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Latest recommendations
Id | Title * | Authors * | Abstract * ▼ | Picture * | Thematic fields * | Recommender | Reviewers | Submission date | |
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28 Nov 2024
![]() Design of a new model yeast consortium for ecological studies of enological fermentationEléonore Pourcelot, Audrey Vigna, Thérèse Marlin, Virginie Galeote, Thibault Nidelet https://doi.org/10.1101/2024.05.06.592697Yeast consortium for novel wine fermentationsRecommended by Francisco Cubillos based on reviews by Pablo Villarreal, Cristian Varela and 3 anonymous reviewersThe article by Pourcelot et al. (2024) brings a novel approach to wine fermentation. Recently, scientific advances have focused on utilizing microbial consortiums rather than individual species alone or even two individuals co-inoculated. However, spontaneous fermentations are complex, and microbes work in communities. This work aims to design a yeast consortium by studying the population changes over time and determining the metabolite production and fermentation kinetics. In this way, the authors present an elegant molecular approach by tagging each strain to construct a wine fermentation consortium. References Eléonore Pourcelot, Audrey Vigna, Thérèse Marlin, Virginie Galeote, Thibault Nidelet (2024) Design of a new model yeast consortium for ecological studies of enological fermentation. bioRxiv, ver.4 peer-reviewed and recommended by PCI Microbiol https://doi.org/10.1101/2024.05.06.592697 | Design of a new model yeast consortium for ecological studies of enological fermentation | Eléonore Pourcelot, Audrey Vigna, Thérèse Marlin, Virginie Galeote, Thibault Nidelet | <p>Wine fermentation involves complex microbial communities of non-<em>Saccharomyces</em> yeast species besides the well-known <em>Saccharomyces cerevisiae</em>. While extensive research has enhanced our understanding of <em>S. cerevisiae</em>, th... | ![]() | Microbial ecology and environmental microbiology | Francisco Cubillos | Cristian Varela, Pablo Villarreal, Anonymous | 2024-05-24 12:17:23 | View |
21 Jan 2025
![]() Factors shaping vaginal microbiota long-term community dynamics in young adult womenTsukushi Kamiya, Nicolas Tessandier, Baptiste Elie, Claire Bernat, Vanina Boue, Sophie Grasset, Soraya Groc, Massilva Rahmoun, Christian Selinger, Michael S. Humphrys, Marine Bonneau, Vincent Foulongne, Christelle Graf, Jacques Reynes, Vincent Tribout, Michel Segondy, Nathalie Boulle, Jacques Ravel, Carmen Lia Murall, Samuel Alizon https://www.medrxiv.org/content/10.1101/2024.04.08.24305448v3Elucidating microbial community transitions within the human vaginal environmentRecommended by Rafael Muñoz-TamayoThe human vaginal microbiota plays a key role in urogenital health. Enhancing our understanding of the dynamics of the vaginal microbiota can provide valuable insights for maintaining health and design strategies to prevent urogenital diseases. Health status evolves over time. The work by Kamiya et al. (2024) addressed the dynamic interplay between vaginal microbiota and health using a robust, high-resolution longitudinal cohort of 125 reproductive-aged women, followed for a median duration of 8.6 months in Montpellier, France. The participants were recruited within the PAPCLEAR study, which aimed to better understand the course and natural history of human papillomaviruses infections in healthy, young women (Murall et al. 2019). Each participant contributed at least three vaginal samples, from which microbiota barcoding was performed. The vaginal microbiota was clustered using the approach developed by Ravel et al. (2011) which categorizes microbial communities in 5 community state types with varying health implications. Transitions between community states were estimated using a hierarchical Bayesian Markov model. These transitions were associated with 16 covariates covering lifestyle, sexual practices and medication. This hierarchical approach allowed for the quantification of individual differences among women. The study characterized the stability of vaginal microbial communities and identified alcohol consumption as the strongest covariate driving community transitions. The results indicated that alcohol consumption promotes non-optimal communities. The modelling approach, however, indicated that individual variability among the women was not