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[hal-04748778] Study of the interactions between plants and a Streptomyces strain with plant defence-eliciting properties
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Alba Noël) 22 Oct 2024
https://hal.science/hal-04748778v1
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[hal-04749383] Activation of plant immunity by galbonolides promotes rhizosphere colonisation by Streptomyces sp. AgN23
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Clément Nicolle) 23 Oct 2024
https://hal.science/hal-04749383v1
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[hal-02941967] Influence of plant genotype and soil on the wheat rhizosphere microbiome: evidences for a core microbiome across eight African and European soils
Here, we assessed the relative influence of wheat genotype, agricultural practices (conventional vs organic) and soil type on the rhizosphere microbiome. We characterized the prokaryotic (archaea and bacteria) and eukaryotic (fungi and protists) communities in soils from four different countries (Cameroon, France, Italy, Senegal) and determined if a rhizosphere core microbiome existed across these different countries. The wheat genotype had a limited effect on the rhizosphere microbiome (2% of variance) as the majority of the microbial taxa were consistently associated to multiple wheat genotypes grown in the same soil. Large differences in taxa richness and in community structure were observed between the eight soils studied (57% variance) and the two agricultural practices (10% variance). Despite these differences between soils, we observed that 177 taxa (2 archaea, 103 bacteria, 41 fungi and 31 protists) were consistently detected in the rhizosphere, constituting a core microbiome. In addition to being prevalent, these core taxa were highly abundant and collectively represented 50% of the reads in our data set. Based on these results, we identify a list of key taxa as future targets of culturomics, metagenomics and wheat synthetic microbiomes. Additionally, we show that protists are an integral part of the wheat holobiont that is currently overlooked.
ano.nymous@ccsd.cnrs.fr.invalid (Marie Simonin) 30 Dec 2023
https://hal.inrae.fr/hal-02941967v1
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[hal-04528599] Characterisation of the spermosphere of the common bean seed (Phaseolus vulgaris)
Seed plants have co-evoluted with microorganisms by forming beneficial relationships in order to facilitate their adaptation to terrestrial lifestyle. Indeed, more and more studies are demonstrating the inter-relationships of the microbiome and their hosts and the resulting impacts of such relationships in terms of the host’s fitness, environmental response, adaptation and evolution. These studies have given rise to a relatively new concept of the holobiont which views the host organism and its associated microbiota as a single functional unit, where evolutionary selection occurs between both the host and its microbiota, as well as among different microbial species within the microbiota. While plant microbiome in the phyllosphere and rhizosphere has been well studied, seed spermosphere and microbiome have remain relatively unnoticed. Yet, seeds have an important distinctive function in the inheritance process by connecting plant generations and serving as a critical point in the continuity of the plant microbiome. However, the fate of seed-borne microorganisms after germination is relatively unexplored. Seed germination, a transient process giving rise to a microenvironment known as the spermosphere, is a critical point for the establishment of the future plant microbiome. Indeed, seed exudation after imbibition is hypothesized to be the driving force for microbial selection, growth and interaction in the spermosphere. The aim of this study is to characterize the germinating bean spermosphere with multi-omics technologies to understand the complex interactions between seed borne microorganisms and seed exudates
ano.nymous@ccsd.cnrs.fr.invalid (Chandrodhay Saccaram) 01 Apr 2024
https://hal.science/hal-04528599v1
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[hal-04599898] Terroir, baker’s practices, wheat varieties and their influence on sourdough microbial diversity
The microbial diversity of many ecosystems has recently been described but the question remains of the extent to which species and varieties develop and evolve within their particular environments. Altenatively, are they essentially ubiquitous, being more frequent in certain localities as a result of the conditions encountered? Is the distribution geographically structured, and/or influenced by other factors ? Using sourdough breadmaking ecosystems as a model and participatory research approach, we are analysing human influence on the dispersion and selection of lactic acid bacteria and yeasts. In France, microbial diversity associated with bread-making has not been well-documented. Bread can be made by two kind of artisans, farmer-bakers and artisan-bakers. Both use sourdough to leaven the bread. Sourdough is a dough composed of wheat and rye flour, or only one of these two ingredients, water, possibly supplemented with salt and subjected to an acidifying natural fermentation, whose function is to ensure the dough raising Décret No. 93- 1074, 13 sept. 1993). This aim of this study was to describe diversity of microbial species in baker's sourdough (yeasts and lactic acid bacteria) and to understand the evolutionary process (dispersion, selection) that shape this diversity.
ano.nymous@ccsd.cnrs.fr.invalid (Elisa Michel) 04 Jun 2024
https://hal.inrae.fr/hal-04599898v1
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[hal-04914263] Century-old herbarium specimen provides insights into Pierce’s disease of grapevines emergence in the Americas
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ano.nymous@ccsd.cnrs.fr.invalid (Monica Donegan) 27 Jan 2025
https://hal.science/hal-04914263v1
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[hal-04906255] Pink-pigmented variant of Clavibacter michiganensis expands phenotypic range of tomato bacterial canker pathogen
Bacterial canker of tomato caused by the Gram-positive corynebacterial species Clavibacter michiganensis is one of the most destructive seed-borne diseases in both open air and greenhouse tomatoes. The pathogen is a regulated agent in all tomato-producing countries as translocation of infected tomato materials transports the bacterium into new areas. Clavibacter michiganensis is generally known to have yellow-pigmented colonies on culture media, which is a key differentiative phenotypic feature in standard diagnostic guidelines. During 2020 and 2021, pink-pigmented corynebacterial strains were isolated from tomato seeds (cv. Sun 6189F1) and plants showing severe canker symptoms in Southern Iran. The six pink-pigmented strains were pathogenic on tomato and pepper seedlings under greenhouse conditions, and gave positive results with C. michiganensis-specific primers pairs described in the literature. Phylogenomics and DNA similarity calculations showed that the pink-pigmented strains were highly similar to the authentic yellow-pigmented members of the pathogen. Thus, they were identified as a new phenotypic variant of tomato bacterial canker pathogen. Whole genome screenings accomplished with PCR-based assays showed that the pink strains contain all pathogenicity determinant genes described in C. michiganensis. Further, orthologous gene clusters in the pink-pigmented strains were more similar to the pathogenic members of C. michiganensis than to those of non-pathogenic tomato-associated Clavibacter species. Results obtained in this study demonstrate the emergence of a new pink-pigmented variant of C. michiganensis and highlight the importance of colony pigmentation/morphology in culture-based detection of the bacterium. The need for updating diagnostic guidelines on the colony variants of the pathogen is further discussed.
