Cara H. Haney

Cara H. Haney
University of British Columbia - Vancouver | UBC · Department of Microbiology and Immunology

Doctor of Philosophy

About

74
Publications
18,538
Reads
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1,018
Citations
Additional affiliations
February 2016 - present
University of British Columbia - Vancouver
Position
  • Professor
September 2004 - January 2011
Stanford University
Position
  • PhD Student

Publications

Publications (74)
Preprint
Full-text available
Pseudomonas fluorescens and related plant root- (“rhizosphere”) associated species contribute to plant health by modulating defenses and facilitating nutrient uptake. To identify bacterial fitness determinants in the rhizosphere of the model plant Arabidopsis thaliana , we performed a Tn-Seq screen using the biocontrol and growth-promoting strain P...
Article
Full-text available
Host-associated bacteria can have both beneficial and detrimental effects on host health. While some of the molecular mechanisms that determine these outcomes are known, little is known about the evolutionary histories of pathogenic or mutualistic lifestyles. Using the model plant Arabidopsis, we found that closely related strains within the Pseudo...
Preprint
Full-text available
Below-ground microbes can induce systemic resistance (ISR) against foliar pests and pathogens on diverse plant hosts. The prevalence of ISR among plant-microbe-pest systems raises the question of host specificity in microbial induction of ISR. To test whether ISR is limited by plant host range, we tested the ISR-inducing ectomycorrhizal (ECM) fungu...
Preprint
Full-text available
Plant root-associated microbes promote plant growth and induce systemic resistance (ISR) to foliar pathogens. In an attempt to find novel growth-promoting and ISR-inducing strains, we previously identified strains of root-associated Pseudomonas spp. that promote plant growth but unexpectedly induced systemic susceptibility (ISS) rather than ISR to...
Article
Full-text available
Maintaining microbiome structure is critical for the health of both plants and animals. By re-screening a collection of Arabidopsis mutants affecting root immunity and hormone crosstalk, we identified a FERONIA (FER) receptor kinase mutant (fer-8) with a rhizosphere microbiome enriched in Pseudomonas fluorescens without phylum-level dysbiosis. Usin...
Article
The gastrointestinal (GI) environment plays a critical role in shaping enteric infections. Host environmental factors create bottlenecks, restrictive events that reduce the genetic diversity of invading bacterial populations. However, the identity and impact of bottleneck events on bacterial infection are largely unknown. We used Citrobacter rodent...
Article
Full-text available
In the face of severe environmental crises that threaten insect biodiversity, new technologies are imperative to monitor both the identity and ecology of insect species. Traditionally, insect surveys rely on manual collection of traps, which provide abundance data but mask the large intra- and interday variations in insect activity, an important fa...
Article
Full-text available
Plants form commensal associations with soil microorganisms, creating a root microbiome that provides benefits, including protection against pathogens. While bacteria can inhibit pathogens through the production of antimicrobial compounds in vitro, it is largely unknown how microbiota contribute to pathogen protection in planta. We developed a gnot...
Preprint
Full-text available
Microbes possess conserved microbe-associated molecular patterns (MAMPs) such as flagellin that are recognized by plant receptors to induce immunity. Despite containing the same MAMPs as pathogens, commensals thrive in the plant rhizosphere microbiome indicating they must suppress or evade host immunity. The beneficial bacteria Pseudomonas capeferr...
Preprint
Full-text available
Members of the bacterial genus Pseudomonas form mutualistic, commensal and pathogenic associations with diverse hosts. The prevalence of host association across the genus suggests that symbiosis may be a conserved ancestral trait and that distinct symbiotic lifestyles may be more recently evolved. Here we show that the ColR/S two-component system,...
Article
Pseudomonas aeruginosa , an opportunistic bacterial pathogen can synthesize and catabolize a number of small cationic molecules known as polyamines. In several clades of bacteria polyamines regulate biofilm formation, a lifestyle-switching process that confers resistance to environmental stress. The polyamine putrescine and its biosynthetic precurs...
Preprint
Full-text available
Despite the importance of the root immune system in the interaction with rhizosphere microbes, the majority of genetic screens for immunity regulators have been performed in leaves. A previous screen identified 27 hsm (hormone-mediated suppression of MAMP-triggered immunity) mutants that are impaired in jasmonic acid (JA)-mediated suppression of pa...
