Biology subjects

Lindow, S. E.

Publications and source records attributed to Lindow, S. E..

9 recordsLinked to original sources

bioRxiv2025

Microbial dispersal from surrounding vegetation influences phyllosphere microbiome assembly of corn and soybean

Non-crop plants surrounding large plantings of agricultural crops can provide numerous ecological services to adjacent agricultural plants but have rarely been considered as a source of microorganisms during the early stages of their growth. In this study we test whether agricultural plants in close proximity to surrounding woodland habitat fragments develop a denser microbiome than plants farther away, and whether the composition of the crop microbiomes more closely resembles the composition of the surrounding vegetation when in close proximity. During the early stages of development, we sampled epiphytic bacteria from corn and soybean leaves over 4 and 3 weekly sampling timepoints, respectively, using a spatially explicit design, and on the final timepoint for both host species we additionally sampled a younger cohort of leaves. To contextualize the source strength of the surrounding vegetation we also sampled the soil at each sampling location. Both crop species exhibited a microbiome density gradient and a decay of microbiome similarity to surrounding vegetation over a distance of 100 m from the field edges at many timepoints. Phyllosphere microbiome similarity to the soil also tended to increase into the field interior. The strength of host plant microbiome filtering also depended on the proximity to the surrounding vegetation, with intermediate to most distant locations exhibiting the highest values of host filtering, reflecting an apparent decrease in immigrant inoculum. The bacterial communities of younger leaves tended to more closely resemble those of the older surrounding conspecific leaves than either the soil or surrounding woodland vegetation, reflecting the growing dominance of inoculum from within developing crop canopies as plants grew. Overall, our study sheds light on the important role that dispersal of bacteria from nearby leaves can play in phyllosphere microbiome assembly and highlights the diminishing role that soil plays in assembly of phyllosphere microbiomes as plant sources are closer or more abundant.

ecology↗

bioRxiv2023

Transmission mode shapes host specialization of the phyllosphere microbiome

The collection of microorganisms inhabiting aboveground plant tissue, termed the phyllosphere microbiome, is shaped by both microbial dispersal and host filtering effects. Because plants often occur in multispecies assemblages, microbiome diversity is likely shaped by plant community composition through microbial transmission between conspecific (same species) and heterospecific (different species) host plants. Although rarely examined, the relative incidence of con-versus heterospecific transmission should impact microbiome-level specialization. Using four species of plants we experimentally tested this idea by passaging an initially diverse microbial community either between conspecific or heterospecific plants in the greenhouse. While conspecific transmission lines exhibited persistent host effects, these effects decreased in the heterospecific transmission lines, suggesting a shift towards more generalist microbiomes. Similarly, when microbiomes were transplanted onto a set of novel host plant species, host effects were weaker for these heterospecific lines than the conspecific lines. Finally, microbiomes conspecifically passaged on tomato plants were found to outcompete those passaged on either bean or pepper when co-inoculated onto tomato hosts, suggesting microbiome-level host specialization under conspecific transmission. Overall, we find that both transmission mode and host association history shape microbiome diversity, that repeated conspecific transmission results in microbiome specialization, and that repeated heterospecific transmission can drive microbiomes to develop generalist characteristics.

ecology↗

bioRxiv2022

Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome

Leaf surface-associated bacterial communities play a significant role in plant health and have therefore been the focus of increasing interest. Despite this, we currently lack a predictive understanding of how leaf-associated bacterial communities are structured within and across hosts, including how leaf traits shape this variation and how community assembly processes may differ across distinct microbial habitats on a leaf. In this study, we characterize the composition of bacterial phyllosphere communities from the upper and lower leaf surfaces of 66 plants across 24 species grown at a common site using 16S rRNA amplicon sequencing. By comparing leaves that vary in pH and stomatal densities and analyzing the leaf surfaces separately, we were able to test the key factors shaping the phyllosphere across host plant species from diverse geographical origins. We found a surprisingly large shared/core microbiome across species, as well as a strong effect of plant species and native origin in shaping composition. Importantly, we found the lower leaf side, where pH values are generally lower and stomatal densities higher, to have lower taxonomic richness relative to the upper leaf side. While the upper leaf side community appears to be more strongly influenced by dispersal effects, the lower leaf appears to be more strongly influenced by plant host filtering effects, as supported by higher relative abundance of shared core taxa and higher signatures of endemism. This work highlights important differences in community assembly processes across the upper and lower leaf microbiomes and underscores the importance of considering differences among habitats within a host when explaining microbial community assembly and composition.

