Plant-Microbiome Interactions for Bacterial Wilt Suppression in Modern Tobacco Production

2020 ◽  
Author(s):  
Raymond O. García-Rodríguez ◽  
Lindsey D. Thiessen
Keyword(s):  
Management Strategies ◽  
Soil Health ◽  
Disease Suppression ◽  
Current Management ◽  
Core Microbiome ◽  
Microbiome Composition ◽  
Sequencing Technologies ◽  
Bacterial Microbiota ◽  
Culture Independent ◽  
Functional Capacities

The soil-borne bacterium Ralstonia solanacearum continues to represent a major threat to flue-cured tobacco (Nicotiana tabacum) production in the southeastern United States and other major producing regions throughout the world. Beneficial microorganisms naturally found in the soil represent an alternative solution for R. solanacearum’s suppression that may reduce soil health impacts of current management strategies. Biological controls and microbiota manipulation together represent a unique opportunity to reduce disease caused by R. solanacearum. Current high-throughput DNA sequencing technologies and advances in bioinformatic analyses enable culture-independent approaches to study root-associated microorganisms and their interactions. The structure and dynamics of tobacco root-associated microbiota, as well as functional capacities of certain taxa, may improve how we apply disease management strategies in the field. Through this review we summarize our current understanding on (i) the role of bacterial microbiota on R. solanacearum survival, (ii) the impacts of current management strategies on the soil bacterial communities, (iii) the rhizospheric and core microbiome composition and inheritance, (iv) the manipulation of the microbiota for enhanced disease suppression, and (v) the shortcomings of the application of plant-associated bacteria for disease suppression.

scholarly journals Wheat Genotype-Specific Recruitment of Rhizosphere Bacterial Microbiota Under Controlled Environments

2021 ◽  
Vol 12 ◽  
Author(s):  
Christine Jade Dilla-Ermita ◽  
Ricky W. Lewis ◽  
Tarah S. Sullivan ◽  
Scot H. Hulbert
Keyword(s):  
Abiotic Stress Tolerance ◽  
Root Disease ◽  
Disease Suppression ◽  
Growth Chamber ◽  
Wheat Genotypes ◽  
Microbiome Composition ◽  
Rhizoctonia Root Rot ◽  
Bacterial Microbiota ◽  
Controlled Environments ◽  
Viable Approach

Plants recruit beneficial microbial communities in the rhizosphere that are involved in a myriad of ecological services, such as improved soil quality, nutrient uptake, abiotic stress tolerance, and soil-borne disease suppression. Disease suppression caused by rhizosphere microbiomes has been important in managing soil-borne diseases in wheat. The low heritability of resistance in wheat to soil-borne diseases like Rhizoctonia root rot has made management of these diseases challenging, particularly in direct-seeded systems. Identification of wheat genotypes that recruit rhizosphere microbiomes that promote improved plant fitness and suppression of the pathogen could be an alternative approach to disease management through genetic improvement. Several growth chamber cycling experiments were conducted using six winter wheat genotypes (PI561725, PI561727, Eltan, Lewjain, Hill81, Madsen) to determine wheat genotypes that recruit suppressive microbiomes. At the end of the third cycle, suppression assays were done by inoculating R. solani into soils previously cultivated with specific wheat genotypes to test suppression of the pathogen by the microbiome. Microbiome composition was characterized by sequencing of 16S rDNA (V1-V3 region). Among the growth cycling lengths, 160-day growth cycles exhibited the most distinct rhizosphere microbiomes among the wheat genotypes. Suppression assays showed that rhizosphere microbiomes of different wheat genotypes resulted in significant differences in shoot length (value of p=0.018) and had an impact on the pathogenicity of R. solani, as observed in the reduced root disease scores (value of p=0.051). Furthermore, soils previously cultivated with the ALMT1 isogenic lines PI561725 and PI561727 exhibited better seedling vigor and reduced root disease. Microbiome analysis showed that Burkholderiales taxa, specifically Janthinobacterium, are differentially abundant in PI561727 and PI561725 cultivated soils and are associated with reduced root disease and better growth. This study demonstrates that specific wheat genotypes recruit different microbiomes in growth chamber conditions but the microbial community alterations were quite different from those previously observed in field plots, even though the same soils were used. Genotype selection or development appears to be a viable approach to controlling soil-borne diseases in a sustainable manner, and controlled environment assays can be used to see genetic differences but further work is needed to explain differences seen between growth chamber and field conditions.