ano.nymous@ccsd.cnrs.fr.invalid (Malihe Haghverdi) 23 Jan 2025
https://hal.science/hal-04906255v1
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[ird-04483657] Celebrating the 20th anniversary of the first Xanthomonas genome sequences – how genomics revolutionized taxonomy, provided insight into the emergence of pathogenic bacteria, enabled new fundamental discoveries and helped developing novel control measures – a perspective from the French network on Xanthomonads
In this Opinion paper, members of the French Network on Xanthomonads give their personal view on what they consider to be some of the groundbreaking discoveries in the field of molecular plant pathology over the past 20 years. By celebrating the 20th anniversary of the first Xanthomonas genome sequences, they explain how genomics revolutionized taxonomy, provided insight into the emergence of pathogenic bacteria, enabled new fundamental discoveries and contributed to the development of novel control measures. Collectively, such new, genomics-enabled perspective will help to ensure sustainable agriculture and conservation of our environment in the future.
ano.nymous@ccsd.cnrs.fr.invalid (Ralf Koebnik) 29 Feb 2024
https://ird.hal.science/ird-04483657v1
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[hal-04908844] Celebrating the 20th anniversary of the first Xanthomonas genome sequences – how genomics revolutionized taxonomy, provided insight into the emergence of pathogenic bacteria, enabled new fundamental discoveries and helped developing novel control measures – a perspective from the French network on Xanthomonads
In this Opinion paper, members of the French Network on Xanthomonads give their personal view on what they consider to be some of the groundbreaking discoveries in the field of molecular plant pathology over the past 20 years. By celebrating the 20th anniversary of the first Xanthomonas genome sequences, they explain how genomics revolutionized taxonomy, provided insight into the emergence of pathogenic bacteria, enabled new fundamental discoveries and contributed to the development of novel control measures. Collectively, such new, genomics-enabled perspective will help to ensure sustainable agriculture and conservation of our environment in the future.
ano.nymous@ccsd.cnrs.fr.invalid (Ralf Koebnik) 23 Jan 2025
https://hal.inrae.fr/hal-04908844v1
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[hal-03834661] Single seed microbiota: assembly and transmission from parent plant to seedling
The seed acts as the primary inoculum source for the plant microbiota. Understanding the processes involved in its assembly and dynamics during germination and seedling emergence has the potential to allow for the improvement of crop establishment. Changes in the bacterial community structure were tracked in 1,000 individual seeds that were collected throughout seed developments of beans and radishes. Seeds were associated with a dominant bacterial taxon that represented more than 75% of all reads. The identity of this taxon was highly variable between the plants and within the seeds of the same plant. We identified selection as the main ecological process governing the succession of dominant taxa during seed filling and maturation. In a second step, we evaluated the seedling transmission of seed-borne taxa in 160 individual plants. While the initial bacterial abundance on seeds was not a good predictor of seedling transmission, the identities of the seed-borne taxa modified the phenotypes of seedlings. Overall, this work revealed that individual seeds are colonized by a few bacterial taxa of highly variable identity, which appears to be important for the early stages of plant development.
ano.nymous@ccsd.cnrs.fr.invalid (Guillaume Chesneau) 05 Sep 2024
https://hal.inrae.fr/hal-03834661v1
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[hal-04670942] Comparative transcriptomics reveals a highly polymorphic Xanthomonas HrpG virulence regulon
Background: Bacteria of the genus Xanthomonas cause economically significant diseases in various crops. Their virulence is dependent on the translocation of type III effectors (T3Es) into plant cells by the type III secretion system (T3SS), a process regulated by the master response regulator HrpG. Although HrpG has been studied for over two decades, its regulon across diverse Xanthomonas species, particularly beyond type III secretion, remains understudied. Results: In this study, we conducted transcriptome sequencing to explore the HrpG regulons of 17 Xanthomonas strains, encompassing six species and nine pathovars, each exhibiting distinct host and tissue specificities. We employed constitutive expression of plasmid-borne hrpG*, which encodes a constitutively active form of HrpG, to induce the regulon. Our findings reveal substantial inter- and intra-specific diversity in the HrpG* regulons across the strains. Besides 21 genes directly involved in the biosynthesis of the T3SS, the core HrpG* regulon is limited to only five additional genes encoding the transcriptional activator HrpX, the two T3E proteins XopR and XopL, a major facility superfamily (MFS) transporter, and the phosphatase PhoC. Interestingly, genes involved in chemotaxis and genes encoding enzymes with carbohydrate-active and proteolytic activities are variably regulated by HrpG*. Conclusions: The diversity in the HrpG* regulon suggests that HrpG-dependent virulence in Xanthomonas might be achieved through several distinct strain-specific strategies, potentially reflecting adaptation to diverse ecological niches. These findings enhance our understanding of the complex role of HrpG in regulating various virulence and adaptive pathways, extending beyond T3Es and the T3SS.
ano.nymous@ccsd.cnrs.fr.invalid (Thomas Quiroz Monnens) 13 Aug 2024
https://hal.inrae.fr/hal-04670942v1
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[hal-03978256] Complete genome sequencing of three clade-1 xanthomonads reveals genetic determinants for a lateral flagellin and the biosynthesis of coronatine-like molecules in Xanthomonas
Evolutionarily early-branching xanthomonads, also referred to as clade-1 xanthomonads, include major plant pathogens, most of which colonize monocotyledonous plants. Seven species have been validly described, among them the two sugarcane pathogens Xanthomonas albilineans and Xanthomonas sacchari, and Xanthomonas translucens, which infects small-grain cereals, diverse grasses, but also asparagus and pistachio trees. Single-gene sequencing and genomic approaches indicated that this clade likely contains more, yet undescribed species. In this study, we sequenced representative strains of three novel species using long-read sequencing technology. Xanthomonas campestris pv. phormiicola strain CFBP 8444 causes bacterial streak on New Zealand flax, another monocotyledonous plant. Xanthomonas sp. strain CFBP 8443 has been isolated from common bean and Xanthomonas sp. strain CFBP 8445 originated from banana. Complete assemblies of the chromosomes confirmed their unique phylogenetic position within clade 1 of Xanthomonas. Genome mining revealed novel genetic features, hitherto undescribed in other members of the Xanthomonas genus. In strain CFBP 8444, we identified genes related to the synthesis of coronatine-like compounds, a phytotoxin produced by several pseudomonads, which raises interesting questions about the evolution and pathogenicity of this pathogen. In addition, strain CFBP 8444 was found to contain a second, atypical flagellar gene cluster in addition to the canonical flagellar gene cluster. Overall, this research represents an important step toward better understanding the evolutionary history and biology of early-branching xanthomonads.