microbiology↗

bioRxiv2021

Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome

Microbial communities associated with plant leaf surfaces (i.e. the phyllosphere) are increasingly recognized for their role in plant health. While accumulating evidence suggests a role for host filtering of its microbiota, far less is known about how community composition is shaped by dispersal, including from neighboring plants. We experimentally manipulated the local plant neighborhood within which tomato, pepper, or bean plants were grown in a three-month field trial. Focal plants were grown in the presence of con- or hetero-specific neighbors (or no neighbors) in a fully factorial combination. At 30-day intervals, focal plants were harvested and replaced with a new age- and species-matched cohort while allowing neighborhood plants to continue growing. 16S community profiling revealed that the strength of host filtering effects (i.e. interspecific differences in composition) decreased over time. In contrast, the strength of neighborhood effects increased over time, suggesting dispersal from neighboring plants becomes more important as neighboring plant biomass increases. We next implemented a cross-inoculation study in the greenhouse using inoculum generated from the field plants to directly test host filtering of microbiomes while controlling for directionality and source of dispersal. This experiment further demonstrated that focal host species, the host from which the microbiome came, and in one case the donor hosts neighbors, contribute to variation in phyllosphere bacterial composition. Overall, our results suggest that local dispersal is a key factor in phyllosphere assembly, and that demographic factors such as nearby neighbor identity and biomass or age are important determinants of phyllosphere microbiome diversity.

ecology↗

bioRxiv2020

Differential virulence contributions of the efflux transporter MexAB-OprM in Pseudomonas syringae infecting a variety of host plants

Efflux transporters such as MexAB-OprM contribute to bacterial resistance to diverse antimicrobial compounds. Here, we show that MexB contributes to epiphytic and apoplastic growth of Pseudomonas syringae strain B728a, as well as lesion formation in common bean (Phaseolus vulgaris). While a mexB deletion mutant formed fewer lesions after topical application to common bean, these lesions contain the same number of cells (105 to 107 cells) as those caused by the wild-type strain. The internalized population size of both the WT and the MexB mutant within small segments of surface-sterilized asymptomatic portions of the leaves varied from undetectably low to as high as 105 cells/cm2. Localized populations of bacteria within the leaf must apparently exceed a threshold size of about 105 cells/cm2 in order for a visible lesion to form. Strain B728a was capable of moderate to extensive apoplastic growth in diverse host plants including lima bean (P. lunatus), fava bean (Vicia faba), pepper (Capsicum annuum), Nicotiana benthamiana, sunflower (Helianthus annuus), and tomato (Solanum lycopersicum). MexB was not required for growth in a subset of these plant species, and in which the duration of growth after inoculation was longer, indicating apparent variation in onset time or magnitude of plant chemical defenses among those hosts. The use of a hyper-susceptible efflux pump mutant strain is an informative strategy to explore the diversity of host chemical immune responses.

microbiology↗

bioRxiv2019

Genome-wide transposon screen of a Pseudomonas syringae mexB mutant reveals the substrates of efflux transporters

Bacteria express numerous efflux transporters that confer resistance to diverse toxicants present in their environment. Due to a high level of functional redundancy of these transporters, it is difficult to identify those that are of most importance in conferring resistance to specific compounds. The resistance-nodulation-division (RND) protein family is one such example of redundant transporters that are widespread among Gram-negative bacteria. Within this family, the MexAB-OprM protein complex is highly-expressed and conserved among Pseudomonas species. We exposed barcoded transposon mutant libraries in isogenic wild-type and {Delta}mexB backgrounds in P. syringae B728a to diverse toxic compounds in vitro to identify mutants with increased susceptibility to these compounds. Mutants in genes encoding both known and novel redundant transporters, but with partially overlapping substrate specificities were observed in a {Delta}mexB background. Psyr_0228, an uncharacterized member of the Major Facilitator Superfamily of transporters, preferentially contributes to tolerance of acridine orange and acriflavine. Another transporter located in the inner membrane, Psyr_0541, contributes to tolerance to acriflavine and berberine. The presence of multiple redundant, genomically encoded, efflux transporters appears to enable bacterial strains to tolerate a diversity of environmental toxins. This genome-wide screen in a hyper-susceptible mutant strain revealed numerous transporters that would otherwise be dispensable in these conditions. Bacterial strains such as P. syringae that likely encounter diverse toxins in their environment such as in association with many different plant species, probably benefit from possessing multiple redundant transporters that enable versatility to tolerate novel toxicants.

microbiology↗

bioRxiv2019

Genome-wide identification of Pseudomonas syringae genes required for competitive fitness during colonization of the leaf surface and apoplast

