Treating all pathogens alike: a call for whole-catchment monitoring of plant-pathogens
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
Recommendation: posted 17 August 2023, validated 29 August 2023
Bizic, M. (2023) Treating all pathogens alike: a call for whole-catchment monitoring of plant-pathogens. Peer Community in Microbiology, 100006. 10.24072/pci.microbiol.100006
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.
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
The recommender in charge of the evaluation of the article and the reviewers declared that they have no conflict of interest (as defined in the code of conduct of PCI) with the authors or with the content of the article. The authors declared that they comply with the PCI rule of having no financial conflicts of interest in relation to the content of the article.
This work was supported by contract ANR-17-CE32-0004 for the project on Strategic preemptive pathogen surveillance of air and water to anticipate plant disease emergence in scenarios of changing land use and the Ec2co project CARTOBACTER 2017-2018.
Evaluation round #2
DOI or URL of the preprint: https://www.biorxiv.org/content/10.1101/2022.09.06.506731v2
Version of the preprint: 2
Author's Reply, 02 Aug 2023
Decision by Mina Bizic, posted 11 Jul 2023, validated 11 Jul 2023
I am sorry for the time it took to evaluate your revised preprint. The original reviewers were unavailable at this time and it took a while to find new reviewers.
Your revised preprint has been now reviewed by one peer who was made aware of the previous comments and revisions. As you can see this reviewer, finds your work very interesting and the manuscript well-written, and has several more suggestions and comments for improvement.
Most of the comments are minor and can be rapidly addressed. With regards to the suggestion to remove the term "seasonality" from the title. Indeed the main focus of the paper is not the seasonality aspect. Though you did sample all seasons across two years, not much emphasis is given to the temporal aspect. Therefore, I suggest considering accepting the suggested title. Alternatively, as also suggested, please enhance the temporal aspect of the discussion and analysis.
I am looking forward to your revised version,
Reviewed by anonymous reviewer 1, 03 Jul 2023
Evaluation round #1
DOI or URL of the preprint: https://doi.org/10.1101/2022.09.06.506731
Version of the preprint: 1
Author's Reply, 12 Apr 2023
Decision by Mina Bizic, posted 15 Feb 2023, validated 16 Feb 2023
As you can see, your manuscript has been thoroughly reviewed by three peers, two of which contributed to the one review. All reviewers like the paper and offered suggestion to improve the manuscript towards a recommendation in PCI.
The reviewers saw a need to improve the introduction including a revision and addition of relevant references. Further suggestions were given for improving the figures.
The reviewers brought up the topic of sampling method using a bucket. This is a rather common method, I agree. However, please specify whether additional means were taken to prevent contamination of one sample by another.
The cts sequences generated in this study are provided in the supplementary material and also submitted to the NCBI. However, there is no mentioning of the accessio numbers and data availability in the main text. Please add this. (If I missed this, I apologize).
Additionaly, please do not use the trem 16S rDNA as this is incorrect - use instead 16S rRNA gene.
Looking forward to reading your revised version,