ano.nymous@ccsd.cnrs.fr.invalid (Chloé Peduzzi) 13 Apr 2023
https://hal.inrae.fr/hal-03978256v1
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[hal-04338621] A novel “ceasefire” model to explain efficient seed transmission of Xanthomonas citri pv. fuscans to common bean
Summary Although seed represents an important means of plant pathogen dispersion, the seed-pathogen dialogue remains largely unexplored. A multi-omic approach ( i.e. dual RNAseq, plant small RNAs and methylome) was performed at different seed developmental stages of common bean ( Phaseolus vulgaris L.) during asymptomatic colonization by Xanthomonas citri pv. fuscans ( Xcf ). In this condition, Xcf did not produce disease symptoms, neither affect seed development. Although, an intense molecular dialogue, via important transcriptional changes, was observed at the early seed developmental stages with down-regulation of plant defense signal transduction, via action of plant miR, and upregulation of the bacterial Type 3 Secretion System. At later seed maturation stages, molecular dialogue between host and pathogen was reduced to few transcriptome changes, but marked by changes in DNA methylation of plant defense and germination genes, in response to Xcf colonization, potentially acting as defense priming to prepare the host for the post-germination battle. This distinct response of infected seeds during maturation, with a more active role at early stages refutes the widely diffused assumption considering seeds as passive carriers of microbes. Finally, our data support a novel plant-pathogen interaction model, specific to the seed tissues, which differs from others by the existence of distinct phases during seed-pathogen interaction with seeds first actively interacting with colonizing pathogens, then both belligerents switch to more passive mode at later stages. We contextualized this observed scenario in a novel hypothetical model that we called “ceasefire”, where both the pathogen and the host benefit from temporarily laying down their weapons until the moment of germination.
ano.nymous@ccsd.cnrs.fr.invalid (Armelle Darrasse) 14 Jan 2025
https://hal.inrae.fr/hal-04338621v1
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[hal-04665363] Molecular dialogue of plant-bacterial interactions during seed transmission
Seed is the vector of dispersion of many phytopathogenic bacteria. The molecular dialogue that is established between the plant and these microorganisms during their transmission remains largely unknown, mainly due to the technological lock of isolating bacterial RNA from infected seeds. In this project, RNA sequencing technologies were used on both plant and bacterial cells in complement to capture technologies for enrichment of specific bacterial RNA. Changes in bacterial and plant transcriptomes, but also plant methylomes were investigated during seed transmission of the plant pathogenic bacteria Xanthomonas citri pv. fuscans (Xcf) on common bean (Phaseolus vulgaris). During the seed filling stage, we observed major transcriptomic changes in both partners. In particular a concomitant differential expression of plant defense genes (e.g. serine peptidases, LRR-kinases, MAPKs, regulators such as bZIP, TIFY, AP2/ERF) and bacterial type II/type III secretion systems effectors occurred during this stage. This intense pathogenic/defense molecular dialogue at early seed developmental stage was shut down in latter stages during seed maturation, and at maturity. We also noted that at maturity, seed transmission of Xcf altered DNA methylation at more than 800 plant genomic regions. These changes included methylation changes within promoter or coding regions of genes involved in plant defense (e.g. WRKY, NB-LR or PUB13) and seed development (e.g. AGL62, FIE2 or LEA proteins). Deep-sequencing of small RNAs at the filling and mature seed stages highlighted potential miRNA (30%) and siRNA (44%) populations originated from P. vulgaris genome. The perspectives are now to integrate all these data to identify which plant miRNAs can mediate transcript repression in plant and bacterial transcriptomes and which plant siRNA can mediate change in plant methylome.
ano.nymous@ccsd.cnrs.fr.invalid (Armelle Darrasse) 31 Jul 2024
https://hal.inrae.fr/hal-04665363v1
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[hal-04665344] Activation of seed defenses through defense priming
Yield losses due to seedborne pathogens have a major economic impact on the global food market. We attempted to develop sustainable strategies to stimulate pathogen resistance from the seed that have a negligeable impact on seed quality parameters, such as germination rate and homogeneity. Our approach consisted in applying defense priming treatments using plant resistance inducers (PRI) such as methyl jasmonate (MeJA) and β-aminobutyric acid (BABA) on developing or mature seeds. After a first stage of technique optimization, results from tomato and bean treated seeds showed extensive transcriptome reprogramming, with a strong effect on defense pathways. To correlate these data with pathogen resistance, we analysed developing and germinating seeds treated with different PRIs and their effects on the growth of different pathogens including bacteria and fungi. First results obtained on tomato showed a marked growth inhibition on A. brassicicola from specific PRI-treated seeds, while the effect on C. michiganensis was minor. Our next step is, now, the identification of the molecules responsible of the fungistatic effect present in treated seeds.
