Plant–Microbe Interaction: Aboveground to Belowground, from the Good to the Bad

Soil health and fertility issues are constantly addressed in the agricultural industry. Through the continuous and prolonged use of chemical heavy agricultural systems, most agricultural lands have been impacted, resulting in plateaued or reduced productivity. As such, to invigorate the agricultural industry, we would have to resort to alternative practices that will restore soil health and fertility. Therefore, in recent decades, studies have been directed towards taking a Magellan voyage of the soil rhizosphere region, to identify the diversity, density, and microbial population structure of the soil, and predict possible ways to restore soil health. Microbes that inhabit this region possess niche functions, such as the stimulation or promotion of plant growth, disease suppression, management of toxicity, and the cycling and utilization of nutrients. Therefore, studies should be conducted to identify microbes or groups of organisms that have assigned niche functions. Based on the above, this article reviews the aboveground and below-ground microbiomes, their roles in plant immunity, physiological functions, and challenges and tools available in studying these organisms. The information collected over the years may contribute toward future applications, and in designing sustainable agriculture.

Download Full-text

Life in mine tailings: microbial population structure across the bulk soil, rhizosphere, and roots of boreal species colonizing mine tailings in northwestern Québec

Annals of Microbiology ◽

10.1186/s13213-020-01582-9 ◽

2020 ◽

Vol 70 (1) ◽

Author(s):

Vanessa Gagnon ◽

Michaël Rodrigue-Morin ◽

Julien Tremblay ◽

Jessica Wasserscheid ◽

Julie Champagne ◽

...

Keyword(s):

Population Structure ◽

Mine Tailings ◽

Microbial Population ◽

Bulk Soil ◽

Boreal Species ◽

Soil Rhizosphere

Download Full-text

Response of Horticultural Soil Microbiota to Different Fertilization Practices

Plants ◽

10.3390/plants9111501 ◽

2020 ◽

Vol 9 (11) ◽

pp. 1501

Author(s):

Iratxe Zarraonaindia ◽

Xabier Simón Martínez-Goñi ◽

Olaia Liñero ◽

Marta Muñoz-Colmenero ◽

Mikel Aguirre ◽

...

Keyword(s):

Organic Fertilizer ◽

Soil Health ◽

Disease Suppression ◽

Glutathione Metabolism ◽

Plant Interactions ◽

Organic Fertilization ◽

Soil Microbiota ◽

Xenobiotic Compound ◽

Soil Prokaryotes ◽

Rapid Shift

Environmentally friendly agricultural production necessitates manipulation of microbe–plant interactions, requiring a better understanding of how farming practices influence soil microbiota. We studied the effect of conventional and organic treatment on soil bacterial richness, composition, and predicted functional potential. 16S rRNA sequencing was applied to soils from adjacent plots receiving either a synthetic or organic fertilizer, where two crops were grown within treatment, homogenizing for differences in soil properties, crop, and climate. Conventional fertilizer was associated with a decrease in soil pH, an accumulation of Ag, Mn, As, Fe, Co, Cd, and Ni; and an enrichment of ammonia oxidizers and xenobiotic compound degraders (e.g., Candidatus Nitrososphaera, Nitrospira, Bacillus, Pseudomonas). Soils receiving organic fertilization were enriched in Ti (crop biostimulant), N, and C cycling bacteria (denitrifiers, e.g., Azoarcus, Anaerolinea; methylotrophs, e.g., Methylocaldum, Methanosarcina), and disease-suppression (e.g., Myxococcales). Some predicted functions, such as glutathione metabolism, were slightly, but significantly enriched after a one-time manure application, suggesting the enhancement of sulfur regulation, nitrogen-fixing, and defense of environmental stressors. The study highlights that even a single application of organic fertilization is enough to originate a rapid shift in soil prokaryotes, responding to the differential substrate availability by promoting soil health, similar to recurrent applications.

