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  • 1
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 375, No. 6586 ( 2022-03-18), p. 1275-1281
    Abstract: A widespread adaptive change in antiherbivore response is seen in a common plant species in urban environments across 160 cities.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2022
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    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
    SSG: 11
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  • 2
    In: Nature Microbiology, Springer Science and Business Media LLC, Vol. 7, No. 11 ( 2022-10-20), p. 1817-1833
    Abstract: Chemical signalling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via an auxin degradation locus was essential for maintaining stereotypic root development in an ecologically relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes iadDE as necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon’s MarR-family repressor with IAA and other auxins. Auxin degradation operons were identified across the bacterial tree of life and we define two distinct types on the basis of gene content and metabolic products: iac -like and iad -like. The structures of MarRs from representatives of each auxin degradation operon type establish that each has distinct IAA-binding pockets. Comparison of representative IAA-degrading strains from diverse bacterial genera colonizing Arabidopsis plants show that while all degrade IAA, only strains containing iad -like auxin-degrading operons interfere with auxin signalling in a complex synthetic community context. This suggests that iad -like operon-containing bacterial strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.
    Type of Medium: Online Resource
    ISSN: 2058-5276
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2845610-5
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  • 3
    Online Resource
    Online Resource
    Proceedings of the National Academy of Sciences ; 2023
    In:  Proceedings of the National Academy of Sciences Vol. 120, No. 11 ( 2023-03-14)
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 120, No. 11 ( 2023-03-14)
    Abstract: TIR domains are NAD-degrading enzymes that function during immune signaling in prokaryotes, plants, and animals. In plants, most TIR domains are incorporated into intracellular immune receptors termed TNLs. In Arabidopsis, TIR-derived small molecules bind and activate EDS1 heterodimers, which in turn activate RNLs, a class of cation channel–forming immune receptors. RNL activation drives cytoplasmic Ca 2+ influx, transcriptional reprogramming, pathogen resistance, and host cell death. We screened for mutants that suppress an RNL activation mimic allele and identified a TNL, SADR1. Despite being required for the function of an autoactivated RNL, SADR1 is not required for defense signaling triggered by other tested TNLs. SADR1 is required for defense signaling initiated by some transmembrane pattern recognition receptors and contributes to the unbridled spread of cell death in lesion simulating disease 1 . Together with RNLs, SADR1 regulates defense gene expression at infection site borders, likely in a non-cell autonomous manner. RNL mutants that cannot sustain this pattern of gene expression are unable to prevent disease spread beyond localized infection sites, suggesting that this pattern corresponds to a pathogen containment mechanism. SADR1 potentiates RNL-driven immune signaling not only through the activation of EDS1 but also partially independently of EDS1. We studied EDS1-independent TIR function using nicotinamide, an NADase inhibitor. Nicotinamide decreased defense induction from transmembrane pattern recognition receptors and decreased calcium influx, pathogen growth restriction, and host cell death following intracellular immune receptor activation. We demonstrate that TIR domains can potentiate calcium influx and defense and are thus broadly required for Arabidopsis immunity.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2023
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 4
    In: ISME Communications, Springer Science and Business Media LLC, Vol. 2, No. 1 ( 2022-02-01)
    Abstract: The symbiont-associated (SA) environmental package is a new extension to the minimum information about any (x) sequence (MIxS) standards, established by the Parasite Microbiome Project (PMP) consortium, in collaboration with the Genomics Standard Consortium. The SA was built upon the host-associated MIxS standard, but reflects the nestedness of symbiont-associated microbiota within and across host-symbiont-microbe interactions. This package is designed to facilitate the collection and reporting of a broad range of metadata information that apply to symbionts such as life history traits, association with one or multiple host organisms, or the nature of host-symbiont interactions along the mutualism-parasitism continuum. To better reflect the inherent nestedness of all biological systems, we present a novel feature that allows users to co-localize samples, to nest a package within another package, and to identify replicates. Adoption of the MIxS-SA and of the new terms will facilitate reports of complex sampling design from a myriad of environments.