ano.nymous@ccsd.cnrs.fr.invalid (Jerome Verdier) 31 Jul 2024
https://hal.inrae.fr/hal-04665344v1
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[hal-04665483] Mise en place d’un pathosystème Brassica napus L./Alternaria brassicicola pour l’étude du déterminisme de la transmission à la semence
Le projet SUCSEED (« Stop the Use of pestiCides on Seeds by proposing alternatives », Projet Prioritaire de Recherche « Cultiver et protéger autrement » ANR 20-PCPA-0009) vise à identifier et développer des solutions de protection des semences innovantes via des approches éco-responsables. Il s’agit plus précisément de lutter contre la transmission des agents pathogènes aux semences et contre les fontes de semis. Alternaria brassicicola est un champignon nécrotrophe, responsable du « black spot » sur les plantes de la famille des Brassicacées et capable de se transmettre aux et par les graines. La contamination des semences compromet leur germination et/ou provoque le développement de symptômes sur les plantes dans la culture suivante. Il est donc essentiel de lutter contre la transmission d’A. brassicicola aux graines. Dans le contexte actuel de nécessité de réduire le recours aux fongicides, la valorisation des défenses de la plante pourrait constituer une opportunité de développement de méthodes de lutte alternative à la lutte chimique. Mais le rôle des réactions de défense de la plante, du fruit et de la graine au cours de la phase de transmission est très mal connu. Des travaux antérieurs [1] sur Arabidopsis thaliana ont mis en évidence l’existence d’un gradient de transmissibilité d’A. brassicicola selon les étages des siliques : les graines des siliques les plus âgées (situées à la base de l’inflorescence) présentent un taux de contamination par A. brassicicola plus élevé que les graines issues des siliques plus jeunes (situées en hauteur). Les raisons de l’existence de ce gradient sont mal connues, en particulier pour ce qui est du rôle des mécanismes de défense de la plante. Pourtant, les composés de défense de la plante sont supposés être déterminants pour la sévérité des symptômes de black spot sur feuille [2]. Le présent travail décrit la mise au point d’un pathosystème pour l’étude du déterminisme de la transmission d’Alternaria brassicicola aux semences de Brassica napus L. Des siliques de la hampe florale principale de plantes de colza ont été inoculées par dépôt de gouttes contenant une suspension de conidies d’A. brassicicola sur les siliques basales (les plus âgées) et apicales (les plus jeunes présentes sur la hampe florale au moment de l’inoculation). Après quelques jours, des symptômes nécrotiques apparaissent sur les siliques, qui ont été récoltées 18 jours après inoculation. Le pathosystème mis au point va permettre l’évaluation du taux de transmission d’A. brassicicola aux semences de colza, mais aussi le décryptage du dialogue moléculaire plante-pathogène au cours de la phase de transmission aux semences.
ano.nymous@ccsd.cnrs.fr.invalid (Agathe Cailleau) 31 Jul 2024
https://hal.inrae.fr/hal-04665483v1
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[hal-04688330] Transmission of synthetic seed bacterial communities to radish seedlings: impact on microbiota assembly and plant phenotype
<div><p>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 unknown. Here, we studied the transmission of bacteria from radish seeds to seedlings using the inoculation of individual seed-borne strains and synthetic communities (SynComs) under in vitro conditions. The SynComs were composed of highly abundant and prevalent, sub-dominant, or rare bacterial seed taxa. We monitored the transmission of each strain alone or in communities using gyrB gene amplicon sequencing and assessed their impacts on germination and seedling phenotype. All strains and Syn-Coms successfully colonized seedlings and we were able to reconstruct a richness gradient (6, 8 and 12 strains) on both seeds and seedlings. Stenotrophomonas rhizophila became dominant on seedlings of the three SynComs but most strains had variable transmission success (i.e increasing, stable or decreasing during seed to seedling transition) that also depended on the SynCom richness. Most individual strains had no effect on seedling phenotypes, with the exception of Pseudomonas viridiflava and Paenibacillus sp. which had detrimental effects on germination and seedling development. Abnormal seedling morphologies were also observed with SynComs but their proportions decreased at the highest richness level. Interestingly, some bacterial strains previously identified as core taxa of radish seeds (Pseudomonas viridiflava, Erwinia persicina) were associated with detrimental effects on seedling phenotypes either in isolation or in SynComs. These results confirm that the plant core microbiome includes pathogenic and not only commensal or mutualistic taxa. Altogether, these results show that SynCom inoculation can effectively manipulate seed and seedling microbiota diversity and thus represents a promising tool to better understand the early stages of plant microbiota assembly. This study also highlights strong differences between native seed-borne taxa in the colonization and survival on plant habitats.</p></div>
ano.nymous@ccsd.cnrs.fr.invalid (Marie Simonin) 04 Sep 2024
https://hal.inrae.fr/hal-04688330v1
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[hal-04852994] Le microbiote des plantes - De son rôle dans la survie végétale à son ingénierie pour une agriculture durable
La majorité des êtres vivants pluricellulaires sont colonisés par une multitude de micro-organismes. C’est le cas notamment des plantes, dont les racines abritent une vaste biodiversité microbienne. Ce microbiote est composé de diverses espèces de bactéries, champignons et protistes, qui étendent le répertoire génétique de la plante, interagissent et contribuent à sa survie. Des recherches récentes illustrent l’importance du microbiote pour la santé des plantes et une agriculture durable.
ano.nymous@ccsd.cnrs.fr.invalid (Anne-Sophie Masson) 21 Dec 2024
https://hal.inrae.fr/hal-04852994v1
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[hal-04844057] Development of Tools to Detect and Identify Strains Belonging to the Pseudomonas syringae Species Complex Responsible for Vein Clearing of Zucchini
Vein clearing of zucchini (VCZ) is a disease caused by seedborne bacteria that affects young plants of Cucurbita pepo subsp. pepo. VCZ agents are distributed into four phylogenetic clusters within clades 2a and 2ba of phylogroup 2 of the Pseudomonas syringae species complex. All these strains are pathogenic to squash, but only certain strains can also attack melon and cucumber. Strains belonging to clades 2b and 2d are sometimes isolated from zucchini seeds but have not been associated with VCZ epidemics. Identification tools for VCZ agents are required to improve disease control. Primers were designed to implement a seven-gene multilocus sequence analysis (MLSA) scheme for a collection of 60 strains isolated from zucchini seeds. The MLSA showed a clear predominance of strains of cluster 2ba-A and the presence of VCZ strains in a fifth cluster (2ba-C). PCR tests were designed to characterize strains in the VCZ clusters, and a multiplex qPCR test was proposed to distinguish strains with a cucurbit host range extended to melon and cucumber, harboring hopZ5 and sylC, from other strains harboring avrRpt2 and sylC. Additional qPCR tests were also designed to gain insights into clade-2b and -2d strains that can be isolated from cucurbits. These tools evaluated in silico with the NCBI database and experimentally with a collection of 112 strains detected all target strains, except for the test dedicated to clade-2b strains, and excluded 96.7 to 100% of nontarget strains. These tools are intended to serve phylogenetic studies, epidemiological monitoring, and seed testing. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license .
