scholarly journals Transcriptome Signatures in Pseudomonas simiae WCS417 Shed Light on Role of Root-Secreted Coumarins in Arabidopsis-Mutualist Communication

2021 ◽  
Vol 9 (3) ◽  
pp. 575
Author(s):  
Ke Yu ◽  
Ioannis A. Stringlis ◽  
Sietske van Bentum ◽  
Ronnie de Jonge ◽  
Basten L. Snoek ◽  
...  
Keyword(s):  
Root Exudates ◽  
Bacterial Genome ◽  
Systemic Resistance ◽  
Beneficial Effects ◽  
Flagellar Biosynthesis ◽  
Signaling Function ◽  
Established Plant ◽  
Local Root ◽  
Bacterial Genes ◽  
Selective Antimicrobial Activity

Pseudomonas simiae WCS417 is a root-colonizing bacterium with well-established plant-beneficial effects. Upon colonization of Arabidopsis roots, WCS417 evades local root immune responses while triggering an induced systemic resistance (ISR) in the leaves. The early onset of ISR in roots shows similarities with the iron deficiency response, as both responses are associated with the production and secretion of coumarins. Coumarins can mobilize iron from the soil environment and have a selective antimicrobial activity that impacts microbiome assembly in the rhizosphere. Being highly coumarin-tolerant, WCS417 induces the secretion of these phenolic compounds, likely to improve its own niche establishment, while providing growth and immunity benefits for the host in return. To investigate the possible signaling function of coumarins in the mutualistic Arabidopsis-WCS417 interaction, we analyzed the transcriptome of WCS417 growing in root exudates of coumarin-producing Arabidopsis Col-0 and the coumarin-biosynthesis mutant f6′h1. We found that coumarins in F6′H1-dependent root exudates significantly affected the expression of 439 bacterial genes (8% of the bacterial genome). Of those, genes with functions related to transport and metabolism of carbohydrates, amino acids, and nucleotides were induced, whereas genes with functions related to cell motility, the bacterial mobilome, and energy production and conversion were repressed. Strikingly, most genes related to flagellar biosynthesis were down-regulated by F6′H1-dependent root exudates and we found that application of selected coumarins reduces bacterial motility. These findings suggest that coumarins’ function in the rhizosphere as semiochemicals in the communication between the roots and WCS417. Collectively, our results provide important novel leads for future functional analysis of molecular processes in the establishment of plant-mutualist interactions.

scholarly journals Reduction of bacterial genome size and expansion resulting from obligate intracellular lifestyle and adaptation to soil habitat.

2001 ◽  
Vol 48 (2) ◽  
pp. 367-381 ◽  
Author(s):  
T Stepkowski ◽  
A B Legocki
Keyword(s):  
Genome Size ◽  
Soil Bacteria ◽  
Bacterial Genome ◽  
Housekeeping Genes ◽  
Eukaryotic Cell ◽  
Genome Reduction ◽  
Mutational Bias ◽  
Effective Population ◽  
Obligate Intracellular ◽  
Bacterial Genes

Prokaryotic organisms are exposed in the course of evolution to various impacts, resulting often in drastic changes of their genome size. Depending on circumstances, the same lineage may diverge into species having substantially reduced genomes, or such whose genomes have undergone considerable enlargement. Genome reduction is a consequence of obligate intracellular lifestyle rendering numerous genes expendable. Another consequence of intracellular lifestyle is reduction of effective population size and limited possibility of gene acquirement via lateral transfer. This causes a state of relaxed selection resulting in accumulation of mildly deleterious mutations that can not be corrected by recombination with the wild type copy. Thus, gene loss is usually irreversible. Additionally, constant environment of the eukaryotic cell renders that some bacterial genes involved in DNA repair are expandable. The loss of these genes is a probable cause of mutational bias resulting in a high A+T content. While causes of genome reduction are rather indisputable, those resulting in genome expansion seem to be less obvious. Presumably, the genome enlargement is an indirect consequence of adaptation to changing environmental conditions and requires the acquisition and integration of numerous genes. It seems that the need for a great number of capabilities is common among soil bacteria irrespective of their phylogenetic relationship. However, this would not be possible if soil bacteria lacked indigenous abilities to exchange and accumulate genetic information. The latter are considerably facilitated when housekeeping genes are physically separated from adaptive loci which are useful only in certain circumstances.