    Type of Medium: Online Resource
    ISSN: 2730-6151
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
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  • 5
    Online Resource
    Online Resource
    Scientific Societies ; 2023
    In:  Molecular Plant-Microbe Interactions® Vol. 36, No. 3 ( 2023-03), p. 165-175
    In: Molecular Plant-Microbe Interactions®, Scientific Societies, Vol. 36, No. 3 ( 2023-03), p. 165-175
    Abstract: The root microbiome is composed of distinct epiphytic (rhizosphere) and endophytic (endosphere) habitats. Differences in abiotic and biotic factors drive differences in microbial community diversity and composition between these habitats, though how they shape the interactions among community members is unknown. Here, we coupled a large-scale characterization of the rhizosphere and endosphere bacterial communities of 30 plant species across two watering treatments with co-occurrence network analysis to understand how root habitats and soil moisture shape root bacterial network properties. We used a novel bootstrapping procedure and null network modeling to overcome some of the limitations associated with microbial co-occurrence network construction and analysis. Endosphere networks had elevated node betweenness centrality versus the rhizosphere, indicating greater overall connectivity among core bacterial members of the root endosphere. Taxonomic assortativity was higher in the endosphere, whereby positive co-occurrence was more likely between bacteria within the same phylum while negative co-occurrence was more likely between bacterial taxa from different phyla. This taxonomic assortativity could be driven by positive and negative interactions among members of the same or different phylum, respectively, or by similar niche preferences associated with phylum rank among root inhabiting bacteria across plant host species. In contrast to the large differences between root habitats, drought had limited effects on network properties but did result in a higher proportion of shared co-occurrences between rhizosphere and endosphere networks. Our study points to fundamentally different ecological processes shaping bacterial co-occurrence across root habitats. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
    Type of Medium: Online Resource
    ISSN: 0894-0282 , 1943-7706
    Language: English
    Publisher: Scientific Societies
    Publication Date: 2023
    detail.hit.zdb_id: 2037108-1
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  • 6
    In: mSphere, American Society for Microbiology, Vol. 5, No. 4 ( 2020-08-26)
    Abstract: Glyphosate is a commonly used herbicide with a broad action spectrum. However, at sublethal doses, glyphosate can induce plant growth, a phenomenon known as hormesis. Most glyphosate hormesis studies have been performed under microbe-free or reduced-microbial-diversity conditions; only a few were performed in open systems or agricultural fields, which include a higher diversity of soil microorganisms. Here, we investigated how microbes affect the hormesis induced by low doses of glyphosate. To this end, we used Arabidopsis thaliana and a well-characterized synthetic bacterial community of 185 strains (SynCom) that mimics the root-associated microbiome of Arabidopsis . We found that a dose of 3.6 × 10 −6 g acid equivalent/liter (low dose of glyphosate, or LDG) produced an ∼14% increase in the shoot dry weight (i.e., hormesis) of uninoculated plants. Unexpectedly, in plants inoculated with the SynCom, LDG reduced shoot dry weight by ∼17%. We found that LDG enriched two Firmicutes and two Burkholderia strains in the roots. These specific strains are known to act as root growth inhibitors (RGI) in monoassociation assays. We tested the link between RGI and shoot dry weight reduction in LDG by assembling a new synthetic community lacking RGI strains. Dropping RGI strains out of the community restored growth induction by LDG. Finally, we showed that individual RGI strains from a few specific phyla were sufficient to switch the response to LDG from growth promotion to growth inhibition. Our results indicate that glyphosate hormesis was completely dependent on the root microbiome composition, specifically on the presence of root growth inhibitor strains. IMPORTANCE Since the introduction of glyphosate-resistant crops, glyphosate has become the most common and widely used herbicide around the world. Due to its intensive use and ability to bind to soil particles, it can be found at low concentrations in the environment. The effect of these remnants of glyphosate in plants has not been broadly studied; however, glyphosate 1,000 to 100,000 times less concentrated than the recommended field dose promoted growth in several species in laboratory and greenhouse experiments. However, this effect is rarely observed in agricultural fields, where complex communities of microbes have a central role in the way plants respond to external cues. Our study reveals how root-associated bacteria modulate the responses of Arabidopsis to low doses of glyphosate, shifting between growth promotion and growth inhibition.