ano.nymous@ccsd.cnrs.fr.invalid (Caroline Lacault) 17 Dec 2024
https://hal.inrae.fr/hal-04844057v1
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[hal-04665509] A stage‐dependent seed defense response to explain efficient seed transmission of Xanthomonas citri pv. fuscans to common bean
Although seed represents an important means of plant pathogen dispersion, the seed–pathogen dialogue remains largely unexplored. A multiomic approach was performed at different seed developmental stages of common bean ( Phaseolus vulgaris L.) during asymptomatic colonization by Xanthomonas citri pv. fuscans ( Xcf ), At the early seed developmental stages, we observed high transcriptional changes both in seeds with bacterial recognition and defense signal transduction genes, and in bacteria with up‐regulation of the bacterial type 3 secretion system. This high transcriptional activity of defense genes in Xcf ‐colonized seeds during maturation refutes the widely diffused assumption considering seeds as passive carriers of microbes. At later seed maturation stages, few transcriptome changes indicated a less intense molecular dialogue between the host and the pathogen, but marked by changes in DNA methylation of plant defense genes, in response to Xcf colonization. We showed examples of pathogen‐specific DNA methylations in colonized seeds acting as plant defense silencing to repress plant immune response during the germination process. Finally, we propose a novel plant–pathogen interaction model, specific to the seed tissues, highlighting the existence of distinct phases during seed–pathogen interaction with seeds being actively interacting with colonizing pathogens, then both belligerents switching to more passive mode at later stages.
ano.nymous@ccsd.cnrs.fr.invalid (Armelle Darrasse) 31 Jul 2024
https://hal.inrae.fr/hal-04665509v1
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[hal-04579728] Interactions shape aquatic microbiome responses to Cu and Au nanoparticle treatments in wetland manipulation experiments
[...]
ano.nymous@ccsd.cnrs.fr.invalid (Zhao Wang) 18 May 2024
https://hal.science/hal-04579728v1
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[hal-04208811] Seasonal Differences and Grazing Pressure Alter the Fate of Gold Nanoparticles in a Microcosm Experiment
Gold nanoparticles (AuNPs) are used as models to track and predict NP fates and effects in ecosystems. Previous work found that aquatic macrophytes and their associated biofilm primarily drove the fate of AuNPs within aquatic ecosystems and that seasonality was an important abiotic factor in the fate of AuNPs. Therefore, the present work aims to study if grazers, by feeding on these interfaces, modify the AuNP fate and if this is altered by seasonal fluctuations. Microcosms were dosed with 44.8 mu g/L of AuNP weekly for 4 weeks and maintained in environmental chambers simulating Spring and Fall light and temperature conditions. We discovered that seasonal changes and the presence of grazers significantly altered the fate of Au. Higher temperatures in the warmer season increased dissolved organic carbon (DOC) content in the water column, leading to stabilization of Au in the water column. Additionally, snail grazing on biofilm growing on the Egeria densa surface led to a transfer of Au from macrophytes to the organic matter above the sediments. These results demonstrate that climate and grazers significantly impacted the fate of Au from AuNPs, highlighting the role that grazers might have in a large and biologically more complex ecosystem.
ano.nymous@ccsd.cnrs.fr.invalid (Christina Bergemann) 20 Dec 2023
https://hal.science/hal-04208811v1
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[hal-04688340] Stable, multigenerational transmission of the bean seed microbiome despite abiotic stress
Seed microbiomes initiate plant microbiome assembly, but the consequences of environmental conditions of the parent plant for seed microbiome assembly and transmission are unknown. We tracked endophytic seed bacterial communities of common bean lines exposed to drought or excess nutrients, and discovered stable transmission of 22 bacterial members regardless of parental plant treatment. This study provides insights into the maintenance of plant microbiomes across generations, even under challenging environmental stress.
ano.nymous@ccsd.cnrs.fr.invalid (Abby Sulesky-Grieb) 05 Sep 2024
https://hal.inrae.fr/hal-04688340v1
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[hal-04292325] At the interfaces of the hydrologic sciences: Connecting water, elements, ecosystems, and people through the major contributions of Dr. Emily Bernhardt
this paper, we describe the major contributions of Professor Emily Bernhardt to the hydrologic sciences. Dr. Bernhardt's work addresses how carbon, nutrient, and contaminant dynamics respond to a wide range of environmental perturbations that alter hydrologic dynamics within and connectivity among ecosystems. Her research leverages intensive and extensive field sampling, experimental manipulations, macroscale data harmonization and exploration, and continental to global-scale synthesis activities to uncover key drivers and patterns of the impacts human perturbations have on water and elemental cycles. Dr. Bernhardt's research program is defined by her ability to ask questions and use approaches that explicitly consider connectivity and interfaces in a variety of ways. Here, we highlight significant contributions from Dr. Bernhardt's work, organized by connectivity, interfaces, and interactions among and across (1) elemental cycles, (2) ecosystems, (3) water-sheds, (4) scales, and (5) disciplines. We conclude with a section on Dr. Bernhardt's impact on the hydrologic sciences and beyond through her exceptional dedication to mentorship, engagement, and service.