scholarly journals Biogeographic traits of dimethyl sulfide and dimethylsulfoniopropionate cycling in polar oceans

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Zhao-Jie Teng ◽  
Qi-Long Qin ◽  
Weipeng Zhang ◽  
Jian Li ◽  
Hui-Hui Fu ◽  
...  
Keyword(s):  
Dimethyl Sulfide ◽  
Bacterial Genome ◽  
Geographic Distance ◽  
Dispersal Limitation ◽  
The Arctic ◽  
Deep Waters ◽  
Solid Foundation ◽  
Polar Oceans ◽  
Polar Ocean ◽  
Bacterial Genes

Abstract Background Dimethyl sulfide (DMS) is the dominant volatile organic sulfur in global oceans. The predominant source of oceanic DMS is the cleavage of dimethylsulfoniopropionate (DMSP), which can be produced by marine bacteria and phytoplankton. Polar oceans, which represent about one fifth of Earth’s surface, contribute significantly to the global oceanic DMS sea-air flux. However, a global overview of DMS and DMSP cycling in polar oceans is still lacking and the key genes and the microbial assemblages involved in DMSP/DMS transformation remain to be fully unveiled. Results Here, we systematically investigated the biogeographic traits of 16 key microbial enzymes involved in DMS/DMSP cycling in 60 metagenomic samples from polar waters, together with 174 metagenome and 151 metatranscriptomes from non-polar Tara Ocean dataset. Our analyses suggest that intense DMS/DMSP cycling occurs in the polar oceans. DMSP demethylase (DmdA), DMSP lyases (DddD, DddP, and DddK), and trimethylamine monooxygenase (Tmm, which oxidizes DMS to dimethylsulfoxide) were the most prevalent bacterial genes involved in global DMS/DMSP cycling. Alphaproteobacteria (Pelagibacterales) and Gammaproteobacteria appear to play prominent roles in DMS/DMSP cycling in polar oceans. The phenomenon that multiple DMS/DMSP cycling genes co-occurred in the same bacterial genome was also observed in metagenome assembled genomes (MAGs) from polar oceans. The microbial assemblages from the polar oceans were significantly correlated with water depth rather than geographic distance, suggesting the differences of habitats between surface and deep waters rather than dispersal limitation are the key factors shaping microbial assemblages involved in DMS/DMSP cycling in polar oceans. Conclusions Overall, this study provides a global overview of the biogeographic traits of known bacterial genes involved in DMS/DMSP cycling from the Arctic and Antarctic oceans, laying a solid foundation for further studies of DMS/DMSP cycling in polar ocean microbiome at the enzymatic, metabolic, and processual levels.

scholarly journals Plant-Based Diets and Hypertension

2019 ◽  
Vol 14 (4) ◽  
pp. 397-405 ◽  
Author(s):  
Shivam Joshi ◽  
Leigh Ettinger ◽  
Scott E. Liebman
Keyword(s):  
Energy Content ◽  
Clinical Trial Data ◽  
Sodium Content ◽  
Adverse Outcomes ◽  
Lifestyle Modifications ◽  
Global Epidemic ◽  
Beneficial Effects ◽  
Treatment Of Hypertension ◽  
Established Plant ◽  
Evidenced Based

Hypertension is a global epidemic and a risk factor for many adverse outcomes, including cardiovascular disease, kidney disease, and death. Lifestyle plays a significant role in the development and maintenance of hypertension, and guidelines from several organizations recommend lifestyle modifications as first-line intervention for hypertensive patients. Data supporting the use of plant-based diets in the treatment of hypertension goes back almost a century. More recently, clinical trial data, including randomized controlled trials, have established plant-based diets as an effective lifestyle intervention for high blood pressure (BP). Plant-based diets differ from the standard American diet in a myriad of ways, with some substances being present in either substantially higher or lower amounts. Although the precise mechanism of a plant-based diet’s beneficial effects on BP is unknown, many of these differences may be responsible. Attributes of a plant-based diet that may lower BP include a lower energy content leading to weight loss, a lower sodium content, an increased potassium content, reduced oxidative stress, higher bioavailability of the vasodilator nitric oxide, and beneficial effects on the microbiome. The evidenced-based benefits of plant-based diets in treating hypertension should lead providers to advocate for this dietary pattern for their patients.

scholarly journals Arabidopsis thaliana Seedlings Influence Bacillus subtilis Spore Formation