scholarly journals Mango Endophyte and Epiphyte Microbiome Composition during Fruit Development and Post-Harvest Stages

Horticulturae ◽  
2021 ◽  
Vol 7 (11) ◽  
pp. 495
Author(s):  
Malick Bill ◽  
Lizyben Chidamba ◽  
Jarishma Keriuscia Gokul ◽  
Lise Korsten
Keyword(s):  
Fruit Development ◽  
Management Strategies ◽  
Development Stage ◽  
Microbial Composition ◽  
Microbiome Composition ◽  
Bacterial Phyla ◽  
Post Harvest ◽  
Bacterial Microbiota ◽  
Target Effect ◽  
Generation Sequencing

The influence of the development stage and post-harvest handling on the microbial composition of mango fruit plays a central role in fruit health. Hence, the composition of fungal and bacterial microbiota on the anthoplane, fructoplane, stems and stem-end pulp of mango during fruit development and post-harvest handling were determined using next-generation sequencing of the internal transcribed spacer and 16S rRNA regions. At full bloom, the inflorescence had the richest fungal and bacterial communities. The young developing fruit exhibited lower fungal richness and diversities in comparison to the intermediate and fully developed fruit stages on the fructoplane. At the post-harvest stage, lower fungal and bacterial diversities were observed following prochloraz treatment both on the fructoplane and stem-end pulp. Ascomycota (52.8%) and Basidiomycota (43.2%) were the most dominant fungal phyla, while Penicillium, Botryosphaeria, Alternaria and Mucor were detected as the known post-harvest decay-causing fungal genera. The Cyanobacteria (35.6%), Firmicutes (26.1%) and Proteobacteria (23.1%) were the most dominant bacterial phyla. Changes in the presence of Bacillus subtilis following post-harvest interventions such as prochloraz suggested a non-target effect of the fungicide. The present study, therefore, provides the primary baseline data on mango fungal and bacterial diversity and composition, which can be foundational in the development of effective disease (stem-end rot) management strategies.

scholarly journals Taxonomic signatures of cause-specific mortality risk in human gut microbiome

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Aaro Salosensaari ◽  
Ville Laitinen ◽  
Aki S. Havulinna ◽  
Guillaume Meric ◽  
Susan Cheng ◽  
...  
Keyword(s):  
Mortality Risk ◽  
Gut Microbiome ◽  
Human Gut ◽  
Cross Sectional ◽  
Microbiome Composition ◽  
Human Gut Microbiome ◽  
Non Invasive ◽  
Sequencing Technologies

AbstractThe collection of fecal material and developments in sequencing technologies have enabled standardised and non-invasive gut microbiome profiling. Microbiome composition from several large cohorts have been cross-sectionally linked to various lifestyle factors and diseases. In spite of these advances, prospective associations between microbiome composition and health have remained uncharacterised due to the lack of sufficiently large and representative population cohorts with comprehensive follow-up data. Here, we analyse the long-term association between gut microbiome variation and mortality in a well-phenotyped and representative population cohort from Finland (n = 7211). We report robust taxonomic and functional microbiome signatures related to the Enterobacteriaceae family that are associated with mortality risk during a 15-year follow-up. Our results extend previous cross-sectional studies, and help to establish the basis for examining long-term associations between human gut microbiome composition, incident outcomes, and general health status.

scholarly journals Application of Nematode Community Analyses-Based Models towards Identifying Sustainable Soil Health Management Outcomes: A Review of the Concepts

