As complex multipartite interactions among the coral host and coral-associated microbial entities including the dinoflagellate symbionts, bacteria, archaea and viruses, have been appreciated, a manipulatable, less-complex study system is desired to deepen our functional understanding of this fascinating symbiotic system. Among experimental manipulation approaches, removal of the algal symbionts using menthol is widely implemented; however, its effect on the rest of the coral-associated symbiotic members has not been explored, which is critical knowledge to assess experimental works using this popular method. This preprint by Puntin et al. (https://doi.org/10.1101/2023.08.23.554380) presents an important observation in this aspect. Their initial observations suggest that menthol-induced coral bleaching introduces stochastic changes in associated bacterial communities, which resemble dysbiosis, making bacterial communities more dissimilar from each other. They also observed low taxonomic diversity in bacterial communities on the corals maintained in aquaria over several months, worth noting as a positive value as an experimental system. Their data are preliminary by nature, while they present intriguing ideas that warrant further studies.

Reference

Puntin G, Wong JCY, Röthig T, Baker DM, Sweet M, Ziegler M (2024). The bacterial microbiome of symbiotic and menthol-bleached polyps of long-term aquarium-reared Galaxea fascicularis (2024). bioRxiv, ver.4., peer-reviewed and recommended by Peer Community In Microbiology. https://doi.org/10.1101/2023.08.23.554380 

The paper "Diversity of bacterial symbionts associated with the tropical plant bug Monalonion velezangeli (Hemiptera: Miridae) revealed by high-throughput 16S rRNA sequencing" by Navarro-Escalante et al. (2023) is a valuable contribution to entomological research, particularly in the context of pest management. This descriptive study, while not delving into the functional characterization of the associated bacterial strains, lays an essential groundwork for understanding the bacterial components of the microbiota of this agricultural pest. This study is interesting because it provides new information on insect microbiota, especially in a family for which the knowledge of the diversity of bacterial symbionts is very limited.

One of the study's core strengths lies in its exploration and definition of the core microbiota of M. velezangeli, which could serve as a foundation for future research aimed at pest control strategies. The use of 16S rRNA sequencing, despite its known limitations, has enabled the profiling of these bacterial communities. The paper highlights the absence of differences in the bacterial communities associated with the nymph and adult stages of the pest, indicating a stable association of these microbes throughout the insect's life cycle.

A standout point in the study is the overwhelming presence of the symbiont Wolbachia, accounting for approximately 92% of the bacterial composition. However, intriguingly, the authors also note the absence of Wolbachia in some individuals, suggesting a more complex dynamic that warrants further investigation. This finding is particularly noteworthy, as it opens up questions about the role of Wolbachia and its impact on the biology and ecology of M. velezangeli.

The researchers have carefully addressed all the reviewers’ comments and suggestions. They also addressed a potential bias in their study - the overwhelming presence of Wolbachia - by analyzing the bacterial community after the removal of Wolbachia sequences. This careful approach enriches the study's credibility and ensures a more accurate representation of the pest's microbiota.

The identification of potentially culturable strains within the core microbiome represents an interesting perspective of this research. This information could be used in future efforts to develop pest control strategies, particularly those employing paratransgenic approaches. The possibility of manipulating these culturable strains to combat M. velezangeli presents an exciting avenue for sustainable pest management.

While the study does not investigate the localization of these associated bacteria, whether in the gut or elsewhere, including potentially in dedicated symbiotic organs, it nevertheless offers a valuable descriptive account. This baseline knowledge will be useful for any subsequent functional or localization studies, which could further unravel the complex interactions between M. velezangeli and its microbial partners.

In conclusion, the work of Navarro-Escalante et al. is a notable effort to set the stage for future research into the biology of M. velezangeli and its associated microbiota. The findings from this study provide a good reference point for further investigations aimed at pest's biology and exploring innovative pest control strategies. It also represents a valuable contribution to understanding the basic biology of insect-bacteria interactions. 

Reference

Navarro-Escalante​ L., Benavides​ P. and Acevedo​, F.E. (2023) Diversity of bacterial symbionts associated with the tropical plant bug Monalonion velezangeli (Hemiptera: Miridae) revealed by high-throughput 16S-rRNA sequencing. Research Square​, ver. 7 peer-reviewed and recommended by PCI Microbiology. https://doi.org/10.21203/rs.3.rs-2022560/v7​

Plant pathogens can cause devastating damage to crop (Strange and Scott 2005) greatly affecting a food resource in growing need on our planet. A significant proportion of global crops require irrigation, and with this, bare the risk of being affected by irrigation-borne pathogens (Lamichhane and Bartoli, 2015). Detection of plant pathogens in irrigation water can effectively be used to minimize this risk. River water makes up a major irrigation water source. Morris et al., (2023), propose monitoring whole river catchments to understand plant pathogen population dynamics and generate models to prevent outbreaks, similar to practices regarding water-borne human pathogens.