2019 ◽  
Vol 32 (9) ◽  
pp. 1188-1195 ◽  
Author(s):  
Vincent Charron-Lamoureux ◽  
Pascale B. Beauregard
Keyword(s):  
Arabidopsis Thaliana ◽  
Bacillus Subtilis ◽  
Systemic Resistance ◽  
Soil System ◽  
Beneficial Effects ◽  
Bacillus Subtilis Spore ◽  
Bacillus Spp ◽  
Plant Growth Promoting ◽  
Growth Promoting

Bacillus subtilis is a Gram-positive plant-growth-promoting rhizobacterium exerting many beneficial effects on plant health. Because they secrete antimicrobial compounds and elicit induced systemic resistance, B. subtilis and phylogenetically related species are of particular interest as antifungals in organic agriculture. These bacteria are also known for their capacity to differentiate phenotypically into endospores able to withstand many environmental stresses. However, although B. subtilis is often inoculated on plants as spores, dynamics of germination and sporulation on roots remain unexplored. Using a hydroponic culture system and a soil system for Arabidopsis thaliana, we observed that B. subtilis spores germinate rapidly on contact with plants. However, the vegetative cells are abundant on roots for only a few days before reversing back to spores. We observed that the germinant receptor GerK and sporulation kinases KinA and KinB identified in vitro control sporulation dynamics on plants. Surprisingly, when plants are inoculated with B. subtilis, free-living cells sporulate more rapidly than plant-associated cells. However, direct contact between plant and bacteria is required for the induction of sporulation in the surrounding B. subtilis. This study has fundamental implications for our understanding of interactions between Bacillus spp. and plants, and particularly for a more efficient usage of B. subtilis as a biofertilizer or biofungicide.

scholarly journals Identification of Pathogenicity-Associated Loci inKlebsiella pneumoniaefrom Hospitalized Patients

mSystems ◽  
2018 ◽  
Vol 3 (3) ◽  
Author(s):  
Rebekah M. Martin ◽  
Jie Cao ◽  
Weisheng Wu ◽  
Lili Zhao ◽  
David M. Manthei ◽  
...  
Keyword(s):  
Health Care ◽  
Klebsiella Pneumoniae ◽  
Association Studies ◽  
Bacterial Genome ◽  
Hospitalized Patients ◽  
Mouse Lung ◽  
Genome Wide Association Studies ◽  
Patient Factors ◽  
Content Type ◽  
Bacterial Genes

ABSTRACTDespite insights gained through experimental models, the set of bacterial genes important for human infection is unclear for many of our most threatening pathogens.Klebsiella pneumoniaeis a leading cause of health care-associated infections (HAIs) and commonly colonizes hospitalized patients, but the factors that determine whether a particular isolate causes disease or remains a colonizer are poorly understood. To identify bacterial genes associated withK. pneumoniaeinfection, a case-control study was performed comparing infected and asymptomatic colonized patients. Comparative bacterial genomics was combined with a conditional logit model that identified patient factors differentiating cases from controls. This method identified five gene loci associated with infection after adjustment for patient factors, including a psicose sugar utilization locus that was validated as a fitness factor during mouse lung infection. These results indicate that bacterial genome-wide association studies of patients can identify loci associated with HAIs and important in infection models.IMPORTANCEKlebsiella pneumoniaeis a common cause of infections in the health care setting. This work supports a paradigm forK. pneumoniaepathogenesis where the accessory genome, composed of genes present in some but not all isolates, influences whether a strain causes infection or asymptomatic colonization, after accounting for patient-level factors. Identification of patients at high risk of infection could allow interventions to prevent or rapidly treatK. pneumoniaeinfections.

scholarly journals Priming negatively affects feeding behaviour and aphid biomass of Rhopalosiphum padi on barley

2021 ◽  
Author(s):  
Gwendolin Wehner ◽  
Adam Schikora ◽  
Frank Ordon ◽  
Torsten Will
Keyword(s):  
Stress Responses ◽  
Feeding Behaviour ◽  
Rhopalosiphum Padi ◽  
Plant Stress ◽  
Systemic Resistance ◽  
Control Group ◽  
Electrical Penetration Graph ◽  
Barley Genotype ◽  
Aphid Infestation ◽  
Beneficial Effects