The foliar plant pathogen Pseudomonas syringae can establish large epiphytic populations on leaf surfaces before infection. However, the bacterial genes that contribute to these lifestyles have not been completely defined. The fitness contributions of most genes in P. syringae pv. syringae B728a were determined by genome-wide fitness profiling with a randomly barcoded transposon mutant library that was grown on the leaf surface and in the apoplast of the susceptible plant Phaseolus vulgaris. Genes within the functional categories of amino acid and polysaccharide (including alginate) biosynthesis contributed most to fitness both on the leaf surface (epiphytic) or in the leaf interior (apoplast), while genes in the type III secretion system and syringomycin synthesis were primarily important in the apoplast. Numerous other genes that had not been previously associated with in planta growth were also required for maximum epiphytic or apoplastic fitness. Many hypothetical proteins and uncategorized glycosyltransferases were also required for maximum competitive fitness in and on leaves. For most genes, no relationship was seen between fitness in planta and either the magnitude of their expression in planta or degree of induction in planta compared to in vitro conditions measured in other studies. A lack of association of gene expression and fitness has important implications for the interpretation of transcriptional information and our broad understanding of plant-microbe interactions.\n\nSignificance StatementMany plant pathogenic bacteria can extensively colonize leaf surfaces before entry and multiplication within the leaf to cause disease. While these habitats presumably require distinct adaptations, the genes required in these habitats and how they would differ was unknown. Using a genome-wide library of barcoded insertional mutants in the plant pathogen Pseudomonas syringae, we ascertained the common and unique genes required to colonize these habitats. A lack of association between gene expression and contribution to fitness suggests that many genes that are highly expressed or induced in planta are dispensable or redundant. As a model bacterium for plant pathogenesis and colonization, our comprehensive genetic dataset allows us to better understand the traits needed for association with leaves.

microbiology↗

bioRxiv2019

Pseudomonas syringae Increases Water Availability in Leaf Microenvironments via Production of Hygroscopic Syringafactin

The epiphytic bacterium Pseudomonas syringae strain B728a produces the biosurfactant syringafactin which is hygroscopic. The water absorbing potential of syringafactin is high. At high relative humidities, syringafactin attracts 250% of its weight in water but is less hygroscopic at lower relative humidities. This suggests that syringafactins benefit to the producing cells is strongly context-dependent. The contribution of syringafactin to the water availability around cells on different matrices was assessed by examining water availability biosensor strains that express gfp via the water-stress activated proU promoter. Wild-type cells exhibited significantly less GFP fluorescence than a syringafactin-deficient strain, on humid but dry filters as well as on leaf surfaces indicating higher water availability. When infiltrated into the leaf apoplast, wild-type cells also subsequently exhibited less GFP fluorescence than a syringafactin-deficient strain. These results suggest that the apoplast is a dry, but humid environment and that, just as on dry but humid leaf surfaces, syringafactin increases liquid water availability and reduces the water stress experienced by P. syringae.\n\nIMPORTANCEMany microorganisms, including the plant pathogen Pseudomonas syringae, produce amphiphilic compounds known as biosurfactants. While biosurfactants are known to disperse hydrophobic compounds and reduce water tension, they have other properties that can benefit the cells that produce them. Leaf colonizing bacteria experience frequent water stress since liquid water is only transiently present on or in leaf sites that they colonize. The demonstration that syringafactin, a biosurfactant produced by P. syringae, is sufficiently hygroscopic to increase water availability to cells, thus relieving water stress, reveals that P. syringae can modify its local habitat both on leaf surfaces and in the leaf apoplast. Such habitat modification may be a common role for biosurfactants produced by other bacterial species that colonize habitats that are not always water saturated such as soil.

microbiology↗

bioRxiv2018

FleN contributes to heterogeneous swimming at high temperatures in Pseudomonas syringae

Motility is generally conserved among many animal and plant pathogens. Environmental conditions, however, significantly impact expression of the motile phenotype. In this study, we describe a novel heterogeneous motility phenotype in Pseudomonas syringae, where under normally suppressive incubation conditions (30{degrees}C) punctate colonies arise that are spatially isolated from the point of inoculation, giving rise to a motility pattern we term constellation swimming (CS). We demonstrate that this phenotype is reproducible, reversible, and dependent on a functioning flagellum. Mirroring the heterogeneous motility phenotype, we demonstrate the existence of a sub-population of cells under non-permissive conditions that express flagellin (fliC) at levels similar to cells incubated under permissive conditions using both quantitative single cell microscopy and flow cytometry. To understand the genetics underlying the CS phenotype, we selected for naturally arising mutants that exhibited a normal swimming phenotype at the warmer incubation temperature. Sequencing these mutants recovered several independent non-synonymous mutations within FleN (also known as FlhG) as well as mutations within the promoter region of FleQ, the master flagellum regulator in Pseudomonas. We further show that nutrient depletion is the likely underlying cause of CS, as reduced nutrients will stimulate both fliC expression and a normal swimming phenotype at 30 {degrees}C.

microbiology↗