Download Full-text

Disruption of Firmicutes and Actinobacteria abundance in tomato rhizosphere causes the incidence of bacterial wilt disease

The ISME Journal ◽

10.1038/s41396-020-00785-x ◽

2020 ◽

Vol 15 (1) ◽

pp. 330-347 ◽

Cited By ~ 1

Author(s):

Sang-Moo Lee ◽

Hyun Gi Kong ◽

Geun Cheol Song ◽

Choong-Min Ryu

Keyword(s):

Bacterial Wilt ◽

Rhizosphere Soil ◽

Plant Protection ◽

Plant Immunity ◽

Disease Suppression ◽

Culturable Bacteria ◽

Gram Positive ◽

Gram Positive Bacteria ◽

Individual Strain ◽

Bacillus Niacini

AbstractEnrichment of protective microbiota in the rhizosphere facilitates disease suppression. However, how the disruption of protective rhizobacteria affects disease suppression is largely unknown. Here, we analyzed the rhizosphere microbial community of a healthy and diseased tomato plant grown <30-cm apart in a greenhouse at three different locations in South Korea. The abundance of Gram-positive Actinobacteria and Firmicutes phyla was lower in diseased rhizosphere soil (DRS) than in healthy rhizosphere soil (HRS) without changes in the causative Ralstonia solanacearum population. Artificial disruption of Gram-positive bacteria in HRS using 500-μg/mL vancomycin increased bacterial wilt occurrence in tomato. To identify HRS-specific and plant-protective Gram-positive bacteria species, Brevibacterium frigoritolerans HRS1, Bacillus niacini HRS2, Solibacillus silvestris HRS3, and Bacillus luciferensis HRS4 were selected from among 326 heat-stable culturable bacteria isolates. These four strains did not directly antagonize R. solanacearum but activated plant immunity. A synthetic community comprising these four strains displayed greater immune activation against R. solanacearum and extended plant protection by 4 more days in comparison with each individual strain. Overall, our results demonstrate for the first time that dysbiosis of the protective Gram-positive bacterial community in DRS promotes the incidence of disease.

Download Full-text

Plants Root Interference Area, A Benefit To The Microbial Community

Bulletin of University of Agricultural Sciences and Veterinary Medicine Cluj-Napoca Horticulture ◽

10.15835/buasvmcn-hort:12302 ◽

2017 ◽

Vol 74 (1) ◽

pp. 1 ◽

Cited By ~ 1

Author(s):

Aurica Breica BOROZAN ◽

Sorina POPESCU ◽

Oana Maria BOLDURA

Keyword(s):

Microbial Community ◽

Plant Growth ◽

Microbial Population ◽

Cumulative Effect ◽

Soil Samples ◽

Herbaceous Plants ◽

Herbaceous Plant ◽

Herbal Plants ◽

Soil Rhizosphere ◽

Micro Organisms

Part of byproducts synthesized by plants through photosynthesis reach the ground, where create selective microenvironments for micro-flora and associations of plant - micro-organisms, which are a benefit for plant growth Setting the interference effect of the root interference area of vines and herbaceous plants and of radicular exudates from vine rhizosphere on microbial community and estimating microbial population present on the vine leaves. The biological material was represented by leaves (Fa, Fb), and soil rhizosphere (Ra, Rb) of two varieties of vines (Tamaioasa Romanian white and black / TA, TN), and from the vine roots interference area with other herbaceous plants (Ma, Mb). The soil has never been chemically treated. The microbiological study of biological samples was performed by classical and molecular methods. Overall, bacteria had a significant presence in soil samples taken from the root interference zone (Ma, Mb). Actinomycetes quantitatively dominated the root interference areaÂ of herbaceous plant with variety TA. The range of actinomycetes species and leaves microflora was reduced. In this study we have shown that significant growth of microorganisms occurs in the interference area of vine with other herbal plants as a result of the cumulative effect of radicular exudates.