AbstractPlants have developed numerous strategies for responding to abiotic and biotic stresses. In particular, the microbiota surrounding plants may have a positive effect on plant stress responses. One is the reaction to rhizobacteria, which can lead to induced systemic resistance. Gram-negative soil bacteria that produce N-acyl homoserine lactones (AHL), for example, Ensifer meliloti, induce a primed state in plants that is part of the inducible resistance phenomenon. Observing Rhopalosiphum padi feeding behaviour on a priming sensitive barley genotype, treated with the AHL-producing E. meliloti strain expR + ch, using electrical penetration graph technique showed decreased ingestion of food. Aphids appear to overcome this effect within the eight-hour observation period, possibly explaining the absence of differences of reproduction. Reproduction was observed for a period of 14 days on primed and control-treated plants. Long-term observations over a period of 40 days after aphid infestation showed a lower aphid biomass in contrast to a control group, interpreted as delayed population growth, and an increase in the biomass of barley plants. Priming-related genotypic effects of the defence response to aphids were observed, with no beneficial effects on the plant genotype when its sensitivity to priming was low. Previously, an AHL-priming sensitive barley genotype showed enhanced resistance against fungi when primed with the expR + ch strain of E. meliloti. The present study reports the same effect against R. padi. These findings suggest that sensitivity to AHL-priming may represent a new approach for plant breeding, targeting multiple pests in parallel by induced plant resistance.

scholarly journals The Constitutive Endopolygalacturonase TvPG2 Regulates the Induction of Plant Systemic Resistance by Trichoderma virens

2017 ◽  
Vol 107 (5) ◽  
pp. 537-544 ◽  
Author(s):  
Sabrina Sarrocco ◽  
Fabiola Matarese ◽  
Riccardo Baroncelli ◽  
Giovanni Vannacci ◽  
Verena Seidl-Seiboth ◽  
...  
Keyword(s):  
Pathogenic Fungi ◽  
Phytopathogenic Fungi ◽  
Plant Roots ◽  
Systemic Resistance ◽  
Trichoderma Spp ◽  
Opportunistic Fungi ◽  
Beneficial Effects ◽  
Tomato Roots

Trichoderma spp. are opportunistic fungi some of which are commonly present in the rhizosphere. Several species, such as T. virens, are also efficient biocontrol agents against phytopathogenic fungi and exert beneficial effects on plants. These effects are the consequence of interactions between Trichoderma and plant roots, which trigger enhanced plant growth and induce plant resistance. We have previously shown that T. virens I10 expresses two endopolygalacturonase genes, tvpg1 and tvpg2, during the interaction with plant roots; tvpg1 is inducible while tvpg2 is constitutively transcribed. Using the same system, the tomato polygalacturonase-inhibitor gene Lepgip1 was induced at the same time as tvpg1. Here we show by gene disruption that TvPG2 performs a regulatory role on the inducible tvpg1 gene and in triggering the plant immune response. A tvpg2-knockout strain fails to transcribe the inducible tvpg1 gene in neither in vitro in inducing media containing pectin or plant cell walls, nor during the in vivo interaction with tomato roots. Likewise, the in vivo induction of Lepgip1 does not occur, and its defense against the pathogen Botrytis cinerea is significantly reduced. Our data prove the importance of a T. virens constitutively produced endopolygalacturonase in eliciting plant induced systemic resistance against pathogenic fungi.

scholarly journals Rapid functional activation of a horizontally transferred eukaryotic gene in a bacterial genome in the absence of selection

2019 ◽  
Vol 47 (12) ◽  
pp. 6351-6359 ◽  
Author(s):  
Zhichao Li ◽  
Ralph Bock
Keyword(s):  
Bacterial Genome ◽  
Marker Gene ◽  
Gene Activation ◽  
Gene Cassette ◽  
Selective Advantage ◽  
Porphyridium Purpureum ◽  
Eukaryotic Genes ◽  
Eukaryotic Gene ◽  
Domains Of Life ◽  
Bacterial Genes

