The emergence of disease‐preventing bacteria within the plant microbiota

Abstract Background Microbiome interactions are important determinants for ecosystem functioning, stability, and health. In previous studies, it was often observed that bacteria suppress potentially pathogenic fungal species that are part of the same plant microbiota; however, the underlying microbe-microbe interplay remains mostly elusive. Here, we explored antagonistic interactions of the fungus Fusarium graminearum and bacterium Streptomyces hygroscopicus at the molecular level. Both are ubiquitous members of the healthy wheat microbiota; under dysbiosis, the fungus causes devastating diseases. Results In co-cultures, we found that Streptomyces alters the fungal acetylome leading to substantial induction of fungal autophagy. The bacterium secrets rapamycin to inactivate the target of rapamycin (TOR), which subsequently promotes the degradation of the fungal histone acetyltransferase Gcn5 through the 26S proteasome. Gcn5 negatively regulates fungal autophagy by acetylating the autophagy-related protein Atg8 at the lysine site K13 and blocking cellular relocalization of Atg8. Thus, degradation of Gcn5 triggered by rapamycin was found to reduce Atg8 acetylation, resulting in autophagy induction in F. graminearum. Conclusions Autophagy homeostasis plays an essential role in fungal growth and competition, as well as for virulence. Our work reveals a novel post-translational regulation of autophagy initiated by a bacterial antibiotic. Rapamycin was shown to be a powerful modulator of bacteria–fungi interactions with potential importance in explaining microbial homeostasis in healthy plant microbiomes. The autophagic process provides novel possibilities and targets to biologically control pathogens.

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Engineering the plant microbiota in the context of the theory of ecological communities

Current Opinion in Biotechnology ◽

10.1016/j.copbio.2021.06.009 ◽

2021 ◽

Vol 70 ◽

pp. 220-225

Author(s):

Asmaâ Agoussar ◽

Etienne Yergeau

Keyword(s):

Ecological Communities ◽

Plant Microbiota

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Climatic Zone and Soil Properties Determine the Biodiversity of the Soil Bacterial Communities Associated to Native Plants from Desert Areas of North-Central Algeria

Microorganisms ◽

10.3390/microorganisms9071359 ◽

2021 ◽

Vol 9 (7) ◽

pp. 1359

Author(s):

Elisa Bona ◽

Nadia Massa ◽

Omrane Toumatia ◽

Giorgia Novello ◽

Patrizia Cesaro ◽

...

Keyword(s):

Soil Properties ◽

Bacterial Communities ◽

Arid Environment ◽

Climatic Zone ◽

Indigenous Plants ◽

North Central ◽

The North ◽

Desert Areas ◽

Plant Microbiota ◽

Semi Arid

Algeria is the largest country in Africa characterized by semi-arid and arid sites, located in the North, and hypersaline zones in the center and South of the country. Several autochthonous plants are well known as medicinal plants, having in common tolerance to aridity, drought and salinity. In their natural environment, they live with a great amount of microbial species that altogether are indicated as plant microbiota, while the plants are now viewed as a “holobiont”. In this work, the microbiota of the soil associated to the roots of fourteen economically relevant autochthonous plants from Algeria have been characterized by an innovative metagenomic approach with a dual purpose: (i) to deepen the knowledge of the arid and semi-arid environment and (ii) to characterize the composition of bacterial communities associated with indigenous plants with a strong economic/commercial interest, in order to make possible the improvement of their cultivation. The results presented in this work highlighted specific signatures which are mainly determined by climatic zone and soil properties more than by the plant species.

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Effect of Enrichment Medium on Real-Time Detection of Salmonella enterica from Lettuce and Tomato Enrichment Cultures

Journal of Food Protection ◽

10.4315/0362-028x-73.6.1047 ◽

2010 ◽

Vol 73 (6) ◽

pp. 1047-1056 ◽

Cited By ~ 7

Author(s):

LISA GORSKI ◽

ANITA S. LIANG

Keyword(s):

Real Time ◽

Pcr Primers ◽

Immunomagnetic Separation ◽

Separation Method ◽

Qualitative Assessment ◽

Detection Methods ◽

Enrichment Cultures ◽

Peptone Water ◽

Immunological Technique ◽

Plant Microbiota

Three enrichment broths commonly used for detection of Salmonella (buffered peptone water [BPW], tryptic soy broth [TSB], and universal preenrichment broth [UPB]) were compared for use in real-time SYBR Green PCR detection of Salmonella introduced into enrichment cultures made from store-bought lettuce and tomatoes. The produce served as a source of normal plant microbiota to measure how well DNA-based detection methods for Salmonella work in a suspension of plant-associated bacteria that may be closely related to Salmonella. A qualitative assessment of the background microbiota that grew in the three enrichment broths cultures from tomato and lettuce samples revealed that different bacteria predominated in the different broths. Results obtained with five produce-related outbreak Salmonella strains and PCR primers directed toward three different Salmonella genes suggest that the ability to detect Salmonella from these enrichment cultures by real-time PCR was 10 to 1,000 times better with TSB enrichment cultures. Detection levels were similar between the different enrichment media when an immunomagnetic separation method was used; however, the immunological technique did not enhance detection from TSB enrichment cultures. Detection could be affected by the medium and by the background microbiota. An immunomagnetic separation method may be useful in BPW and UPB enrichment cultures but not in TSB enrichment cultures.