Monitoring 270 km of the river Durance, Morris et al., (2023) reveal that two groups of bacteria known to host pathogenic strains, Pseudomonas syringae and the Soft Rot Pectobacteriaceae are present in relatively high numbers across the entire catchment or significant parts of it, respectively, with their abundance mostly correlated to water temperature. Nevertheless, despite their presence no major outbreaks have been reported in recent years. The authors suggest that the current environmental conditions in the lower, agriculture-dominated part of the catchment may not generate the necessary environment for an outbreak. Alternatively, as also suggested, though some potentially pathogenic variants were detected in the study, they may not match the crops currently grown in the area (Morris et al., 2023).

The authors thus bring up the need for large scale monitoring and call for observations on potential land-use changes in the area that may alter the sensitive and seemingly stable conditions in such a way that outbreaks will be triggered. Change of land use, specifically from rural to agricultural use, has been repeatedly recognized to influence biodiversity (e.g., Ionescu et al., 2022). Furthermore, agricultural environments, with a dense network of irrigation channels, natural and man-made ponds, and larger reservoirs, will accelerate the spread of organisms through multiple biotic and abiotic vectors (Karnatak and Wollrab, 2020), and with this likely plant- (and other) pathogens. Overall, the work by Morris et al., (2023) highlights that studying the presence and distribution of plant pathogens in water used for irrigation across large areas, is bound to identify which potential pathogens are omnipresent, awaiting for the right condition for an outbreak; and which are rather spread from, isolated, local sources and thus can be effectively mitigated.

References

Strange, R. N., and Scott, P. R. (2005). Plant disease: a threat to global food security. Annu. Rev. Phytopathol. 43, 83–116. https://doi.org/10.1146/annurev.phyto.43.113004.133839

Lamichhane, J.R. and Bartoli, C. (2015), Plant pathogenic bacteria in open irrigation systems: what risk for crop health? Plant Pathol, 64: 757-766. https://doi.org/10.1111/ppa.12371

C.E. Morris, C. Lacroix, C. Chandeysson, C. Guilbaud, C. Monteil, S. Piry, Rochelle Newall E., S. Fiorini, F. Van Gijsegem, M.A. Barny, O. Berge (2023) Comparative abundance and diversity of populations of the Pseudomonas syringae and Soft Rot Pectobacteriaceae species complexes throughout the Durance River catchment from its French Alps sources to its delta. bioRxiv, 2022.09.06.506731, ver. 3 peer-reviewed and recommended by Peer Community in Microbiology. https://doi.org/10.1101/2022.09.06.506731 

Ionescu, D., Bizic, M., Karnatak, R., Musseau, C. L., Onandia, G., Kasada, M., Berger, S. A., et al. (2022). From Microbes to Mammals: Pond Biodiversity Homogenization across Different Land-Use Types in an Agricultural Landscape. Ecological Monographs 92(3): e1523. https://doi.org/10.1002/ecm.1523

Shrimp aquaculture ponds are an established technology that helps answer the demand for high-protein food while reducing the impact of fishing on the oceans.

However, as a closed system, high in organic matter, aquaculture ponds in general and those used for shrimp in particular tend to develop anoxic sediments and favour sulfate reduction to H2S. The development of hydrogen sulphide, in return, is toxic to the shrimp and can lead to lower yields.

A standard solution to the problem is to inject air into the sediments. However, this solution requires additional infrastructure, is costly to operate, and can also disturb other essential life forms in the pond, such as benthic plants. 

In this work by Torun et al. (2024), the authors used a carefully designed lab model of shrimp ponds to show that the addition of molybdate at concentrations as low as 5 mg/l delayed the accumulation of H2S and pushed the zone rich in sulphide deeper into the sediment.

The postulated mechanism for the inhibition in H2S production is that molybdate binds to the ATP sulfurylase in sulphate-reducing bacteria (SRB), and together with ATP, they generate adenosine 5′-phosphosulfate (APS) that cannot be used as an electron acceptor.

Surprisingly, however, the growth of SRB was stimulated rather than inhibited in this experiment. While the exact cause remains unknown, the authors postulate that SRB resorted to alternative metabolic pathways such as fermentation.

Overall, while this work was done on a model system in the lab, adding molybdate to shrimp aquaculture ponds is a promising technique and should be tested on a larger scale.

Reference

Torun F, Hostins B, Schryver PD, Boon N, Vrieze JD. (2024). Molybdate delays sulphide formation in the sediment and transfer to the bulk liquid in a model shrimp pond. bioRxiv, ver.3, peer-reviewed and recommended by Peer Community In Microbiology. https://doi.org/10.1101/2023.11.16.567380

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