Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes DOI Creative Commons
Kerrigan B. Gilbert, Emily Holcomb, Robyn L. Allscheid

et al.

PLoS ONE, Journal Year: 2019, Volume and Issue: 14(7), P. e0219207 - e0219207

Published: July 24, 2019

The distribution and diversity of RNA viruses in fungi is incompletely understood due to the often cryptic nature mycoviral infections focused study primarily pathogenic and/or economically important fungi. As most that are known infect possess either single-stranded or double-stranded genomes, transcriptomic data provides opportunity query for diverse fungal samples without any a priori knowledge virus infection. Here we describe systematic survey all datasets from belonging subphylum Pezizomycotina. Using simple but effective computational pipeline uses reads discarded during normal RNA-seq analyses, followed by identification viral RNA-dependent polymerase (RdRP) motif de novo assembled contigs, 59 44 different were identified. Among identified, 88% determined be new species 68% are, our knowledge, first described species. Comprehensive analyses both nucleotide inferred protein sequences characterize phylogenetic relationships between these set support classification up four families two genera. Thus results provide deeper understanding scope while also increasing hosts. Further, this demonstrates suitability analyzing facilitate rapid discovery viruses.

Language: Английский

Plant–microbiome interactions: from community assembly to plant health DOI
Pankaj Trivedi, Jan E. Leach, Susannah G. Tringe

et al.

Nature Reviews Microbiology, Journal Year: 2020, Volume and Issue: 18(11), P. 607 - 621

Published: Aug. 12, 2020

Language: Английский

Citations

2361
Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival DOI Creative Commons
Paloma Durán,

Thorsten Thiergart,

Rubén Garrido‐Oter

et al.

Cell, Journal Year: 2018, Volume and Issue: 175(4), P. 973 - 983.e14

Published: Nov. 1, 2018

Language: Английский

Citations

835
Root microbiota drive direct integration of phosphate stress and immunity DOI
Gabriel Castrillo, Paulo José Pereira Lima Teixeira, Sur Herrera Paredes

et al.

Nature, Journal Year: 2017, Volume and Issue: 543(7646), P. 513 - 518

Published: March 1, 2017

Language: Английский

Citations

823
The Plant Microbiota: Systems-Level Insights and Perspectives DOI
Daniel Müller, Christine Vogel, Yang Bai

et al.

Annual Review of Genetics, Journal Year: 2016, Volume and Issue: 50(1), P. 211 - 234

Published: Sept. 20, 2016

Plants do not grow as axenic organisms in nature, but host a diverse community of microorganisms, termed the plant microbiota. There is an increasing awareness that microbiota plays role growth and can provide protection from invading pathogens. Apart intense research on crop plants, Arabidopsis emerging valuable model system to investigate drivers shaping stable bacterial communities leaves roots tool decipher intricate relationship among its colonizing microorganisms. Gnotobiotic experimental systems help establish causal relationships between genotypes phenotypes test hypotheses biotic abiotic perturbations systematic way. We highlight major recent findings using comparative profiling omics analyses, discuss these approaches light establishment beneficial traits like nutrient acquisition health.

Language: Английский

Citations

723
Understanding and exploiting plant beneficial microbes DOI Creative Commons
Omri M. Finkel, Gabriel Castrillo, Sur Herrera Paredes

et al.

Current Opinion in Plant Biology, Journal Year: 2017, Volume and Issue: 38, P. 155 - 163

Published: June 14, 2017

After a century of incremental research, technological advances, coupled with need for sustainable crop yield increases, have reinvigorated the study beneficial plant-microbe interactions attention focused on how microbiomes alter plant phenotypes. We review recent advances in microbiome and describe potential applications increasing productivity. The phylogenetic diversity is increasingly well characterized, their functional becoming more accessible. Large culture collections are available controlled experimentation, to come. Genetic resources being brought bear questions function. expect that microbial amendments varying complexities will expose rules governing contributing growth promotion disease resistance, enabling agriculture.

Language: Английский

Citations

604
Root Endophyte Colletotrichum tofieldiae Confers Plant Fitness Benefits that Are Phosphate Status Dependent DOI Creative Commons
Kei Hiruma,

Nina Gerlach,

Soledad Sacristán

et al.