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Assessment of the structural and functional diversities of plant microbiota: Achievements and challenges – A review

Journal of Advanced Research ◽

10.1016/j.jare.2019.04.007 ◽

2019 ◽

Vol 19 ◽

pp. 3-13 ◽

Cited By ~ 6

Author(s):

Anton Hartmann ◽

Doreen Fischer ◽

Linda Kinzel ◽

Soumitra Paul Chowdhury ◽

Andreas Hofmann ◽

...

Keyword(s):

Plant Microbiota

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The effects of soil phosphorous content on microbiota are driven by the plant phosphate starvation response

10.1101/608133 ◽

2019 ◽

Cited By ~ 2

Author(s):

Omri M. Finkel ◽

Isai Salas-González ◽

Gabriel Castrillo ◽

Stijn Spaepen ◽

Theresa F. Law ◽

...

Keyword(s):

Indirect Effects ◽

Plant Immunity ◽

Phosphate Starvation ◽

Drop Out ◽

Microbiota Composition ◽

Positive Interaction ◽

Starvation Response ◽

Soil P ◽

Phosphate Starvation Response ◽

Plant Microbiota

AbstractPhosphate starvation response (PSR) in non-mycorrhizal plants comprises transcriptional reprogramming resulting in severe physiological changes to the roots and shoots and repression of plant immunity. Thus, plant-colonizing microorganisms – the plant microbiota – are exposed to direct influence by the soil’s phosphorous (P) content itself, as well as to the indirect effects of soil P on the microbial niches shaped by the plant. The individual contribution of these factors to plant microbiota assembly remains unknown. To disentangle these direct and indirect effects, we planted PSR-deficient Arabidopsis mutants in a long-term managed soil P gradient, and compared the composition of their shoot and root microbiota to wild type plants across different P concentrations. PSR-deficiency had a larger effect on the composition of both bacterial and fungal plant-associated microbiota composition than P concentrations in both roots and shoots. The fungal microbiota was more sensitive to P concentrationsper sethan bacteria, and less depended on the soil community composition.Using a 185-member bacterial synthetic community (SynCom) across a wide P concentration gradient in an agar matrix, we demonstrated a shift in the effect of bacteria on the plant from a neutral or positive interaction to a negative one, as measured by rosette size. This phenotypic shift is accompanied by changes in microbiota composition: the genusBurkholderiais specifically enriched in plant tissue under P starvation. Through a community drop-out experiment, we demonstrate that in the absence ofBurkholderiafrom the SynCom, plant shoots accumulate higher phosphate levels than shoots colonized with the full SynCom, only under P starvation, but not under P-replete conditions. Therefore, P-stressed plants allow colonization by latent opportunistic competitors found within their microbiome, thus exacerbating the plant’s P starvation.

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The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ

10.1101/225755 ◽

2017 ◽

Author(s):

Na Wei ◽

Tia-Lynn Ashman

Keyword(s):

Sexual Dimorphism ◽

Host Species ◽

Complete Separation ◽

Host Interactions ◽

Type Host ◽

Β Diversity ◽

Organ Type ◽

In The Wild ◽

Host Genetic ◽

Plant Microbiota

ABSTRACTPlant-associated microbiomes profoundly influence host interactions with below- and aboveground environments. Characterizing plant-associated microbiomes in experimental settings have revealed important drivers of microbiota assemblies within host species. However, it remains unclear how important these individual drivers (e.g., organ type, host species, host sexual phenotype) are in structuring the patterns of plant–microbiota association in the wild.Using 16s rRNA sequencing, we characterized root, leaf and flower microbiomes in three closely related, sexually polymorphic Fragaria species, in the broadly sympatric portion of their native ranges in Oregon, USA. Taking into account the potential influence of broad-scale abiotic environments, we quantified the relative effects of organ type, host species and sex on the α- and β-diversity of bacterial communities in these wild populations. Our statistical models showed that organ type explained the largest variation of compositional and phylogenetic α- and β-diversity of plant microbiomes, and its overall effect exceeded that of host plant species. Yet, the influence of host species increased from root to leaf to flower microbiomes. We found strong sexual dimorphism in flower and leaf microbiomes, especially in host species with the most complete separation of sexes. Our results provide the first demonstration of enhanced effects of host species and sexual dimorphism from root to flower microbiomes. While these findings await manipulative experiments to disentangle contributions of micro-environment and the residing microbiota from host genetic effects, we anticipate that such phenotypic patterns of host species–microbiota association may be broadly applicable to other plants in the wild.

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Humic acids enrich the plant microbiota with bacterial candidates for the suppression of pathogens

10.1101/2020.07.18.210427 ◽

2020 ◽

Author(s):

Maura Santos Reis de Andrade da Silva ◽

Orlando Carlos Huertas Tavares ◽

Thiago Gonçalves Ribeiro ◽

Camilla Santos Reis de Andrade da Silva ◽

Carolina Santos Reis de Andrade da Silva ◽

...

