The degree of fidelity between microbes and their hosts varies considerably among different animal groups but also along the host's developmental stages and depends on the stability of their microbial communities. Cheutin et al. showcase experimentally the stability of whole body bacterial microbiome in a dermapteran insect species, the European earwig Forficula auricularia. The carefully designed experiments, which include a large number of investigated families and the related methodologies along with the data analysis, revealed that the bacterial communities of this insect are highly dynamic during the early developmental stages, but these changes are rather specific to each developmental stage and rather irrelevant to moulting. Some of these changes were reflected in the dominant predicted metabolic pathways. Another important finding of this study was that maternal care of the eggs has a detectable impact on the future shaping of the adult insect bacterial microbiome.

The findings of this paper clearly answer its working hypotheses, but they also generate a set of specific novel hypotheses for future studies. These hypotheses are of interest to the general field of animal-microbe interactions and, more specifically, to the driving forces of transmissability of microbes from one generation to the next one. This study also depicts some of the most likely important metabolic pathways in this insect-microbe relationship that could be the focus of future studies with more specific methodologies.

References

Cheutin M-C, Boucicot M, Meunier J. (2024). Microbiome turnover during offspring development varies with maternal care, but not moult, in a hemimetabolous insect. bioRxiv, ver.3, peer-reviewed and recommended by Peer Community In Microbiology. https://www.biorxiv.org/content/10.1101/2024.03.26.586808v3

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

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​

Engineering plant microbiota can improve plant health and growth sustainably. Emergent approaches include rational Synthetic Communities (SynCom) design or soil amendments and specific agricultural practices to shift resident microbiota and to understand its impact (Moreira et al. 2023). 

In this context, the impact of seed microbiota on the early stages of plant development is becoming an essential topic in the study of plant–microbiota interactions. Behind the well-studied seed-borne pathogens, the seed microbiota can host many other commensal and beneficial organisms that have been neglected in the past. 

The study of Simonin et al. (2023) applies single isolates and synthetic communities (SynCom)  on radish seeds to answer two key questions: what is the role of seed microbiota during the early stages of plant development? How can SynCom influence the seedling health and its microbiota? The study describes an elegant approach to cope with the variability of natural microbiota using SynCom following a gradient of complexity. 

Overall, the study highlighted a contrasted impact of the bacterial strains when applied in isolation or SynCom. The composition and complexity of the SynCom had also an impact on plant seedlings. Importantly, contrasting evolution from seeds to seedlings was observed for 3 strains of Pseudomonas fluorescens within the SynComs, underlining the importance of intra-species level diversity and precluding any generalization of results at species level.  

References 

Moreira, Z. P. M., Chen, M. Y., Ortuno, D. L. Y., & Haney, C. H. (2023). Engineering plant microbiomes by integrating eco-evolutionary principles into current strategies. Current Opinion in Plant Biology, 71, 102316. https://doi.org/10.1016/j.pbi.2022.102316

Simonin, M., Préveaux, A., Marais, C., Garin, T., Arnault, G., Sarniguet, A., & Barret, M. (2023). Transmission of synthetic seed bacterial communities to radish seedlings: impact on microbiota assembly and plant phenotype. bioRxiv, 2023-02. ver. 3 peer-reviewed and recommended by Peer Community in Microbiology. https://doi.org/10.1101/2023.02.14.527860

Improved characterization of food microbial ecosystems, especially those fermented is key to the development of food sustainability. Short-read metabarcoding is one of the most popular ways to study microbial communities. However, this approach remains complex because of the locks and biases it may entail particularly when applied to fungal communities. 

Building and using four mock communities from fermented food (bread, wine, cheese, fermented meat), Rué et al., 2023 demonstrate that combined DADA2 denoising algorithm followed to the FROGS tools gives a more accurate description of fungal communities compared to several commonly used bioinformatic workflows, dealing with all amplicon lengths. Moreover, Rué et al., 2023 provide guidance on which barcode to use (ITS1, ITS2, D1/D2 and RPB2), depending on the fermented food studied.

Practices in metabarcoding of fungi have been recently reviewed by Tedersoo et al., 2022 and their synthesis comes to the same conclusion as Rué et al., 2023.  As the reference databases are far from being complete notably for food ecosystems, the development of specific sequences public databases will enable the scientific community to lift the veil on this whole area of microbial ecology. 

The study conducted by Rué et al. (2023) provides a particularly detailed approach from a technical point of view, which contributes to improving the general practices in the metabarcoding of fungi. The design and the use of mock communities to compare the performances of the different pipelines is a strong point of this study. Another key element is the creation and use of an in-house database of fungal barcode sequences which improved the species-level affiliations

However, the study of fungal communities by metabarcoding is still a promising avenue of research in agri-food sciences. Thus, short-read sequencing, combined with suitable pipelines and databases, should remain of interest to the microbial ecology community (Pauvert et al., 2019; Furneaux et al., 2021). 

References

Furneaux, B., Bahram, M., Rosling, A., Yorou, N. S., & Ryberg, M. (2021). Long‐and short‐read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities. Molecular Ecology Resources, 21(6), 1833-1849. https://doi.org/10.1111/1755-0998.13387

Pauvert, C., Buée, M., Laval, V., Edel-Hermann, V., Fauchery, L., Gautier, A., ... & Vacher, C. (2019). Bioinformatics matters: The accuracy of plant and soil fungal community data is highly dependent on the metabarcoding pipeline. Fungal Ecology, 41, 23-33. https://doi.org/10.1016/j.funeco.2019.03.005

Rué, O., Coton, M., Dugat-Bony, E., Howell, K., Irlinger, F., Legras, J. L., ... & Sicard, D. (2023). Comparison of metabarcoding taxonomic markers to describe fungal communities in fermented foods. BioRxiv,  2023-0113.523754, ver.3 peer-reviewed and recommended by Peer Community in Microbiology. https://doi.org/10.1101/2023.01.13.523754

Tedersoo, L., Bahram, M., Zinger, L., Nilsson, R. H., Kennedy, P. G., Yang, T., ... & Mikryukov, V. (2022). Best practices in metabarcoding of fungi: From experimental design to results. Molecular ecology, 31(10), 2769-2795. https://doi.org/10.1111/mec.16460