Preprint
Full-text available
Plants form commensal associations with soil microorganisms, creating a root microbiome that provides benefits to the host including protection against pathogens. While bacteria can inhibit pathogens through production of antimicrobial compounds in vitro, it is largely unknown how microbiota contribute to pathogen protection in planta. We developed...
Preprint
Full-text available
Beneficial root-associated bacteria can induce systemic resistance (ISR) to foliar pathogens and there is known transcriptional and genetic overlap in the root response to iron deficiency and ISR. A previous study found that there is natural variation in ISR among Arabidopsis accessions. The Ws accession is deficient in ISR, and the responsible rec...
Preprint
Full-text available
Circadian clocks are paramount to insect survival and drive many aspects of their physiology and behaviour. While insect circadian behaviours have been extensively studied in the laboratory, their circadian activity within natural settings is poorly understood. The study of circadian activity necessitates measuring biological variables (e.g., locom...
Article
Plants restructure their microbiomes as a ‘cry for help’ against biotic and abiotic stress. A recent study shows that prolonged drought stress causes a permanent shift in the rhizosphere microbiome, and provides clues to which drought-induced microbiome changes might sustain plant health.
Article
Full-text available
Phytopathogenic Verticillia cause Verticillium wilt on numerous economically important crops. Plant infection begins at the roots, where the fungus is confronted with rhizosphere inhabiting bacteria. The effects of different fluorescent pseudomonads, including some known biocontrol agents of other plant pathogens, on fungal growth of the haploid Ve...
Article
The use of genetically tractable plant–microbe pairs has driven research in plant immunity and mutualistic symbiosis. Clear functional readouts for the outcomes of symbiosis or immunity have facilitated forward genetic screening and identification of signals, molecules and mechanisms that determine the outcome of these interactions. Plants also ass...
Article
Full-text available
This article is part of the Top 10 Unanswered Questions in MPMI invited review series. That plants recruit beneficial microbes while simultaneously restricting pathogens is critical to their survival. Plants must exclude pathogens; however, most land plants are able to form mutualistic symbioses with arbuscular mycorrhizal fungi. Plants also associ...
Chapter
Toward the end of August 2000, the 6.3 Mbp whole genome sequence of Pseudomonas aeruginosa strain PAO1 was published. With 5570 open reading frames (ORFs), PAO1 had the largest microbial genome sequenced up to that point in time—including a large proportion of metabolic, transport and antimicrobial resistance genes supporting its ability to coloniz...
Preprint
Full-text available
Maintaining microbiome structure is critical for the health of both plants ¹ and animals ² . In plants, enrichment of beneficial bacteria is associated with advantageous outcomes including protection from biotic and abiotic stress 3,4 . However, the genetic and molecular mechanisms by which plants enrich for specific beneficial microbes without gen...
Article
Full-text available
Plant-associated microorganisms, such as bacteria and fungi, can grow on and survive in healthy plant tissues, making up the plant microbiome. Members of the plant microbiome can provide benefits to their host, and emerging research suggests that plants can reshape the composition of their microbiomes in response to environmental cues. The plant mi...
Article
Full-text available
Plant root-associated microbes promote plant growth and elicit induced systemic resistance (ISR) to foliar pathogens. In an attempt to find novel growth-promoting and ISR-inducing strains, we previously identified strains of root-associated Pseudomonas spp. that promote plant growth but unexpectedly elicited induced systemic susceptibility (ISS) ra...
Article
Full-text available
Below‐ground microbes can induce systemic resistance (ISR) against foliar pests and pathogens on diverse plant hosts. The prevalence of ISR among plant‐microbe‐pest systems raises the question of host specificity in microbial induction of ISR. To test whether ISR is limited by plant host range, we tested the ISR‐inducing ectomycorrhizal fungus Lacc...
Article
The root microbiome consists of commensal, pathogenic, and plant-beneficial microbes [1]. Most members of the root microbiome possess microbe-associated molecular patterns (MAMPs) similar to those of plant pathogens [2]. Their recog- nition can lead to the activation of host immunity and suppression of plant growth due to growth- defense tradeoffs...
Article
The plant immune system is essential for plants to perceive and defend against bacterial, fungal and insect pests and pathogens. Induced systemic resistance (ISR) is a systemic immune response that occurs upon root colonization by beneficial microbes. A well-studied model for ISR is the association of specific beneficial strains of Pseudomonas spp....