fully accounted for by the selected 16 covariates, suggesting the need to explore additional key factors, including dynamic covariates. The authors clearly identified several potential limitations of the study, including the variability associated to home sampling, the resolution of the microbial categories, and the impact of the clustering method on the analysis. My decision to recommend this manuscript is supported by the solid and rigorous analysis of the study, strengthened by the clear presentation of methods, data and analysis. While applying advanced computational techniques, the authors provide a solid biological interpretation of their results. This work makes a substantial contribution by expanding the understanding of vaginal microbiota dynamics and its interplay with health. It sets a framework for further evaluation of strategies aimed at promoting vaginal health. Moreover, it presents a generic methodology that could be applied to other microbial ecosystems. References Kamiya T, Tessandier N, Elie B, Bernat C, Boué V, Grasset S, Groc S, Rahmoun M, Selinger C, Humphrys MS, Bonneau M, Graf C, Foulongne V, Reynes J, Tribout V, Segondy M, Boulle N, Ravel J, Murall CL, Alizon S (2024) Factors shaping vaginal microbiota long-term community dynamics in young adult women. medRxiv, 2024.04.08.24305448, ver.3 peer-reviewed and recommended by PCI Microbiol. https://doi.org/10.1101/2024.04.08.24305448 Murall CL, Rahmoun M, Selinger C, Baldellou M, Bernat C, Bonneau M, Boué V, Buisson M, Christophe G, D’Auria G, Taroni F De, Foulongne V, Froissart R, Graf C, Grasset S, Groc S, Hirtz C, Jaussent A, Lajoie J, Lorcy F, Picot E, Picot MC, Ravel J, Reynes J, Rousset T, Seddiki A, Teirlinck M, Tribout V, Tuaillon É, Waterboer T, Jacobs N, Bravo IG, Segondy M, Boulle N, Alizon S (2019) Natural history, dynamics, and ecology of human papillomaviruses in genital infections of young women: protocol of the PAPCLEAR cohort study. BMJ Open, 9, e025129. https://doi.org/10.1136/BMJOPEN-2018-025129 Ravel J, Gajer P, Abdo Z, Schneider GM, Koenig SSK, McCulle SL, Karlebach S, Gorle R, Russell J, Tacket CO, Brotman RM, Davis CC, Ault K, Peralta L, Forney LJ (2011) Vaginal microbiome of reproductive-age women. Proceedings of the National Academy of Sciences of the United States of America, 108. https://doi.org/10.1073/pnas.1002611107
| Factors shaping vaginal microbiota long-term community dynamics in young adult women | Tsukushi Kamiya, Nicolas Tessandier, Baptiste Elie, Claire Bernat, Vanina Boue, Sophie Grasset, Soraya Groc, Massilva Rahmoun, Christian Selinger, Michael S. Humphrys, Marine Bonneau, Vincent Foulongne, Christelle Graf, Jacques Reynes, Vincent Tri... | <p>The vaginal microbiota is known to affect women’s health. Yet, there is a notable paucity of high-resolution follow-up studies lasting several months, which would be required to interrogate the long-term dynamics and associations with demograph... | ![]() | Mathematical modeling of microbial processes and ecosystems, Microbe-microbe and microbe-host interactions, Microbial ecology and environmental microbiology, Microbiomes | Rafael Muñoz-Tamayo | Simon Labarthe, Anonymous | 2024-09-02 17:27:41 | View |
11 Aug 2023
![]() Comparison of enrichment methods for efficient nitrogen fixation on a biocathodeAxel Rous, Gaëlle Santa-Catalina, Elie Desmond-Le Quéméner, Eric Trably, Nicolas Bernet https://doi.org/10.1101/2023.03.02.530809Toward a low-energy bioelectrochemical fixation of N2 via mixed cultures electroactive biofilmsRecommended by Jo De VriezeNitrogen 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. | Comparison of enrichment methods for efficient nitrogen fixation on a biocathode | Axel Rous, Gaëlle Santa-Catalina, Elie Desmond-Le Quéméner, Eric Trably, Nicolas Bernet | <p>The production of nitrogen fertilizers in modern agriculture is mostly based on the Haber-Bosch process, representing nearly 2% of the total energy consumed in the world. Low-energy bioelectrochemical fixation of N2 to microbial biomass was pre... | ![]() | Biofilms, microbial mats, Microbial biotechnology, Microbial ecology and environmental microbiology | Jo De Vrieze | Anonymous, Anonymous | 2023-03-07 08:27:42 | View |
19 Jul 2024