ano.nymous@ccsd.cnrs.fr.invalid (Ashley Helton) 17 Nov 2023
https://hal.inrae.fr/hal-04292325v1
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[hal-02516590] Assembly of seed-associated microbial communities within and across successive plant generations
<p>Background and aims</p> <p>Seeds are involved in the transmission of microorganisms from one plant generation to another and consequently may act as the initial inoculum source for the plant microbiota. In this work, we assessed the structure and composition of the seed microbiota of radish (Raphanus sativus) across three successive plant generations.</p> <p>Methods</p> <p>Structure of seed microbial communities were estimated on individual plants through amplification and sequencing of genes that are markers of taxonomic diversity for bacteria (gyrB) and fungi (ITS1). The relative contribution of dispersal and ecological drift in inter-individual fluctuations were estimated with a neutral community model.</p> <p>Results</p> <p>Seed microbial communities of radish display a low heritability across plant generations. Fluctuations in microbial community profiles were related to changes in community membership and composition across plant generations, but also to variation between individual plants. Ecological drift was an important driver of the structure of seed bacterial communities, while dispersal was involved in the assembly of the fungal fraction of the seed microbiota.</p> <p>Conclusions</p> <p>These results provide a first glimpse of the governing processes driving the assembly of the seed microbiota.</p>
ano.nymous@ccsd.cnrs.fr.invalid (Samir Rezki) 13 Apr 2023
https://univ-angers.hal.science/hal-02516590v1
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[hal-04691991] A survey of common bacterial blight in Central Brazil reveals a third Xanthomonas species infecting common bean
A survey of common bacterial blight (CBB) was conducted in common bean fields in Brazil, in the state of Goi &amp; aacute;s and in the Federal District. Isolation from symptomatic leaves on a semi-selective medium yielded yellow, mucoid colonies typical of Xanthomonas, and 161 pure cultures were obtained. PCR with specific primers for X. phaseoli pv. phaseoli and X. citri pv. fuscans was performed and confirmed the presence of both fuscans and GL2 strains of X. citri pv. fuscans and the presence of X. phaseoli pv. phaseoli. However, for 81 isolates, PCR results were negative. Housekeeping genes gyrB and rpoD sequences placed these strains in the provisionally named X. cannabis species clade, clustering pv. zinniae, pv. esculenti, and the strain Nyagatare, isolated from beans in Rwanda in 2013. The identification of a subset of 20 strains was complemented by a positive PCR with Xanthomonas-specific primers that amplify a portion of the gumD gene and the induction of hypersensitive reaction in tomato leaves within 24-48 hours. Pathogenicity was confirmed by inoculation on the French common bean cv. Flavert and the Brazilian common bean cv. BRS &amp; Aacute;rtico. Symptoms such as white spots along the leaf blade, leaf curling, and wilting developed in inoculated plants. Partial gyrB and rpoD sequences analyses revealed identity values ranging from 98.3 to 100% between the Brazilian isolates and strain Nyagatare, proposed as X. cannabis pv. phaseoli.
ano.nymous@ccsd.cnrs.fr.invalid (Bruna Alícia R. Paiva) 09 Sep 2024
https://hal.inrae.fr/hal-04691991v1
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[inserm-04492349] Emergence and spread of Mycobacterium ulcerans at different geographic scales
ABSTRACT The classical lineage of Mycobacterium ulcerans is the most prevalent clonal group associated with Buruli ulcer in humans. Its reservoir is strongly associated with the environment. We analyzed together 1,045 isolates collected from 13 countries on two continents to define the evolutionary history and population dynamics of this lineage. We confirm that this lineage spread over 7,000 years from Australia to Africa with the emergence of outbreaks in distinct waves in the 18th and 19th centuries. In sharp contrast with its global spread over the last century, transmission chains are now mostly local, with little or no dissemination between endemic areas. This study provides new insights into the phylogeography and population dynamics of M. ulcerans, highlighting the importance of comparative genomic analyses to improve our understanding of pathogen transmission. IMPORTANCE Mycobacterium ulcerans is an environmental mycobacterial pathogen that can cause Buruli ulcer, a severe cutaneous infection, mostly spread in Africa and Australia. We conducted a large genomic study of M. ulcerans , combining genomic and evolutionary approaches to decipher its evolutionary history and pattern of spread at different geographic scales. At the scale of villages in an endemic area of Benin, the circulating genotypes have been introduced in recent decades and are not randomly distributed along the river. On a global scale, M. ulcerans has been spreading for much longer, resulting in distinct and compartmentalized endemic foci across Africa and Australia.
ano.nymous@ccsd.cnrs.fr.invalid (Martial Briand) 28 Mar 2024
https://inserm.hal.science/inserm-04492349v1
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[hal-04688341] The type VI secretion system of Stenotrophomonas rhizophila CFBP13503 limits the transmission of Xanthomonas campestris pv. campestris 8004 from radish seeds to seedlings
Stenotrophomonas rhizophila CFBP13503 is a seedborne commensal bacterial strain, which is efficiently transmitted to seedlings and can outcompete the phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc8004). The type VI secretion system (T6SS), an interference contact‐dependent mechanism, is a critical component of interbacterial competition. The involvement of the T6SS of S. rhizophila CFBP13503 in the inhibition of Xcc8004 growth and seed‐to‐seedling transmission was assessed. The T6SS cluster of S. rhizophila CFBP13503 and nine putative effectors were identified. Deletion of two T6SS structural genes, hcp and tssB , abolished the competitive advantage of S. rhizophila against Xcc8004 in vitro. The population sizes of these two bacterial species were monitored in seedlings after inoculation of radish seeds with mixtures of Xcc8004 and either S. rhizophila wild‐type (wt) strain or isogenic hcp mutant. A significant decrease in the population size of Xcc8004 was observed during confrontation with the S. rhizophila wt in comparison with T6SS‐deletion mutants in germinated seeds and seedlings. We found that the T6SS distribution among 835 genomes of the Stenotrophomona s genus is scarce. In contrast, in all available S. rhizophila genomes, T6SS clusters are widespread and mainly belong to the T6SS group i4. In conclusion, the T6SS of S. rhizophila CFBP13503 is involved in the antibiosis against Xcc8004 and reduces seedling transmission of Xcc8004 in radish. The distribution of this T6SS cluster in the S. rhizophila complex could make it possible to exploit these strains as biocontrol agents against X. campestris pv. campestris .