Download Full-text

In search of biological indicators for soil health and disease suppression

Applied Soil Ecology ◽

10.1016/s0929-1393(00)00068-8 ◽

2000 ◽

Vol 15 (1) ◽

pp. 13-24 ◽

Cited By ~ 302

Author(s):

A.H.C. van Bruggen ◽

A.M. Semenov

Keyword(s):

Soil Health ◽

Biological Indicators ◽

Disease Suppression ◽

Health And Disease

Download Full-text

Below-Ground Attack by the Root Knot Nematode Meloidogyne graminicola Predisposes Rice to Blast Disease

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-11-16-0225-r ◽

2017 ◽

Vol 30 (3) ◽

pp. 255-266 ◽

Cited By ~ 9

Author(s):

Tina Kyndt ◽

Henok Yimer Zemene ◽

Ashley Haeck ◽

Richard Singh ◽

David De Vleesschauwer ◽

...

Keyword(s):

Oxidative Stress ◽

Stress Responses ◽

Plant Immunity ◽

Blast Disease ◽

Root Knot Nematode ◽

Promoting Effect ◽

Meloidogyne Graminicola ◽

Oxidative Stress Level ◽

Below Ground ◽

Oxidative Stress Responses

Magnaporthe oryzae (rice blast) and the root-knot nematode Meloidogyne graminicola are causing two of the most important pathogenic diseases jeopardizing rice production. Here, we show that root-knot nematode infestation on rice roots leads to important above-ground changes in plant immunity gene expression, which is correlated with significantly enhanced susceptibility to blast disease. A detailed metabolic analysis of oxidative stress responses and hormonal balances demonstrates that the above-ground tissues have a disturbed oxidative stress level, with accumulation of H2O2, as well as hormonal disturbances. Moreover, double infection experiments on an oxidative stress mutant and an auxin-deficient rice line indicate that the accumulation of auxin in the above-ground tissue is at least partly responsible for the blast-promoting effect of root-knot nematode infection.

Download Full-text

Brassica Biofumigants for Improved Soil Health

Proceedings ◽

10.3390/proceedings2019036077 ◽

2020 ◽

Vol 36 (1) ◽

pp. 77

Author(s):

Rajagopal ◽

Duff ◽

Hall

Keyword(s):

Cover Crops ◽

Management Practices ◽

Biomass Yield ◽

Irrigation Management ◽

Sclerotium Rolfsii ◽

Soil Health ◽

Field Capacity ◽

Macrophomina Phaseolina ◽

Disease Suppression ◽

Irrigation Treatments

Biofumigation involves growing specialised cover crops that have the ability to suppress certain soil-borne diseases. Species such as those in the Brassicaceae family, (e.g., radish, mustard and rocket) are known to have this capability. Biofumigation activity is initiated by the degradation of glucosinolates within the tissues of the plant when the crop is incorporated into the soil at approx. 25% flowering rate. In this experiment, nine bio-fumigant varieties were assessed over six planting dates for biomass yield, irrigation management, glucosinolate concentration and efficacy against three soilborne pathogens, namely; Sclerotium rolfsii, Sclerotinia sclerotiorum and Macrophomina phaseolina. Preliminary results showed incorporation dates varied across varieties and planting times. Winter planting had highest biomass yield across all varieties, compared with the summer plantings (e.g., 14.82 t/ha in winter, versus 5.02 t/ha in summer for Caliente). The efficacy of disease suppression was variable between variety and planting date. For example, Nemfix and BQ Mulch produced a higher percentage mortality rate (100% and 98%) against S. sclerotiorum, compared with autumn (22% and 12%) and winter (37% and 13%) planting. High glucosinolate production was observed during the summer plantings, where irrigation treatments including drought conditions (Low; 0.75 ML/ha), moderate watering (Medium; 2 ML/ha) and field capacity (High; 2.5 ML/ha) were applied. Increased glucosinolate concentrations were observed in the Low irrigation treatments (e.g., Mustclean; 32.31 μmol/g DW), versus High irrigation (e.g., Mustclean; 17.11 μmol/g DW). Summer data pending analysis. These findings can help growers to identify biofumigant varieties that compliment rotation program and optimise disease management practices.