![]() Microbiome turnover during offspring development varies with maternal care, but not moult, in a hemimetabolous insectMarie-Charlotte Cheutin, Manon Boucicot, Joel Meunier https://doi.org/10.1101/2024.03.26.586808Stability in a microbe-insect interactionRecommended by Konstantinos KormasThe 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 | Microbiome turnover during offspring development varies with maternal care, but not moult, in a hemimetabolous insect | Marie-Charlotte Cheutin, Manon Boucicot, Joel Meunier | <p>The ecological success of insects often depends on their association with beneficial microbes. However, insect development involves repeated moults, which can have dramatic effects on their microbial communities. Here, we investigated whether a... | ![]() | Microbial ecology and environmental microbiology, Microbial physiology, ecophysiology and metabolism, Microbiomes | Konstantinos Kormas | 2024-03-28 12:24:50 | View | |
09 May 2023
![]() Interactions between Mycoplasma mycoides subsp. mycoides and bovine macrophages under physiological conditionsPhilippe Totté, Tiffany Bonnefois, Lucia Manso-Silvan https://doi.org/10.1101/2022.12.06.519279Interaction of bovine macrophages with Mycoplasma mycoides subsp. mycoidesRecommended by Pablo Zunino based on reviews by 2 anonymous reviewersMycoplasma mycoides subsp. mycoides (Mmm), a pathogenic wall-less bacterium, is the etiological agent of contagious bovine pleuropneumonia (CBPP). This highly contagious respiratory disease may develop in severe pneumonia, with associated high mortality rates in cattle. Mmm can display different immune evasion mechanisms; in addition, a host uncontrolled inflammatory response stands for lung lesions and chronic carrier animals. Macrophages are among the most important lines of defense against Mmm of the lower respiratory tract. Although their importance in defense and immune response modulation is known, results about their role and mechanisms of action are scarce and sometimes conflicting. In the present study, Totté et al. (1) aimed to investigate the interaction of bovine macrophages (isolated from cattle peripheral blood mononuclear cells) with Mmm, under in vitro conditions. The authors highlight that the study was performed under physiological conditions (in the presence of complement prepared from the same cell donor). In their study, using different approaches, the authors provide interesting and original results, proposing a pivotal role of complement in controlling the inflammatory response, which is crucial in the CBPP pathogenesis. The authors reported that macrophages did not kill Mmm in the presence of a non-bactericidal concentration of bovine serum. However, Mmm inactivation was observed when antiserum from CBPP convalescent animals was used. They also observed that Mmm induced the production of TNF by macrophages (when a high MOI was assessed). However, complement could even abolish Mmm-induced TNF response when used at bactericidal activity concentrations. This role of complement could be combined with the development of potentially protective antibodies against particular Mmm antigens involved in the interaction with identified macrophage receptors to propose control strategies against CBPP. Overall, the study by Totté et al. provides new fundamental insight for the research on preventive or therapeutic strategies for a poorly understood disease that still represents a serious concern for livestock production. REFERENCES 1. Totté, P., Bonnefois, T., Manso-Silván, L. Interactions between Mycoplasma mycoides subsp. mycoides and bovine macrophages under physiological conditions. bioRxiv 2022.12.06.519279, ver. 2 peer-reviewed and recommended by Peer Community In Microbiology. https://doi.org/10.1101/2022.12.06.519279 | Interactions between *Mycoplasma mycoides* subsp. *mycoides* and bovine macrophages under physiological conditions | Philippe Totté, Tiffany Bonnefois, Lucia Manso-Silvan | <p style="text-align: justify;">We investigated the interactions of unopsonized and opsonized *Mycoplasma mycoides* subsp. *mycoides* (Mmm) with bovine macrophages *in vitro*. Mmm survived and proliferated extracellularly on bovine macrophage cell... | ![]() | Microbe-microbe and microbe-host interactions | Pablo Zunino | Anonymous, Anonymous | 2022-12-09 15:12:53 | View |
17 Aug 2023