Abstract Horizontal gene transfer has occurred between organisms of all domains of life and contributed substantially to genome evolution in both prokaryotes and eukaryotes. Phylogenetic evidence suggests that eukaryotic genes horizontally transferred to bacteria provided useful new gene functions that improved metabolic plasticity and facilitated adaptation to new environments. How these eukaryotic genes evolved into functional bacterial genes is not known. Here, we have conducted a genetic screen to identify the mechanisms involved in functional activation of a eukaryotic gene after its transfer into a bacterial genome. We integrated a eukaryotic selectable marker gene cassette driven by expression elements from the red alga Porphyridium purpureum into the genome of Escherichia coli. Following growth under non-selective conditions, gene activation events were indentified by antibiotic selection. We show that gene activation in the bacterial recipient occurs at high frequency and involves two major types of spontaneous mutations: deletion and gene amplification. We further show that both mechanisms result in promoter capture and are frequently triggered by microhomology-mediated recombination. Our data suggest that horizontally transferred genes have a high probability of acquiring functionality, resulting in their maintenance if they confer a selective advantage.

scholarly journals From iron to antibiotics: Identification of conserved bacterial-fungal interactions across diverse partners

2020 ◽  
Author(s):  
Emily C. Pierce ◽  
Manon Morin ◽  
Jessica C. Little ◽  
Roland B. Liu ◽  
Joanna Tannous ◽  
...  
Keyword(s):  
Bacterial Species ◽  
Microbial Interactions ◽  
Interaction Mechanisms ◽  
Beneficial Effects ◽  
Specific Effects ◽  
Antibiotic Compounds ◽  
Bacterial Genes ◽  
Species Specific ◽  
Fungal Interactions ◽  
And Function

ABSTRACTMicrobial interactions are major determinants in shaping microbiome structure and function. Although fungi are found across diverse microbiomes, the mechanisms through which fungi interact with other species remain largely uncharacterized. In this work, we explore the diversity of ways in which fungi can impact bacteria by characterizing interaction mechanisms across 16 different bacterial-fungal pairs, involving 8 different fungi and 2 bacteria (Escherichia coli and Pseudomonas psychrophila). Using random barcode transposon-site sequencing (RB-TnSeq), we identified a large number of bacterial genes and pathways important in fungal interaction contexts. Within each interaction, fungal partners elicit both antagonistic and beneficial effects. Using a panel of phylogenetically diverse fungi allowed us to identify interactions that were conserved across all species. Our data show that all fungi modulate the availability of iron and biotin, suggesting that these may represent conserved bacterial-fungal interactions. Several fungi also appear to produce previously uncharacterized antibiotic compounds. Generating a mutant in a master regulator of fungal secondary metabolite production showed that fungal metabolites are key shapers of bacterial fitness profiles during interactions. This work demonstrates a diversity of mechanisms through which fungi are able to interact with bacterial species. In addition to many species-specific effects, there appear to be conserved interaction mechanisms which may be important across microbiomes.

scholarly journals Potential of the indirect and direct beneficial effects of the use of Trichoderma koningii, Aspergillus niger and Mucor sp. on eggplants plants: Plant growth and systemic resistance induction

2021 ◽  
Vol 20 (1) ◽  
pp. e809
Author(s):  
Abdulnabi Abbdul Ameer Matrood ◽  
Abdelhak Rhouma
Keyword(s):  
Aspergillus Niger ◽  
Integrated Management ◽  
Management Strategies ◽  
Total Yield ◽  
Dry Weight ◽  
Systemic Resistance ◽  
Symbiotic Interaction ◽  
Beneficial Effects ◽  
Trichoderma Koningii ◽  
Plant Length

Several pathogens fungi responsible for total yield losses are worldwide spread notably in Iraq. The alternatives strategies to decrease disease development are those able to destruct a total or partial population density using eco-friendly approach treatments. In this investigation, we demonstrate the symbiotic interaction with Trichoderma koningii, Aspergillus niger and Mucor sp. on the eggplant plants growth and development, and on the defence response induction. The results revealed that the highest fungal frequency from eggplant rhizosphere was registered for A. niger, followed by Mucor sp. and T. koningii. Seeds treatment with T. koningii showed a higher value of length of shoots (2.83 cm), roots (3.00 cm), and leaves (3.50 cm). Obtained results revealed that T. koningii ameliorates the seedling fresh (3.91 g), dry weight (0.24 g), and accelerates plant length (48.67 cm). Obtained results revealed increasing of peroxidase activity (12.53, 12.68, and 11.28 10-1 units.g.mL.min-1, respectively) and chlorophyll content (2.11, 1.70, and 1.90 mg.g-1 fresh weight, respectively) eggplants treated with combination Mucor sp. + A. niger + T. koningii, T. koningii + Mucor sp., and T. koningii alone. To control pathogens fungi within integrated management strategies, the biological control should be taken into consideration.  

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