last years) received the necessary public attention. Hence, novel techniques for (1) reactive nitrogen recovery, (2) energy-effective removal, and (3) sustainable nitrogen fixation are essential to prevent the nitrogen cycle from spinning out of control without also putting an additional burden on our precious natural resources or increasing the emission of greenhouse gasses.

In this research paper by Rous et al. (2023), the authors investigated the use of a biocathode in a bioelectrochemical system (BES) for sustainable fixation of N2 into NH3, using electricity as a sustainable energy source and CO2 as the only carbon source. A critical element in their study was the enrichment of N2-fixating bacteria, starting from soil samples, in an effort to achieve effective nitrogen fixation. A comparison between the enriched culture and a pure culture of diazotrophic hydrogenotrophic bacteria confirmed comparable results for N2 fixation, indicating that the enrichment process was a viable and successful approach. Although pure culture biotechnological processes have their merits, it is clear that the usage of an enriched microbial culture allows for a more simple, robust, and open microbial process, compared to pure culture systems.

This approach does enable a sustainable way of N2 (and by extension CO2) fixation, as it relies on electricity directly (or indirectly through H2) and CO2 only, but it does suffer from low coulombic efficiencies (<5%). This indicates that, even though the results are promising, there is room for optimization, especially concerning the production of (unwanted) side products, such as acetate and other microbial metabolites. This reflects a key challenge and potential disadvantage of mixed or enriched cultures compared to pure cultures.

It is in that framework that this study provides an interesting, highly relevant view on the potential of bioelectrochemical nitrogen fixation using enriched cultures, yet, it also implies the need to either find a purpose for the byproducts, such as acetate, and/or achieve a more effective enrichment strategy to achieve an increased coulombic efficiency towards sustainable nitrogen fixation.

Reference

Rous A., Santa-Catalina G., Desmond-Le Quéméner E., Eric Trably E. and Nicolas Bernet N. (2023). Comparison of enrichment methods for efficient nitrogen fixation on a biocathode. bioRxiv, 2023.03.02.530809, ver 5, peer-reviewed and recommended by Peer Community in Microbiology. https://doi.org/10.1101/2023.03.02.530809​

The Burkholderia sensu lato group is predominant in the rhizosphere of rice. It includes both plant growth promoting rhizobacteria (typically members of the Paraburkholderia genus) and phytopathogens (typically members of the Burkholderia genus). Better understanding the interaction between Burkholderia sensu lato and their host plant is therefore crucial to advance our knowledge of the ecology of rice, a plant that feeds more than half of the humans on the planet.

The perception of root exudates from their host is key for rhizobacteria. Is the response to root exudates more related to the phylogeny of the bacteria, i.e. genus-dependent, or is it strain-specific? This question is not trivial for the Burkholderia sensu lato group, which has experienced shifting outlines over the last twenty years. During the early stages of rice root colonization, Wallner et al. [1] investigated the transcriptomic regulation of three strains of each Burkholderia and Paraburkholderia genera, in addition to a genomic comparison, in order to better understand their early colonization strategies. 

While these six strains possess a large proportion of gene homologues, their experiment shows their response to root exudates to be strain-specific. In the study, rice root exudates affected several metabolic pathways of interest in most strains, noticeably including i) the Entner-Doudoroff pathway, which had never been reported to be activated in relation to root colonization and ii) the putrescine pathway, which may reflect signaling controlling root colonization. 

The work by Wallner et al. provides new insights on the strain-level response of the transcriptomic regulation of Burkholderia sensu lato in response to root exudates in the early stages of root colonization. Beyond this, the next steps will hopefully shed light on what happens in more complex environments, within a complex bacterial community and during later colonization stages.

Reference

Wallner A, Klonowska A, Guigard L, King E, Rimbault I, Ngonkeu E, Nguyen P, Béna G, Moulin L (2022) Comparative genomics and transcriptomic response to root exudates of six rice root-associated Burkholderia sensu lato species. BioRxiv, 2022.10.04.510755, version 2 peer-reviewed and recommended by PCI Microbiol. https://doi.org/10.1101/2022.10.04.510755