Preprint
Full-text available
Plant root-associated microbes promote plant growth and induce systemic resistance (ISR) to foliar pathogens. In an attempt to find novel growth-promoting and ISR-inducing strains, we previously identified strains of root-associated Pseudomonas spp. that promote plant growth but unexpectedly induced systemic susceptibility (ISS) rather than ISR to...
Article
Full-text available
Pseudomonas fluorescens and related plant root (“rhizosphere”)-associated species contribute to plant health by modulating defenses and facilitating nutrient uptake. To identify bacterial fitness determinants in the rhizosphere of the model plant Arabidopsis thaliana, we performed a high-throughput transposon sequencing (Tn-Seq) screen using the bi...
Preprint
Full-text available
Host-associated bacteria can have both beneficial and detrimental effects on host health, but little is known about the evolution of these distinct outcomes. Using the model plant Arabidopsis, we found that closely related strains within the Pseudomonas fluorescens species complex (Pfl) promote plant growth and occasionally cause disease. To elucid...
Article
Full-text available
The formation of nitrogen fixing root nodules by Medicago truncatula and Sinorhizobium meliloti requires communication between both organisms and coordinated differentiation of plant and bacterial cells. After an initial signal exchange, the bacteria invade the tissue of the growing nodule via plant-derived tubular structures, called infection thre...
Article
Full-text available
What allows bacteria, both pathogens and mutualists alike, to survive in close association with a eukaryotic host? A new study performed a large-scale comparative genomics analysis to identify novel genetic and genomic traits that are enriched in plant-associated bacterial taxa.
Article
Full-text available
The acquisition of a virulence plasmid is sufficient to turn a beneficial strain of Rhodococcus bacteria into a pathogen.
Article
Full-text available
Just as the number of petals in a flower or the number of limbs on an animal follow predictable rules, host-associated microbial communities (“microbiomes”) have predictable compositions. At the level of bacterial phylum, the structure of the host-associated microbiome is conserved across individuals of a species (1, 2). The consistency and predict...
Article
Full-text available
Just as the number of petals in a flower or the number of limbs on an animal follow predictable rules, host-associated microbial communities (“microbiomes”) have predictable compositions. At the level of bacterial phylum, the structure of the host-associated microbiome is conserved across individuals of a species (1, 2). The consistency and predict...
Data
Gene expression values used to construct the PCA of root samples.Shoot fresh weight (FW), shoot area, lateral root number and primary root length of plants grown in different containers and media.DOI: http://dx.doi.org/10.7554/eLife.07597.007
Data
Two way ANOVA p-values comparing plants grown in MS media vs plants grown in soil (pots or rhizotrons) and plants collected at day or night.We used p-value < 0.00065 threshold based on Bonferroni adjustment for multiple testing.DOI: http://dx.doi.org/10.7554/eLife.07597.005
Data
Ground truth and GLO-RIA measured values of directionality, depth and width use for validation.DOI: http://dx.doi.org/10.7554/eLife.07597.060
Data
Shape predictor values (TPS format) from Bay-0, Col-0 and Sha used to perform PCA.DOI: http://dx.doi.org/10.7554/eLife.07597.022
Data
Distances to boundary between plants.Shoot FW, root system architecture and shoot area of single and pairs of plants grown in the same rhizotron.DOI: http://dx.doi.org/10.7554/eLife.07597.028
Data
Pixel intensity and water content values used to construct calibration curve.DOI: http://dx.doi.org/10.7554/eLife.07597.034
Data
Directionality values of Bay-0, Col-0, miz1, tir1-1 grown under WW, WD and high and control temperature conditions.DOI: http://dx.doi.org/10.7554/eLife.07597.038
Data
Directionality, root system architecture traits and shoot area values of Col-0 plants grown under different phosphorus concentrations.DOI: http://dx.doi.org/10.7554/eLife.07597.039
Data
Luminescence intensity values of the different luciferase isoforms across the emission spectrum.DOI: http://dx.doi.org/10.7554/eLife.07597.006
Data
Gene expression values used to construct the PCA of shoot samples.DOI: http://dx.doi.org/10.7554/eLife.07597.008
Data
Directionality and whole root system architecture trait values from the time series.DOI: http://dx.doi.org/10.7554/eLife.07597.018
Data