ano.nymous@ccsd.cnrs.fr.invalid (Tiffany Garin) 05 Sep 2024
https://hal.inrae.fr/hal-04688341v1
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[hal-02901652] Genome-Scale Investigation of the Metabolic Determinants Generating Bacterial Fastidious Growth
High proliferation rate and robustness are vital characteristics of bacterial pathogens that successfully colonize their hosts. The observation of drastically slow growth in some pathogens is thus paradoxical and remains unexplained. In this study, we sought to understand the slow (fastidious) growth of the plant pathogen Xylella fastidiosa. Using genome-scale metabolic network reconstruction, modeling, and experimental validation, we explored its metabolic capabilities. Despite genome reduction and slow growth, the pathogen's metabolic network is complete but strikingly minimalist and lacking in robustness. Most alternative reactions were missing, especially those favoring fast growth, and were replaced by less efficient paths. We also found that the production of some virulence factors imposes a heavy burden on growth. Interestingly, some specific determinants of fastidious growth were also found in other slow-growing pathogens, enriching the view that these metabolic peculiarities are a pathogenicity strategy to remain at a low population level.IMPORTANCE Xylella fastidiosa is one of the most important threats to plant health worldwide, causing disease in the Americas on a range of agricultural crops and trees, and recently associated with a critical epidemic affecting olive trees in Europe. A main challenge for the detection of the pathogen and the development of physiological studies is its fastidious growth, as the generation time can vary from 10 to 100 h for some strains. This physiological peculiarity is shared with several human pathogens and is poorly understood. We performed an analysis of the metabolic capabilities of X. fastidiosa through a genome-scale metabolic model of the bacterium. This model was reconstructed and manually curated using experiments and bibliographical evidence. Our study revealed that fastidious growth most probably results from different metabolic specificities such as the absence of highly efficient enzymes or a global inefficiency in virulence factor production. These results support the idea that the fragility of the metabolic network may have been shaped during evolution to lead to the self-limiting behavior of X. fastidiosa.
ano.nymous@ccsd.cnrs.fr.invalid (Léo Gerlin) 04 Sep 2024
https://hal.inrae.fr/hal-02901652v1
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[hal-04688333] Seedling microbiota engineering using bacterial synthetic community inoculation on seeds
Synthetic Communities (SynComs) are being developed and tested to manipulate plant microbiota and improve plant health. To date, only few studies proposed the use of SynCom on seed despite its potential for plant microbiota engineering. We developed and presented a simple and effective seedling microbiota engineering method using SynCom inoculation on seeds. The method was successful using a wide diversity of SynCom compositions and bacterial strains that are representative of the common bean seed microbiota. First, this method enables the modulation of seed microbiota composition and community size. Then, SynComs strongly outcompeted native seed and potting soil microbiota and contributed on average to 80% of the seedling microbiota. We showed that strain abundance on seed was a main driver of an effective seedling microbiota colonization. Also, selection was partly involved in seed and seedling colonization capacities since strains affiliated to Enterobacteriaceae and Erwiniaceae were good colonizers while Bacillaceae and Microbacteriaceae were poor colonizers. Additionally, the engineered seed microbiota modified the recruitment and assembly of seedling and rhizosphere microbiota through priority effects. This study shows that SynCom inoculation on seeds represents a promising approach to study plant microbiota assembly and its consequence on plant fitness.
ano.nymous@ccsd.cnrs.fr.invalid (Gontran Arnault) 05 Sep 2024
https://hal.inrae.fr/hal-04688333v1
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[tel-04688332] Pilotage du microbiote des graines pour améliorer la santé des plantes
Après une thèse au laboratoire d’Écologie Microbienne de Lyon (Université Claude Bernard Lyon 1), puis un post-doctorat de 3 ans à Duke University (NC, USA), suivi d’un post-doctorat de 9 mois à IPME (IRD, Montpellier), j’ai intégré en octobre 2019 l’équipe EmerSys de l’Institut de Recherche en Horticulture et Semences (IRHS, Angers) pour développer une thématique de recherche sur le pilotage de la composition du microbiote des semences pour améliorer la santé des plantes. Mon projet de recherche vise à caractériser la fraction du microbiote des graines qui est transmise à la plante (i.e. son inoculum primaire) et son impact sur le phénotype de la plantule. Ces connaissances fondamentales permettent d’identifier des leviers de pilotage du microbiote des graines en favorisant la présence de certains consortia microbiens ou de fonctions microbiennes permettant d’améliorer la vigueur des graines et ainsi proposer des solutions alternatives aux pesticides appliqués sur les semences. Mon projet se structure autour de 3 axes principaux, dont les principaux résultats sont détaillés dans ce document : 1) Synthèse des connaissances sur le microbiote des graines : Méta-analyse de données de metabarcoding. 2) Étude de la transmission du microbiote des graines et impact sur le phénotype de la plantule – Approche par reconstruction de microbiotes synthétiques. 3) Contribution du microbiote des graines à la fitness et productivité de la plante – études transgénérationnelles et évolution expérimentale. Dans leur ensemble, ces travaux permettent d’obtenir des résultats originaux basées sur l’utilisation de communautés synthétiques pour établir les liens entre microbiote et santé de la plante, ainsi que sur la validation (ou invalidation) expérimentale du concept d’holobionte.
ano.nymous@ccsd.cnrs.fr.invalid (Marie Simonin) 05 Sep 2024
https://hal.inrae.fr/tel-04688332v1
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[hal-04688338] Alkaline mine drainage drives stream sediment microbial community structure and function
With advances in eDNA metabarcoding, environmental microbiomes are increasingly used as cost-effective tools for monitoring ecosystem health. Stream ecosystems in Central Appalachia, heavily impacted by alkaline drainage from mountaintop coal mining, present ideal opportunities for biomonitoring using stream microbiomes, but the structural and functional responses of microbial communities in different environmental compartments are not well understood. We investigated sediment microbiomes in mining impacted streams to determine how community composition and function respond to mining and to look for potential microbial bioindicators. Using 16s rRNA gene amplicon sequencing, we found that mining leads to shifts in microbial community structure, with the phylum Planctomycetes enriched by 1-6% at mined sites. We observed ~51% increase in species richness in bulk sediments. In contrast, of the 31 predicted metabolic pathways that changed significantly with mining, 23 responded negatively. Mining explained 15-18% of the variance in community structure and S, Se, %C and %N were the main drivers of community and functional pathway composition. We identified 12 microbial indicators prevalent in the ecosystem and sensitive to mining. Overall, alkaline mountaintop mining drainage causes a restructuration of the sediment microbiome, and our study identified promising microbial indicators for the long-term monitoring of these impacted streams.