Within-species variation in the gut microbiome of medaka (Oryzias latipes) is driven by the interaction of light intensity and genetic backgroundCharlotte Evangelista, Stefaniya Kamenova, Beatriz Diaz Pauli, Joakim Sandkjenn, Leif Asbjørn Vøllestad, Eric Edeline, Pål Trosvik, Eric Jacques de Muinck https://doi.org/10.1101/2023.02.17.528956Getting closer to the host-microbe evolutionary relationshipRecommended by Konstantinos KormasThe issue of whether there is a clear and detectable relationship -either deterministic or stochastic- of fish gut microbiota with evolutionary processes is far from being resolved. Studies on fish microbiota are more perplexed as this animal group includes species both from wild and farmed populations (for food production, ornamental fish and animal models), with variable life cycles and ecophysiologies, and all these features expand the type of interactions to be studied. Based on this biological features variability, multiple methodological limitations, especially for the species with wild populations, are perhaps among of the central reasons for this knowledge gap. Therefore, experimental approaches, which can eliminate some of this variability, seem to be the best approach. The preprint by Evangelista et al. (2023) entitled "Within-species variation in the gut microbiome of medaka (Oryzias latipes) is driven by the interaction of light intensity and genetic background" is an example of such a targeted study with a freshwater fish species. Due to the paper's finely detailed experimental design, the interdisciplinary skills of the participating co-authors and exhaustive data analysis, this paper manages to draw solid and reproducible results and conclusions. This renders it not only an insightful contribution towards the more general host-microbe interactions in an evolutionary framework, but also a perfect example on how current and future relevant research should be conducted. I feel confident that this paper will assist other scientits of the field to move forward with their current working hypotheses but also to generate novel ones. Reference : Evangelista C, Kamenova S, Diaz Pauli B, Sandkjenn J, Vollestad A, Edeline E, Trosvik P, de Muinck E (2023) Within-species variation in the gut microbiome of medaka (Oryzias latipes) is driven by the interaction of light intensity and genetic background. bioRxiv, 2023.02.17.528956, ver. 2 peer-reviewed and recommended by Peer Community in Microbiology. https://doi.org/10.1101/2023.02.17.528956 | Within-species variation in the gut microbiome of medaka (*Oryzias latipes*) is driven by the interaction of light intensity and genetic background | Charlotte Evangelista, Stefaniya Kamenova, Beatriz Diaz Pauli, Joakim Sandkjenn, Leif Asbjørn Vøllestad, Eric Edeline, Pål Trosvik, Eric Jacques de Muinck | <p style="text-align: justify;">Unravelling evolution-by-environment interactions on the gut microbiome is particularly relevant considering the unprecedented level of human-driven disruption of the ecological and evolutionary trajectories of spec... | Microbiomes | Konstantinos Kormas | 2023-03-30 16:53:31 | View | ||
25 Apr 2023
![]() Genomic Changes During the Evolution of the Coxiella Genus Along the Parasitism-Mutualism Continuum.Diego Santos-Garcia, Olivier Morel, Hélène Henri, Adil El Filali, Marie Buysse, Valérie Noël, Karen D. McCoy, Yuval Gottlieb, Lisa Klasson, Lionel Zenner, Olivier Duron, Fabrice Vavre https://doi.org/10.1101/2022.10.26.513839Lifestyle transitions in endosymbiosisRecommended by Daniel TamaritHost-microbe symbioses are an essential component of many ecological systems, playing critical roles in the physiology and evolution of all involved partners. In this context, the bacterial family that includes Coxiella burnetii, the causative agent of Q fever, is of particular interest. The Coxiellaceae family is a complex group with members that have adopted a variety of specializations. Closely related lineages to C. burnetii are tick mutualists (Coxiella-like endosymbionts) and aquatic bacteria that may include both free living and symbiotic species. Additionally, four related genera within this family include symbionts of insects and amoebae. Exactly how and when pathogenicity and mutualism evolved in this lineage is not clear, thus remaining a valuable line of enquiry that can help establish general principles on these lifestyle transitions. A new study by Santos-Garcia and colleagues (2023) places the spotlight on this bacterial group, obtaining new insights through comparative genomics. The authors add two genomes, one of them a circular contig representing a highly reduced (0.9 Mb) chromosome, that