Cell, Journal Year: 2016, Volume and Issue: 165(2), P. 464 - 474

Published: March 17, 2016

Highlights•Colletotrichum tofieldiae (Ct) is a fungal root endophyte of Arabidopsis•Ct transfers the macronutrient phosphorus to Arabidopsis shoots•Ct-mediated plant growth promotion needs an intact phosphate starvation response•A branch innate immune system essential for beneficial Ct activitiesSummaryA staggering diversity endophytic fungi associate with healthy plants in nature, but it usually unclear whether these represent stochastic encounters or provide host fitness benefits. Although most characterized species genus Colletotrichum are destructive pathogens, we show here that C. endemic natural thaliana populations central Spain. Colonization by initiates roots can also spread systemically into shoots. shoots, promotes growth, and increases fertility only under phosphorus-deficient conditions, nutrient status might have facilitated transition from pathogenic lifestyles. The host's response (PSR) controls colonization needed (PGP). PGP requires PEN2-dependent indole glucosinolate metabolism, component responses, indicating functional link between immunity PSR during interactions Ct.Graphical abstract

Language: Английский

Citations

564
Interplay Between Innate Immunity and the Plant Microbiota DOI
Stéphane Hacquard, Stijn Spaepen, Rubén Garrido‐Oter

et al.

Annual Review of Phytopathology, Journal Year: 2017, Volume and Issue: 55(1), P. 565 - 589

Published: June 24, 2017

The innate immune system of plants recognizes microbial pathogens and terminates their growth. However, recent findings suggest that at least one layer this is also engaged in cooperative plant-microbe interactions influences host colonization by beneficial communities. This involves sensing microbe-associated molecular patterns (MAMPs) pattern recognition receptors (PRRs) initiate quantitative responses to control host-microbial load, whereas diversification MAMPs PRRs emerges as a mechanism locally sculpts assemblages plant populations. suggests more complex management role the for controlled accommodation microbes pathogen elimination. finding similar strategies are deployed symbionts dampen consistent with hypothesis but implies different selective pressures on due contrasting outcomes fitness. reciprocal interplay between microbiota likely plays critical shaping plant-microbiota combinations maintaining homeostasis.

Language: Английский

Citations

447
Pattern recognition receptors and signaling in plant–microbe interactions DOI Creative Commons
Yusuke Saijo, Eliza P.I. Loo, Shigetaka Yasuda

et al.

The Plant Journal, Journal Year: 2017, Volume and Issue: 93(4), P. 592 - 613

Published: Dec. 20, 2017

Summary Plants solely rely on innate immunity of each individual cell to deal with a diversity microbes in the environment. Extracellular recognition microbe‐ and host damage‐associated molecular patterns leads first layer inducible defenses, termed pattern‐triggered ( PTI ). In plants, pattern receptors PRR s) described date are all membrane‐associated receptor‐like kinases or proteins, reflecting prevalence apoplastic colonization plant‐infecting microbes. An increasing inventory elicitor‐active s indicates that large number them limited certain range plant groups/species, pointing dynamic convergent evolution specificities. addition common principles signaling, recent studies have revealed substantial diversification between their functions regulatory mechanisms. This serves confer robustness plasticity whole system natural infections, wherein different simultaneously engaged faced microbial assaults. We review functional significance basis ‐mediated pathogen disease resistance, also an emerging role for homeostatic association beneficial commensal

Language: Английский

Citations

402
Systems Biology of Plant-Microbiome Interactions DOI Creative Commons
Patricia A. Rodriguez, Michael Rothballer, Soumitra Paul Chowdhury

et al.

Molecular Plant, Journal Year: 2019, Volume and Issue: 12(6), P. 804 - 821

Published: May 23, 2019

In natural environments, plants are exposed to diverse microbiota that they interact with in complex ways. While plant–pathogen interactions have been intensely studied understand defense mechanisms plants, many microbes and microbial communities can substantial beneficial effects on their plant host. Such include improved acquisition of nutrients, accelerated growth, resilience against pathogens, resistance abiotic stress conditions such as heat, drought, salinity. However, the bacterial strains or consortia host often cultivar species specific, posing an obstacle general application. Remarkably, signals trigger immune responses molecularly highly similar identical pathogenic microbes. Thus, it is unclear what determines outcome a particular microbe–host interaction which factors enable distinguish beneficials from pathogens. To unravel network genetic, microbial, metabolic interactions, including signaling events mediating comprehensive quantitative systems biology approaches will be needed.

Language: Английский

Citations

397
Notes on currently accepted species of Colletotrichum DOI Creative Commons
Ruvishika S. Jayawardena

Mycosphere, Journal Year: 2016, Volume and Issue: 7(8), P. 1192 - 1260

Published: Jan. 1, 2016

Colletotrichum is an economically important plant pathogenic genus worldwide, but can also have endophytic or saprobic lifestyles.The has undergone numerous revisions in the past decades with addition, typification and synonymy of many species.In this study, we provide account 190 currently accepted species, one doubtful species excluded that molecular data.Species are listed alphabetically annotated their habit, host geographic distribution, phylogenetic position, sexual morphs uses (if there any known).There eleven complexes 23 singleton species.The main characters each complex detailed illustrations.Phylogenetic trees provided for whole complex.Genes combination genes be used identification suggested.Specific given when possible.

Language: Английский

Citations

314