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

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

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

Host-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

Fermented vegetables, traditionally consumed in Asian and Eastern countries, are gaining increasing interest in Western countries due to the growing demand for more natural, healthy, and sustainable food. Their potential health effects have only recently begun to be scientifically studied (Thierry et al., 2023).

The manufacturing process of fermented vegetables consists of cutting and packing raw vegetables with salt or brine, that will draw water and nutrients out from the vegetable tissue, thus providing microorganisms with the necessary substrates to initiate spontaneous fermentation (Buckenhueskes, 2015). Various parameters, including the cutting method, which may influence the rate of solute diffusion from vegetable tissue, can affect fermentation speed and, consequently, the quality of fermented vegetables. However, the role of cutting type has rarely been addressed.

The study by Valence et al. (2025) used a comprehensive range of methods to investigate how cutting types and a slight reduction in salt concentration influence the spontaneous fermentation of two vegetables, carrot and cabbage. Two cutting types, finely or roughly cut, and two salt levels, 1% (the minimum concentration usually used) and a lower salt level in line with health recommendations (0.8%), were tested. Carrot and cabbage fermentations were performed under controlled conditions in duplicate, and microbiological and biochemical characteristics were monitored over one month by combining several approaches and extensive experiments in culturomics, 16S rRNA gene and gyrB metataxonomics for bacterial community analysis, and targeted metabolomics.

The study shows the sequential establishment of microbial communities during the fermentation of both vegetables. In the early stages, Enterobacteriaceae replaced the initial microbiota, but they were rapidly outcompeted by Lactic Acid Bacteria (LAB). LAB growth acidified the medium, inhibiting enterobacteria and ensuring microbial safety. Their dominance was attributed to their ability to ferment carbohydrates into lactic acid and possibly the production of antimicrobial compounds. The results of targeted metabolomic analysis show that the main fermentation byproducts are mannitol, lactic acid, and acetic acid, which is consistent with previous studies on fermented vegetables.​

Most notably, this study demonstrated for the first time that the type of vegetable cutting has a major impact on fermentation dynamics by influencing the release of solutes into the brine. Finer cuts, which provide a greater surface area, facilitate nutrient diffusion, thereby promoting LAB proliferation and acidification.

​​​​​​The study also shows that salt addition improved solute release, though the microbial effects were less clear due to variability between replicates. Indeed, significant variability between jars was noted, affecting microbial composition, metabolite profiles, and acidification rates.

The work of Valence et al. (2025) highlights for the first time the crucial role of cutting type in vegetable fermentation, demonstrating that finer cuts accelerate acidification, improve microbial safety, and enhance fermentation efficiency. Their findings contribute to the optimization of fermentation processes, providing valuable insights for enhancing the quality of fermented vegetables.​​​​​

​​​References:
Buckenhueskes HJ. Quality improvement and fermentation control in vegetables. Advances in Fermented Foods and Beverages. Elsevier, 2015, 515–39. https://doi.org/10.1016/B978-1-78242-015-6.00022-0

Thierry A, Baty C, Marché L, Chuat V, Picard O, Lortal S, Valence F. Lactofermentation of vegetables: An ancient method of preservation matching new trends. Trends Food Sci Technol. 2023. https://doi.org/10.1016/j.tifs.2023.07.009

Valence F, Junker R, Baty C, Rué O, Mariadassou M, Madec M, Maillard M, Bage A, Chuat V, Marché L, Thierry A. The cutting type of vegetables influences the spontaneous fermentation rate. HAL, ver.2 2025. https://hal.science/hal-04701063v2​

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