Soil Systems ◽  
2021 ◽  
Vol 5 (2) ◽  
pp. 32
Author(s):  
Haddish Melakeberhan ◽  
Gregory Bonito ◽  
Alexandra N. Kravchenko
Keyword(s):  
Nutrient Cycling ◽  
Health Management ◽  
Management Strategies ◽  
Soil Health ◽  
Agricultural Practices ◽  
Nematode Community ◽  
Parasitic Nematodes ◽  
Worst Case ◽  
Pests And Diseases ◽  
Water Holding

Soil health connotes the balance of biological, physicochemical, nutritional, structural, and water-holding components necessary to sustain plant productivity. Despite a substantial knowledge base, achieving sustainable soil health remains a goal because it is difficult to simultaneously: (i) improve soil structure, physicochemistry, water-holding capacity, and nutrient cycling; (ii) suppress pests and diseases while increasing beneficial organisms; and (iii) improve biological functioning leading to improved biomass/crop yield. The objectives of this review are (a) to identify agricultural practices (APs) driving soil health degradations and barriers to developing sustainable soil health, and (b) to describe how the nematode community analyses-based soil food web (SFW) and fertilizer use efficiency (FUE) data visualization models can be used towards developing sustainable soil health. The SFW model considers changes in beneficial nematode population dynamics relative to food and reproduction (enrichment index, EI; y-axis) and resistance to disturbance (structure index, SI; x-axis) in order to identify best-to-worst case scenarios for nutrient cycling and agroecosystem suitability of AP-driven outcomes. The FUE model visualizes associations between beneficial and plant-parasitic nematodes (x-axis) and ecosystem services (e.g., yield or nutrients, y-axis). The x-y relationship identifies best-to-worst case scenarios of the outcomes for sustainability. Both models can serve as platforms towards developing integrated and sustainable soil health management strategies on a location-specific or a one-size-fits-all basis. Future improvements for increased implementation of these models are discussed.

scholarly journals Uncovering the Core Microbiome and Distribution of Palmerolide in Synoicum adareanum Across the Anvers Island Archipelago, Antarctica

Marine Drugs ◽  
2020 ◽  
Vol 18 (6) ◽  
pp. 298
Author(s):  
Alison E. Murray ◽  
Nicole E. Avalon ◽  
Lucas Bishop ◽  
Karen W. Davenport ◽  
Erwan Delage ◽  
...  
Keyword(s):  
Marine Invertebrate ◽  
Bioactive Compound ◽  
Rrna Gene ◽  
Sequence Variants ◽  
Specific Sequence ◽  
Core Microbiome ◽  
Microbiome Composition ◽  
The Core ◽  
Synoicum Adareanum ◽  
Palmerolide A

Polar marine ecosystems hold the potential for bioactive compound biodiscovery, based on their untapped macro- and microorganism diversity. Characterization of polar benthic marine invertebrate-associated microbiomes is limited to few studies. This study was motivated by our interest in better understanding the microbiome structure and composition of the ascidian, Synoicum adareanum, in which palmerolide A (PalA), a bioactive macrolide with specificity against melanoma, was isolated. PalA bears structural resemblance to a hybrid nonribosomal peptide-polyketide that has similarities to microbially-produced macrolides. We conducted a spatial survey to assess both PalA levels and microbiome composition in S. adareanum in a region of the Antarctic Peninsula near Anvers Island (64°46′ S, 64°03′ W). PalA was ubiquitous and abundant across a collection of 21 ascidians (3 subsamples each) sampled from seven sites across the Anvers Island Archipelago. The microbiome composition (V3–V4 16S rRNA gene sequence variants) of these 63 samples revealed a core suite of 21 bacterial amplicon sequence variants (ASVs)—20 of which were distinct from regional bacterioplankton. ASV co-occurrence analysis across all 63 samples yielded subgroups of taxa that may be interacting biologically (interacting subsystems) and, although the levels of PalA detected were not found to correlate with specific sequence variants, the core members appeared to occur in a preferred optimum and tolerance range of PalA levels. These results, together with an analysis of the biosynthetic potential of related microbiome taxa, describe a conserved, high-latitude core microbiome with unique composition and substantial promise for natural product biosynthesis that likely influences the ecology of the holobiont.

