Ecology and Evolution of Plant Microbiomes

Annual Review of Microbiology, Journal Year: 2019, Volume and Issue: 73(1), P. 69 - 88

Published: May 15, 2019

Microorganisms colonizing plant surfaces and internal tissues provide a number of life-support functions for their host. Despite increasing recognition the vast functional capabilities microbiome, our understanding ecology evolution taxonomically hyperdiverse microbial communities is limited. Here, we review current knowledge genotypic phenotypic traits as well allogenic autogenic factors that shape microbiome composition functions. We give specific emphasis to impact domestication on assembly how insights into microbiomes wild relatives native habitats can contribute reinstate or enrich microorganisms with beneficial effects growth, development, health. Finally, introduce new concepts perspectives in research, particular community theory mechanistic framework unravel interplay distinct ecological processes-i.e., selection, dispersal, drift, diversification-that structure microbiome.

Language: Английский

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Revisiting Plant–Microbe Interactions and Microbial Consortia Application for Enhancing Sustainable Agriculture: A Review

Frontiers in Microbiology, Journal Year: 2020, Volume and Issue: 11

Published: Dec. 21, 2020

The present scenario of agricultural sector is dependent hugely on the use chemical-based fertilizers and pesticides that impact nutritional quality, health status, productivity crops. Moreover, continuous release these chemical inputs causes toxic compounds such as metals to accumulate in soil move plants with prolonged exposure, which ultimately human health. Hence, it becomes necessary bring out alternatives pesticides/fertilizers for improvement outputs. rhizosphere plant an important niche abundant microorganisms residing it. They possess properties growth promotion, disease suppression, removal compounds, assimilating nutrients plants. Utilizing beneficial microbes crop presents efficient way modulate yield by maintaining healthy status quality through bioformulations. To understand microbial formulation compositions, essential processes going well their concrete identification better utilization diversity growth–promoting bacteria arbuscular mycorrhizal fungi. this background, review article highlights microbiome aboveground belowground, importance inoculants various species, subsequent interactive mechanisms sustainable agriculture.

Language: Английский

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Genomes and secretomes of Ascomycota fungi reveal diverse functions in plant biomass decomposition and pathogenesis

BMC Genomics, Journal Year: 2019, Volume and Issue: 20(1)

Published: Dec. 1, 2019

Abstract Background The dominant fungi in arid grasslands and shrublands are members of the Ascomycota phylum. important drivers carbon nitrogen cycling ecosystems. These play roles soil stability, plant biomass decomposition, endophytic interactions with plants. They may also form symbiotic associations biocrust components or be latent saprotrophs pathogens that live on tissues. However, their functional potential soils, where organic matter, nutrients water very low only periodically available, is poorly characterized. Results Five were isolated from different crust microhabitats rhizosphere soils around native bunchgrass Pleuraphis jamesii an grassland near Moab, UT, USA. Putative genera Coniochaeta , lichen biocrust, Embellisia cyanobacteria Chaetomium below Phoma a moss microhabitat, Aspergillus soil. grown replicate cultures sources (chitin, pine wood) relevant to sources. Secretomes produced by each substrate demonstrate these likely interact primary producers (biocrust plants) secreting wide range proteins facilitate associations. Each fungal isolates secreted enzymes degrade biomass, small effector proteins, involved either beneficial virulence. expressed more degrading when grass- pine-containing than chitin. similar numbers under all conditions, while grass-containing cultures. Conclusions This study genomes secretomes provides insights about lifestyles grassland, exact nature those interactions, whether any true endophytes, opportunistic phytopathogens, will topic future studies.

Language: Английский

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Hiding in plain sight: New virus genomes discovered via a systematic analysis of fungal public transcriptomes

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

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Experimental evidence of microbial inheritance in plants and transmission routes from seed to phyllosphere and root

Environmental Microbiology, Journal Year: 2021, Volume and Issue: 23(4), P. 2199 - 2214

Published: Jan. 15, 2021

While the environment is considered primary origin of plant microbiome, potential role seeds as a source transmitting microorganisms has not received much attention. Here we tested hypothesis that microbiome partially inherited through vertical transmission. An experimental culturing device was constructed to grow oak seedlings in microbe-free while keeping belowground and aboveground tissues separated. The microbial communities associated with acorn's embryo pericarp developing seeding's phyllosphere root systems were analysed using amplicon sequencing fungal ITS bacterial 16S rDNA. Results showed seed diverse non-randomly distributed within an acorn. composition strongly resembled found embryo, whereas roots each had less distinct community. Our findings demonstrate high level diversity spatial partitioning community both seedling, indicating inheritance, niche differentiation divergent transmission routes for establishment communities.

Language: Английский

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Genera of phytopathogenic fungi: GOPHY 4

Studies in Mycology, Journal Year: 2022, Volume and Issue: 101(1), P. 417 - 564

Published: March 1, 2022

Language: Английский

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Do all fungi have ancestors with endophytic lifestyles?

Fungal Diversity, Journal Year: 2023, Volume and Issue: 125(1), P. 73 - 98

Published: March 16, 2023

Language: Английский

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Pervasive associations between dark septate endophytic fungi with tree root and soil microbiomes across Europe

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Jan. 2, 2024

Abstract Trees interact with a multitude of microbes through their roots and root symbionts such as mycorrhizal fungi endophytes. Here, we explore the role fungal predictors soil root-associated microbiomes widespread broad-leaved trees across European latitudinal gradient. Our results suggest that, alongside factors climate, soil, vegetation properties, colonization by ectomycorrhizal, arbuscular mycorrhizal, dark septate endophytic also shapes tree-associated microbiomes. Notably, structure our sites is more strongly consistently associated endophyte than many abiotic factors. Root endophytes has consistent negative association relative abundance diversity nutrient cycling genes. study not only indicates that root-symbiotic interactions are an important factor structuring communities functions in forest ecosystems, but hitherto less studied likely to be central players these interactions.

Language: Английский

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Genetic determinants of endophytism in the Arabidopsis root mycobiome

Nature Communications, Journal Year: 2021, Volume and Issue: 12(1)

Published: Dec. 10, 2021

Abstract The roots of Arabidopsis thaliana host diverse fungal communities that affect plant health and disease states. Here, we sequence the genomes 41 isolates representative A. root mycobiota for comparative analysis with other 79 plant-associated fungi. Our analyses indicate members evolved from ancestors lifestyles retain large repertoires cell wall-degrading enzymes (PCWDEs) effector-like small secreted proteins. We identify a set 84 gene families associated endophytism, including genes encoding PCWDEs acting on xylan (family GH10) cellulose AA9). Transcripts these are also part conserved transcriptional program activated by phylogenetically-distant upon contact. Recolonization experiments individual fungi strains detrimental effects in mono-association colonize more aggressively than those beneficial activities, dominate natural samples. Furthermore, show pectin-degrading enzyme family PL1_7 links aggressiveness endophytic colonization to health.

Language: Английский

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Dark septate endophytes improve the growth of host and non-host plants under drought stress through altered root development

Plant and Soil, Journal Year: 2019, Volume and Issue: 439(1-2), P. 259 - 272

Published: April 10, 2019

Language: Английский

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