increase the resolution of key branches in the Coxiella evolutionary tree. These include a sister group to C. burnetii and the group immediately subtending them, both entirely containing Coxiella-like endosymbionts. By analyzing genetic potential for metabolism, cell dimorphism, virulence and acidophily, the authors find evidence for the ancestrality of genes associated with a pathogenic lifestyle, and support a scenario by which mutualism arose multiple times in a parasitic lineage. In this context shines a pathogenicity island acquired in the common ancestor of this group and subsequently eroded in mutualistic lineages. This scenario highlights the importance of pre-adaptations that facilitate evolutionary specializations, such as the capabilities for B vitamin biosynthesis (key feature in the adaptation to a mutualistic relationship with organisms with B-vitamin-poor diets) and pH homeostasis (harnessed by C. burnetii for infection). Microbial groups at the crossroads of parasitism and mutualism help us understand the mechanisms underpinning these evolutionary strategies (see e.g. Drew et al, 2021). Transitions in endosymbiosis, including shifts in the parasitism-mutualism continuum, adaptation to new partners, or switches between free-living and host-associated lifestyles, affect the structure of ecological networks, and understanding them can yield crucial insights into how to manipulate microbial symbioses for health outcomes, sustainable agriculture or ecosystem conservation. The Coxiellaceae, by including a diverse set of mutualistic, parasitic and possibly free-living lineages, are a fantastic model group to tackle these questions. Together with other host-associated bacteria, such as Sodalis (Clayton et al, 2012) or Pantoea (Walterson and Stavrinides, 2015) species, these ecologically diverse microbes are valuable assets in the quest to decipher the molecular basis of lifestyle transitions in endosymbiosis. REFERENCES Clayton, A.L., et al (2012). A novel human-infection-derived bacterium provides insights into the evolutionary origins of mutualistic insect–bacterial symbioses. PLoS Genetics, 8: e1002990. https://doi.org/10.1371/journal.pgen.1002990 Drew, G.C., Stevens, E.J., King, K.C. (2021). Microbial evolution and transitions along the parasite-mutualist continuum. Nature Reviews Microbiology, 19: 623-638. https://doi.org/10.1038/s41579-021-00550-7 Santos-Garcia, D., et al. (2023) Genomic changes during the evolution of the Coxiella genus along the parasitism-mutualism continuum. bioRxiv, 2022.10.26.513839, ver. 4 peer-reviewed and recommended by Peer Community In Microbiology. https://doi.org/10.1101/2022.10.26.513839 Walterson, A.M., Stavrinides, J. (2015). Pantoea: insights into a highly versatile and diverse genus within the Enterobacteriaceae. FEMS Microbiology Reviews, 39: 968-984. https://doi.org/10.1093/femsre/fuv027 | Genomic Changes During the Evolution of the Coxiella Genus Along the Parasitism-Mutualism Continuum. | Diego Santos-Garcia, Olivier Morel, Hélène Henri, Adil El Filali, Marie Buysse, Valérie Noël, Karen D. McCoy, Yuval Gottlieb, Lisa Klasson, Lionel Zenner, Olivier Duron, Fabrice Vavre | <p style="text-align: justify;">The Coxiellaceae family is composed of five genera showing lifestyles ranging from free-living to symbiosis. Among them, <em>Coxiella burnetii </em>is a well-known pathogen causing Q fever in humans. This bacterium ... | ![]() | Bioinformatics dedicated to microbial studies, Genomic and evolutionary studies, Microbe-microbe and microbe-host interactions, Microbial symbiosis | Daniel Tamarit | 2022-10-27 12:55:14 | View | |
20 Sep 2023
![]() Transmission of synthetic seed bacterial communities to radish seedlings: impact on microbiota assembly and plant phenotypeMarie Simonin, Anne Preveaux, Coralie Marais, Tiffany Garin, Gontran Arnault, Alain Sarniguet, Matthieu Barret https://doi.org/10.1101/2023.02.14.527860Seed synthetic community matters and its impact on seedling is strain- and not species-dependantRecommended by Sebastien Massart based on reviews by Cindy Morris, Sebastian Pfeilmeier and 1 anonymous reviewerEngineering 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 | Transmission of synthetic seed bacterial communities to radish seedlings: impact on microbiota assembly and plant phenotype | Marie Simonin, Anne Preveaux, Coralie Marais, Tiffany Garin, Gontran Arnault, Alain Sarniguet, Matthieu Barret | <p style="text-align: justify;">Seed-borne microorganisms can be pioneer taxa during germination and seedling emergence. Still, the identity and phenotypic effects of these taxa that constitute a primary inoculum of plant microbiota is mostly unkn... | ![]() | Microbe-microbe and microbe-host interactions, Microbial ecology and environmental microbiology, Microbiomes | Sebastien Massart | 2023-02-15 10:27:26 | View | |