    Type of Medium: Online Resource
    ISSN: 2379-5042
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 2020
    detail.hit.zdb_id: 2844248-9
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  • 7
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2022
    In:  Behavioral Ecology and Sociobiology Vol. 76, No. 8 ( 2022-08)
    In: Behavioral Ecology and Sociobiology, Springer Science and Business Media LLC, Vol. 76, No. 8 ( 2022-08)
    Type of Medium: Online Resource
    ISSN: 0340-5443 , 1432-0762
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 1458476-1
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  • 8
    Online Resource
    Online Resource
    Wiley ; 2020
    In:  The Bulletin of the Ecological Society of America Vol. 101, No. 3 ( 2020-07)
    In: The Bulletin of the Ecological Society of America, Wiley, Vol. 101, No. 3 ( 2020-07)
    Abstract: Senior positions in academia such as tenured faculty and editorial positions often exhibit large gender imbalances across a broad range of research disciplines. The forces driving these imbalances have been the subject of extensive speculation and a more modest body of research. Given the central role publications play in determining individual outcomes and progress in academic settings, unequal patterns of authorship across gender could be a potent driver of observed gender imbalance in academia. Here, we investigate patterns of co‐authorship across four journals in ecology and evolutionary biology at four time‐points spanning four decades. Co‐authorship patterns are of interest because collaborations are important in scientific research, affecting individual researcher productivity, and increasingly, funding opportunities. Based on inferred gender from set criteria, we found significant differences between male and female researchers in their tendency to publish with female co‐authors. Specifically, compared to women, male researchers in the last author position were more likely to co‐author papers with other males. While we did find that the proportion of female co‐authors has increased modestly over the last thirty years, this is strongly correlated with an increase in the average number of authors per paper over time. Additionally, the proportion of female co‐authors on papers remains well below the proportion of PhDs awarded to females in biology.
    Type of Medium: Online Resource
    ISSN: 0012-9623 , 2327-6096
    URL: Issue
    Language: English
    Publisher: Wiley
    Publication Date: 2020
    detail.hit.zdb_id: 2040812-2
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  • 9
    Online Resource
    Online Resource
    Elsevier BV ; 2023
    In:  Cell Vol. 186, No. 21 ( 2023-10), p. 4496-4513
    In: Cell, Elsevier BV, Vol. 186, No. 21 ( 2023-10), p. 4496-4513
    Type of Medium: Online Resource
    ISSN: 0092-8674
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    Language: English
    Publisher: Elsevier BV
    Publication Date: 2023
    detail.hit.zdb_id: 187009-9
    detail.hit.zdb_id: 2001951-8
    SSG: 12
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  • 10
    In: Annual Review of Microbiology, Annual Reviews, Vol. 74, No. 1 ( 2020-09-08), p. 81-100
    Abstract: Methodological advances over the past two decades have propelled plant microbiome research, allowing the field to comprehensively test ideas proposed over a century ago and generate many new hypotheses. Studying the distribution of microbial taxa and genes across plant habitats has revealed the importance of various ecological and evolutionary forces shaping plant microbiota. In particular, selection imposed by plant habitats strongly shapes the diversity and composition of microbiota and leads to microbial adaptation associated with navigating the plant immune system and utilizing plant-derived resources. Reductionist approaches have demonstrated that the interaction between plant immunity and the plant microbiome is, in fact, bidirectional and that plants, microbiota, and the environment shape a complex chemical dialogue that collectively orchestrates the plantmicrobiome. The next stage in plant microbiome research will require the integration of ecological and reductionist approaches to establish a general understanding of the assembly and function in both natural and managed environments.
    Type of Medium: Online Resource
    ISSN: 0066-4227 , 1545-3251
    URL: Issue
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    Language: English
    Publisher: Annual Reviews
    Publication Date: 2020
    detail.hit.zdb_id: 1470471-7
    SSG: 12
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