Relative water content of leaves from plants grown under WW and WD conditions and high or control temperatures.DOI: http://dx.doi.org/10.7554/eLife.07597.042
Data
Shoot Fresh Weight (FW) and primary root length of plants grown with or without luciferin.DOI: http://dx.doi.org/10.7554/eLife.07597.009
Data
Directionality, whole root system architectural trait values and shape predictors from Bay-0, Col-0 and Sha.DOI: http://dx.doi.org/10.7554/eLife.07597.021
Data
Whole root system architecture trait values from Bay-0, Col-0 and Sha.DOI: http://dx.doi.org/10.7554/eLife.07597.023
Data
Data for ProZAT12:LUC reporter gene expression in root segments extracted from a whole root system.DOI: http://dx.doi.org/10.7554/eLife.07597.026
Data
Luciferase intensity values from the root tip to maturation zone of ProUBQ10:LUC2o, ProZAT12:LUC and ProDR5:LUC+.DOI: http://dx.doi.org/10.7554/eLife.07597.027
Data
Depth of Brachypodium primary roots grown in petri plates and rhizotrons.DOI: http://dx.doi.org/10.7554/eLife.07597.052
Data
Blueprints of the holders, clear sheets, and spacers needed to build the rhizotrons. Additional details are provided in the ‘Materials and methods’. Files are provided in Adobe Illustrator .ai and Autocad .dxf formats. DOI: http://dx.doi.org/10.7554/eLife.07597.054
Data
Directionality values at different depths of the rhizotron for Col-0 plants exposed to light in the top third of the rhizotron.DOI: http://dx.doi.org/10.7554/eLife.07597.041
Data
Individual root segment traits of plants growing under WW and WD conditions.DOI: http://dx.doi.org/10.7554/eLife.07597.050
Data
Vector maps of all the constructs used in this work. DOI: http://dx.doi.org/10.7554/eLife.07597.056
Data
Directionality values of Col-0 and phot1/2 plants grown with the root system in the dark or exposed to light in the top third of the rhizotron.DOI: http://dx.doi.org/10.7554/eLife.07597.040
Data
Primers used in the qPCR experiment. DOI: http://dx.doi.org/10.7554/eLife.07597.055
Preprint
Full-text available
Root systems develop different root types that individually sense cues from their local environment and integrate this information with systemic signals. This complex multi-dimensional amalgam of inputs enables continuous adjustment of root growth rates, direction and metabolic activity that define a dynamic physical network. Current methods for an...
Article
Full-text available
Host-associated microbiomes influence host health. However, it is unclear whether genotypic variations in host organisms influence the microbiome in ways that have adaptive consequences for the host. Here, we show that wild accessions of Arabidopsis thaliana differ in their ability to associate with the root-associated bacterium Pseudomonas fluores...
Article
Full-text available
Plants and animals must avoid becoming a free meal to microbes, which vastly outnumber eukaryotic life in both quantity and diversity. Adaptive immunity in the strict sense, whereby the host creates an immunological memory after exposure to a pathogen, is limited to vertebrates. Both plants and animals (including insects and mammals) have an innate...
Article
Full-text available
Plants and animals must avoid becoming a free meal to microbes, which vastly outnumber eukaryotic life in both quantity and diversity. Adaptive immunity in the strict sense, whereby the host creates an immunological memory after exposure to a pathogen, is limited to vertebrates. Both plants and animals (including insects and mammals) have an innate...
Article
Full-text available
The Medicago truncatula DMI2 gene encodes a leucine rich-repeat receptor-like kinase that is essential for symbiosis with nitrogen-fixing rhizobia. While phenotypic analyses have provided a description for the host's responses mediated by DMI2, a lack of tools for in vivo biochemical analysis has hampered efforts to elucidate the mechanisms by whic...
Article
Full-text available
To form nitrogen-fixing symbioses, legume plants recognize a bacterial signal, Nod Factor (NF). The legume Medicago truncatula has two predicted NF receptors that direct separate downstream responses to its symbiont Sinorhizobium meliloti. NOD FACTOR PERCEPTION encodes a putative low-stringency receptor that is responsible for calcium spiking and t...
Article
Full-text available
To establish compatible rhizobial-legume symbioses, plant roots support bacterial infection via host-derived infection threads (ITs). Here, we report the requirement of plant flotillin-like genes (FLOTs) in Sinorhizobium meliloti infection of its host legume Medicago truncatula. Flotillins in other organisms have roles in viral pathogenesis, endocy...