29 Aug 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 deltaC.E. Morris, C. Lacroix, C. Chandeysson, C. Guilbaud, C. Monteil, S. Piry, E. Rochelle Newall, S. Fiorini, F. Van Gijsegem, M.A. Barny, O. Berge https://doi.org/10.1101/2022.09.06.506731Treating all pathogens alike: a call for whole-catchment monitoring of plant-pathogensRecommended by Mina Bizic based on reviews by António Machado, Tiffany Lowe-Power ? and 1 anonymous reviewerPlant 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 | 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 | C.E. Morris, C. Lacroix, C. Chandeysson, C. Guilbaud, C. Monteil, S. Piry, E. Rochelle Newall, S. Fiorini, F. Van Gijsegem, M.A. Barny, O. Berge | <p style="text-align: justify;">Rivers, creeks, streams are integrators of biological, chemical and physical processes occurring in a catchment linking land cover from the headwaters to the outlet. The dynamics of human and animal pathogens in cat... | ![]() | Microbial ecology and environmental microbiology | Mina Bizic | 2022-12-22 12:04:32 | View | |
13 Oct 2023
![]() Fine-scale congruence in bacterial community structure from marine sediments sequenced by short-reads on Illumina and long-reads on NanoporeAlice Lemoinne, Guillaume Dirberg, Myriam Georges, Tony Robinet https://doi.org/10.1101/2023.06.06.541006ONT long-read sequencing and Illumina short-read sequencing of 16S rDNA amplicons give comparable results in terms of bacterial community structure in marine sedimentsRecommended by Aymé SporONT long-read high-throughput sequencing is not routinely used for metabarcoding studies of microbial communities. Even though this technology is supposed to considerably improve phylogenetic coverage and taxonomic resolution, it initially suffered from relatively poor read accuracy. Assessment of the performance of this new approach in comparison with routinely used 16S rDNA short-read sequencing is therefore needed to validate its use. The study by Lemoinne et al. (2023) offers a comprehensive comparison of two 16S rDNA metabarcoding approaches on marine sediment samples. By comparing Illumina short-read sequencing with ONT long-read sequencing, the authors conclude that bacterial community structures inferred from both technologies were similar. They also found that differences observed between sampling sites and along the sea-land orientation were comparable between the two technologies. However, the choice of technology still has an impact on the obtained results, notably in terms of bacterial diversity retrieved, taxonomic resolution, and replicability between biological replicates. Altogether, these results validate the use of ONT long-read sequencing for 16S metabarcoding approaches in marine sediments. Comparisons of such kinds targeting other remote environments are needed, as they might offer new opportunities for field scientists with no access to sequencing platforms to study the structure and composition of microbial communities. Reference Lemoinne, A., Dirberg, G., Georges, M., & Robinet, T. (2023). Fine-scale congruence in bacterial community structure from marine sediments sequenced by short-reads on Illumina and long-reads on Nanopore. biorXiv, version 3 peer-reviewed and recommended by Peer Community in Microbiology. https://doi.org/10.1101/2023.06.06.541006 | Fine-scale congruence in bacterial community structure from marine sediments sequenced by short-reads on Illumina and long-reads on Nanopore | Alice Lemoinne, Guillaume Dirberg, Myriam Georges, Tony Robinet | <p style="text-align: justify;">Following the development of high-throughput sequencers, environmental prokaryotic communities are usually described by metabarcoding with genetic markers on the 16S domain. However, short-read sequencing encounters... | ![]() | Microbial ecology and environmental microbiology, Molecular microbiology | Aymé Spor | 2023-06-07 17:48:08 | View |
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