Keyword(s):

Bacterial Community ◽

Humic Acids ◽

Positive Influence ◽

Growth Promoters ◽

Plant Growth Promoters ◽

Nematode Eggs ◽

Plant Microbiota ◽

Relationship Of ◽

First Time ◽

The Relationship

AbstractHumic acids (HAs) stimulate the growth of several plant species by regulating their hormonal and redox metabolisms. Nevertheless, studies on the relationship of these substances with the plant-associated microbiota are almost nonexistent. Here, we hypothesized that the effect of HAs occurs in parallel with the regulation of the plant-associated bacterial community. Our results show the positive influence of HAs on the growth of rice and its stimulation of the root system. Metataxonomics revealed that the structure and composition of root bacterial communities were affected upon the application of HAs. Chitinophaga and Mucilaginibacter were the predominant genera in HA-treated roots. These bacteria produce enzymes that degrade compounds like those present in the wall of fungi, oomycetes, and nematode eggs. Pseudomonas and the Gp 1 group of Acidobacteria, both siderophore-producers and plant-growth promoters were also enriched, although with lower abundances. Given these results, we suggest that plants recruit these microorganisms in response to the stress caused by the HA-root interaction. For the first time, our findings indicate that HA-stimulated plants adopt the ecological strategy of recruiting members of the bacterial community that are candidates for the suppression of pathogens and, therefore, involved in plant defense.

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Dissecting the co-transcriptome landscape of plants and microbiota members

10.1101/2021.04.25.440543 ◽

2021 ◽

Author(s):

Tatsuya Nobori ◽

Yu Cao ◽

Frederickson Entila ◽

Eik Dahms ◽

Yayoi Tsuda ◽

...

Keyword(s):

Pathogenic Bacteria ◽

Early Stage ◽

Building Blocks ◽

Niche Separation ◽

In Planta ◽

Bacterial Strains ◽

Transcriptional Responses ◽

Associated Bacteria ◽

Plant Microbiota ◽

And Function

AbstractInteractions between plants and each neighboring microbial species are fundamental building blocks that collectively determine the structure and function of the plant microbiota, but the molecular basis of such interactions is poorly characterized. Here, we monocolonized Arabidopsis leaves with nine plant-associated bacteria from all major phyla of the plant microbiota and profiled co-transcriptomes of plants and bacteria. These strains elicited quantitatively different plant transcriptional responses including typical pattern-triggered immunity responses. Genes of non-pathogenic bacteria involved in general metabolism and energy production were commonly suppressed in planta in contrast to a virulent pathogen. Various nutrient acquisition pathways that are frequently encoded in the genomes of plant-associated bacteria were induced in planta in a strain-specific manner, shedding light on bacterial adaptation to the plant environment and identifying a potential driving force of niche separation. Integrative analyses of plant and bacterial transcriptomes suggested that the transcriptional reprogramming of plants is largely uncoupled from that of bacteria at an early stage of interactions. This study provides insights into how plants discriminate among bacterial strains and sets the foundation for in-depth mechanistic dissection of plant-microbiota interactions.

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Experimental evidence pointing to rain as a reservoir of tomato phyllosphere microbiota

Phytobiomes Journal ◽

10.1094/pbiomes-04-21-0025-r ◽

2021 ◽

Author(s):

Marco Enrique Mechan Llontop ◽

Long Tian ◽

Parul Sharma ◽

Logan Heflin ◽

Vivian Angelica Bernal Galeano ◽

...

Keyword(s):

Relative Abundance ◽

Microbial Population ◽

Amplicon Sequencing ◽

Crop Productivity ◽

Sterile Water ◽

Tomato Plants ◽

Operational Taxonomic Units ◽

16S Rrna Amplicon Sequencing ◽

Plant Microbiota

Plant microbiota play essential roles in plant health and crop productivity. Comparisons of community composition have suggested seeds, soil, and the atmosphere as reservoirs of phyllosphere microbiota. After finding that leaves of tomato (Solanum lycopersicum) plants exposed to rain carried a higher microbial population size than leaves of tomato plants not exposed to rain, we experimentally tested the hypothesis that rain is a so far neglected reservoir of phyllosphere microbiota. Rain microbiota were thus compared with phyllosphere microbiota of tomato plants either treated with concentrated rain microbiota, filter-sterilized rain, or sterile water. Based on 16S rRNA amplicon sequencing, one-hundred and four operational taxonomic units (OTUs) significantly increased in relative abundance after inoculation with concentrated rain microbiota but no OTU significantly increased after treatment with either sterile water or filter-sterilized rain. Some of the genera to which these 104 OTUs belonged were also found at higher relative abundance on tomatoes exposed to rain outdoors than on tomatoes grown protected from rain in a commercial greenhouse. Taken together, these results point to precipitation as a reservoir of phyllosphere microbiota and show the potential of controlled experiments to investigate the role of different reservoirs in the assembly of phyllosphere microbiota.

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