Integration of culture-dependent and independent methods provides a more coherent picture of the pig gut microbiome

2020 ◽  
Vol 96 (3) ◽  
Author(s):  
Gavin J Fenske ◽  
Sudeep Ghimire ◽  
Linto Antony ◽  
Jane Christopher-Hennings ◽  
Joy Scaria
Keyword(s):  
Bacterial Communities ◽  
Bacterial Species ◽  
Shotgun Metagenomics ◽  
Culture Techniques ◽  
Microbiome Composition ◽  
Culture Independent ◽  
Health And Disease ◽  
The Media ◽  
And Function ◽  
Culture Dependent

ABSTRACT Bacterial communities resident in the hindgut of pigs, have profound impacts on health and disease. Investigations into the pig microbiome have utilized either culture-dependent, or far more commonly, culture-independent techniques using next generation sequencing. We contend that a combination of both approaches generates a more coherent view of microbiome composition. In this study, we surveyed the microbiome of Tamworth breed and feral pigs through the integration high throughput culturing and shotgun metagenomics. A single culture medium was used for culturing. Selective screens were added to the media to increase culture diversity. In total, 46 distinct bacterial species were isolated from the Tamworth and feral samples. Selective screens successfully shifted the diversity of bacteria on agar plates. Tamworth pigs are highly dominated by Bacteroidetes primarily composed of the genus Prevotella whereas feral samples were more diverse with almost equal proportions of Firmicutes and Bacteroidetes. The combination of metagenomics and culture techniques facilitated a greater retrieval of annotated genes than either method alone. The single medium based pig microbiota library we report is a resource to better understand pig gut microbial ecology and function. It allows for assemblage of defined bacterial communities for studies in bioreactors or germfree animal models.

Pathophysiology, Diagnosis, and Current Management Strategies for Chest Pain in Patients With Normal Findings on Angiography

2001 ◽  
Vol 76 (8) ◽  
pp. 813-822 ◽  
Author(s):  
Jassim Al Suwaidi ◽  
Stuart T. Higano ◽  
David R. Holmes ◽  
Amir Lerman
Keyword(s):  
Chest Pain ◽  
Management Strategies ◽  
Current Management

scholarly journals Nematode Community-Based Soil Food Web Analysis of Ferralsol, Lithosol and Nitosol Soil Groups in Ghana, Kenya and Malawi Reveals Distinct Soil Health Degradations

Diversity ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 101
Author(s):  
Haddish Melakeberhan ◽  
ZinThuZar Maung ◽  
Isaac Lartey ◽  
Senol Yildiz ◽  
Jenni Gronseth ◽  
...  
Keyword(s):  
Food Web ◽  
Health Management ◽  
Management Strategies ◽  
Soil Health ◽  
Principal Component ◽  
Trophic Group ◽  
Sub Saharan Africa ◽  
Soil Food Web ◽  
Soil Group ◽  
Soil Groups

Determining if the vast soil health degradations across the seven major soil groups (orders) of Sub-Saharan Africa (SSA) can be managed on the basis of a one-size-fits-all or location-specific approach is limited by a lack of soil group-based understanding of soil health degradations. We used the relationship between changes in nematode population dynamics relative to food and reproduction (enrichment, EI) and resistance to disturbance (structure, SI) indices to characterize the soil food web (SFW) and soil health conditions of Ferralsol, Lithosol and Nitosol soil groups in Ghana, Kenya and Malawi. We applied bivariate correlations of EI, SI, soil pH, soil organic carbon (SOC), and texture (sand, silt and clay) to identify integrated indicator parameters, and principal component analysis (PCA) to determine how all measured parameters, soil groups, and countries align. A total of 512 georeferenced soil samples from disturbed (agricultural) and undisturbed (natural vegetation) landscapes were analyzed. Nematode trophic group abundance was low and varied by soil group, landscape and country. The resource-limited and degraded SFW conditions separated by soil groups and by country. EI and SI correlation with SOC varied by landscape, soil group or country. PCA alignment showed separation of soil groups within and across countries. The study developed the first biophysicochemical proof-of-concept that the soil groups need to be treated separately when formulating scalable soil health management strategies in SSA.

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