Download Full-text

Changes of soil-rhizosphere microbiota after organic amendment application in a Hordeum vulgare L. short-term greenhouse experiment

Plant and Soil ◽

10.1007/s11104-020-04637-7 ◽

2020 ◽

Vol 455 (1-2) ◽

pp. 489-506 ◽

Cited By ~ 1

Author(s):

Michael M. Obermeier ◽

Eva-Maria L. Minarsch ◽

Abilash C. Durai Raj ◽

Francois Rineau ◽

Peter Schröder

Keyword(s):

Hordeum Vulgare ◽

Microbial Activity ◽

Crop Production ◽

Soil Health ◽

Organic Amendments ◽

Mineral Fertilizer ◽

Greenhouse Experiment ◽

Plant Performance ◽

Short Term ◽

Soil Rhizosphere

Abstract Aims In order to counteract the enduring decreases in the quality of agricultural land, mechanistic studies for a more sustainable agricultural crop production were performed. They aimed to assess the effects of organic amendments in combination with mineral fertilizer on soil-rhizosphere microbiota and their influence on soil health and plant performance. Methods In a short-term greenhouse experiment, the effects of pelletized spent mushroom substrate, with different combinations of biochar and mineral fertilizer, on agricultural soil and performance of Hordeum vulgare L were scrutinized. To evaluate improved soil quality, different soil biological and chemical properties, microbial activity, bacterial diversity and plant performance were assessed. Results Plant performance increased across all fertilizer combinations. Bacterial β-diversity changed from the initial to the final sampling, pointing at a strong influence of plant development on the rhizosphere with increasing abundances of Acidobacteria and decreasing abundances of Actinobacteria, Chloroflexi, and Bacteroidetes. Microbial activity (FDA), potential enzyme activity and metabolic diversity of the microbial community (BIOLOG) were not affected by the amendments, whereas bacterial community structure changed on family level, indicating functional redundancy. Treatments containing biochar and the highest amount of mineral fertilizer (B_MF140) caused the strongest changes, which were most pronounced for the families Xanthobacteraceae, Mycobacteriaceae, and Haliangiaceae. Conclusion Applying organic amendments improved plant performance and maintained soil health, contributing to more sustainable crop production. Nevertheless, long-term field studies are recommended to verify the findings of this short-term experiment.

Download Full-text

Influence of Earthworm Activity on Soil Microbes and Soilborne Diseases of Vegetables

Plant Disease ◽

10.1094/pdis-93-2-0175 ◽

2009 ◽

Vol 93 (2) ◽

pp. 175-179 ◽

Cited By ~ 41

Author(s):

Wade H. Elmer

Keyword(s):

Soil Health ◽

Solanum Melongena ◽

Lumbricus Terrestris ◽

Disease Suppression ◽

Asparagus Officinalis ◽

Trichoderma Spp ◽

Soilborne Diseases ◽

Progress Curve ◽

Race 1 ◽

Earthworm Activity

Earthworm densities have been regarded as reliable indicators of soil health, but their role in suppression of plant disease has not received much attention. Several greenhouse studies were done to determine if soils infested with soilborne pathogens and augmented with earthworms (Lumbricus terrestris) could reduce disease of susceptible cultivars of asparagus (Asparagus officinalis), eggplant (Solanum melongena), and tomato (Solanum lycopersicum). Soils planted with asparagus were infested with Fusarium oxysporum f. sp. asparagi and F. proliferatum, eggplant with Verticillium dahliae, and tomato with F. oxysporum f. sp. lycopersici Race 1. In each host–disease system, earthworm activity was associated with an increase in plant growth and a decrease in disease. In general, plant weights were increased 60 to 80% and estimates of disease (area under the disease progress curve, percent vascular discoloration, and percent root lesions) were reduced 50 to 70% when soils were augmented with earthworms. Soil dilutions on selective media revealed that densities of fluorescent pseudomonads and filamentous actinomycetes were consistently higher for rhizosphere soils augmented with earthworms. In the studies with Verticillium wilt of eggplant, compared to the controls, the densities of total bacteria and Mn-transforming microbes were reduced in the presence of earthworms while population densities of bacilli and Trichoderma spp. were not affected. Disease suppression may have been mediated through microbiological activity. These studies suggest that strategies to increase earthworm densities in soil should suppress soilborne diseases.

Download Full-text