ano.nymous@ccsd.cnrs.fr.invalid (Lingrong Jin) 05 Sep 2024
https://hal.inrae.fr/hal-04688338v1
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[hal-04111816] Chronic Engineered Nanoparticle Additions Alter Insect Emergence and Result in Metal Flux from Aquatic Ecosystems into Riparian Food Webs
Freshwater ecosystems are exposed to engineered nanoparticles (NPs) through discharge from wastewater and agricultural runoff. We conducted a 9-month mesocosm experiment to examine the combined effects of chronic NP additions on insect emergence and insect-mediated contaminant flux to riparian spiders. Two NPs (copper, gold, plus controls) were crossed by two levels of nutrients in 18 outdoor mesocosms open to natural insect and spider colonization. We collected adult insects and two riparian spider genera, Tetragnatha and Dolomedes, for 1 week on a monthly basis. We estimated a significant decrease in cumulative insect emergence of 19% and 24% after exposure to copper and gold NPs, irrespective of nutrient level. NP treatments led to elevated copper and gold tissue concentrations in adult insects, which resulted in terrestrial fluxes of metals. These metal fluxes were associated with increased gold and copper tissue concentrations for both spider genera. We also observed about 25% fewer spiders in the NP mesocosms, likely due to reduced insect emergence and/or NP toxicity. These results demonstrate the transfer of NPs from aquatic to terrestrial ecosystems via emergence of aquatic insects and predation by riparian spiders, as well as significant reductions in insect and spider abundance in response to NP additions.
ano.nymous@ccsd.cnrs.fr.invalid (Brittany G Perrotta) 31 May 2023
https://hal.inrae.fr/hal-04111816v1
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[hal-03299428] Transmission of Seed and Soil Microbiota to Seedling
The seed microbial community constitutes an initial inoculum for plant microbiota assembly. Still, the persistence of seed microbiota when seeds encounter soil during plant emergence and early growth is barely documented. We characterized the encounter event of seed and soil microbiota and how it structured seedling bacterial and fungal communities by using amplicon sequencing. We performed eight contrasting encounter events to identify drivers influencing seedling microbiota assembly. To do so, four contrasting seed lots of two Brassica napus genotypes were sown in two soils whose microbial diversity levels were manipulated by serial dilution and recolonization. Seedling root and stem microbiota were influenced by soil but not by initial seed microbiota composition or by plant genotype. A strong selection on the seed and soil communities occurred during microbiota assembly, with only 8% to 32% of soil taxa and 0.8% to 1.4% of seed-borne taxa colonizing seedlings. The recruitment of seedling microbiota came mainly from soil (35% to 72% of diversity) and not from seeds (0.3% to 15%). Soil microbiota transmission success was higher for the bacterial community than for the fungal community. Interestingly, seedling microbiota was primarily composed of initially rare taxa (from seed, soil, or unknown origin) and intermediate-abundance soil taxa.
ano.nymous@ccsd.cnrs.fr.invalid (Aude Rochefort) 25 Oct 2021
https://hal.inrae.fr/hal-03299428v1
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[hal-03299446] Seed microbiota revealed by a large-scale meta-analysis including 50 plant species
Seed microbiota constitutes a primary inoculum for plants that is gaining attention owing to its role for plant health and productivity. Here, we performed a meta-analysis on 63 seed microbiota studies covering 50 plant species to synthesize knowledge on the diversity of this habitat. Seed microbiota are diverse and extremely variable, with taxa richness varying from one to thousands of taxa. Hence, seed microbiota presents a variable (i.e. flexible) microbial fraction but we also identified a stable (i.e. core) fraction across samples. Around 30 bacterial and fungal taxa are present in most plant species and in samples from all over the world. Core taxa, such as Pantoea agglomerans, Pseudomonas viridiflava, P. fluorescens, Cladosporium perangustum and Alternaria sp., are dominant seed taxa. The characterization of the core and flexible seed microbiota provided here will help uncover seed microbiota roles for plant health and design effective microbiome engineering.
ano.nymous@ccsd.cnrs.fr.invalid (Marie Simonin) 26 Jul 2021
https://hal.inrae.fr/hal-03299446v1
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[hal-04097465] Density declines, richness increases, and composition shifts in stream macroinvertebrates
Documenting trends of stream macroinvertebrate biodiversity is challenging because biomonitoring often has limited spatial, temporal, and taxonomic scopes. We analyzed biodiversity and composition of assemblages of >500 genera, spanning 27 years, and 6131 stream sites across forested, grassland, urban, and agricultural land uses throughout the United States. In this dataset, macroinvertebrate density declined by 11% and richness increased by 12.2%, and insect density and richness declined by 23.3 and 6.8%, respectively, over 27 years. In addition, differences in richness and composition between urban and agricultural versus forested and grassland streams have increased over time. Urban and agricultural streams lost the few disturbance-sensitive taxa they once had and gained disturbance-tolerant taxa. These results suggest that current efforts to protect and restore streams are not sufficient to mitigate anthropogenic effects.
ano.nymous@ccsd.cnrs.fr.invalid (Samantha Rumschlag) 15 May 2023
https://hal.inrae.fr/hal-04097465v1
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[hal-04494294] Mean species responses predict effects of environmental change on coexistence
Abstract Environmental change research is plagued by the curse of dimensionality: the number of communities at risk and the number of environmental drivers are both large. This raises the pressing question if a general understanding of ecological effects is achievable. Here, we show evidence that this is indeed possible. Using theoretical and simulation‐based evidence for bi‐ and tritrophic communities, we show that environmental change effects on coexistence are proportional to mean species responses and depend on how trophic levels on average interact prior to environmental change. We then benchmark our findings using relevant cases of environmental change, showing that means of temperature optima and of species sensitivities to pollution predict concomitant effects on coexistence. Finally, we demonstrate how to apply our theory to the analysis of field data, finding support for effects of land use change on coexistence in natural invertebrate communities.
ano.nymous@ccsd.cnrs.fr.invalid (Frederik de Laender) 07 Mar 2024
https://hal.inrae.fr/hal-04494294v1
