Shifts in the Active Rhizobiome Paralleling Low Meloidogyne chitwoodi Densities in Fields Under Prolonged Organic Soil Management

Harkes, Paula; Steenbrugge, Joris J.M. van; Elsen, S.J.J. van den; Suleiman, Afnan Khalil Ahmad; Haan, J.J. de; Holterman, M.H.M.; Helder, J.

doi:10.3389/fpls.2019.01697

Cited by 29 publications

(19 citation statements)

References 61 publications

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“…Biplot results revealed an increase in the relative abundance of ASVs assigned to Pseudomonas in J2s from all time points, and early season roots, compared to other sample classes (Fig. 3B), in line with the results of Harkes et al (48), as well as the increase in ASVs assigned to Azospirillum and Reinheimera.…”

Section: Resultssupporting

confidence: 89%

Bacterial Community Structure Dynamics in Meloidogyne incognita -Infected Roots and Its Role in Worm-Microbiome Interactions

Yergaliyev

Alexander-Shani

Dimerets

et al. 2020

mSphere

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Plant parasitic nematodes such as Meloidogyne incognita have a complex life cycle, occurring sequentially in various niches of the root and rhizosphere. They are known to form a range of interactions with bacteria and other microorganisms that can affect their densities and virulence. High-throughput sequencing can reveal these interactions in high temporal and geographic resolutions, although thus far we have only scratched the surface. In this study, we have carried out a longitudinal sampling scheme, repeatedly collecting rhizosphere soil, roots, galls, and second-stage juveniles from 20 plants to provide a high-resolution view of bacterial succession in these niches, using 16S rRNA metabarcoding. Our findings indicate that a structured community develops in the root, in which gall communities diverge from root segments lacking a gall, and that this structure is maintained throughout the crop season. We describe the successional process leading toward this structure, which is driven by interactions with the nematode and later by an increase in bacteria often found in hypoxic and anaerobic environments. We present evidence that this structure may play a role in the nematode’s chemotaxis toward uninfected root segments. Finally, we describe the J2 epibiotic microenvironment as ecologically deterministic, in part, due to the active bacterial attraction of second-stage juveniles. IMPORTANCE The study of high-resolution successional processes within tightly linked microniches is rare. Using the power and relatively low cost of metabarcoding, we describe the bacterial succession and community structure in roots infected with root-knot nematodes and in the nematodes themselves. We reveal separate successional processes in galls and adjacent non-gall root sections, which are driven by the nematode’s life cycle and the progression of the crop season. With their relatively low genetic diversity, large geographic range, spatially complex life cycle, and the simplified agricultural ecosystems they occupy, root-knot nematodes can serve as a model organism for terrestrial holobiont ecology. This perspective can improve our understanding of the temporal and spatial aspects of biological control efficacy.

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Section: Resultssupporting

confidence: 89%

Bacterial Community Structure Dynamics in Meloidogyne incognita -Infected Roots and Its Role in Worm-Microbiome Interactions

Yergaliyev

Alexander-Shani

Dimerets

et al. 2020

mSphere

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“…The observed taxonomic structures have common traits with the earlier described wheat and pea rhizospheric microbiomes but differ from those by shifts in abundance of few taxonomic groups only [73][74][75][76], e.g., representatives of Proteobacteria, Firmicutes and Thaumarchaeota. Analysis of the alpha-diversity showed no significant differences in diversity indices between treatments with different soil conditions, plant genotype and microbial inoculation.…”

Section: Rhizosphere Bacterial Communitiessupporting

confidence: 64%

The Role of Symbiotic Microorganisms, Nutrient Uptake and Rhizosphere Bacterial Community in Response of Pea (Pisum sativum L.) Genotypes to Elevated Al Concentrations in Soil

Belimov

Шапошников

Syrova

et al. 2020

Plants

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Aluminium being one of the most abundant elements is very toxic for plants causing inhibition of nutrient uptake and productivity. The aim of this study was to evaluate the potential of microbial consortium consisting of arbuscular mycorrhizal fungus (AMF), rhizobia and PGPR for counteracting negative effects of Al toxicity on four pea genotypes differing in Al tolerance. Pea plants were grown in acid soil supplemented with AlCl3 (pHKCl = 4.5) or neutralized with CaCO3 (pHKCl = 6.2). Inoculation increased shoot and/or seed biomass of plants grown in Al-supplemented soil. Nodule number and biomass were about twice on roots of Al-treated genotypes after inoculation. Inoculation decreased concentrations of water-soluble Al in the rhizosphere of all genotypes grown in Al-supplemented soil by about 30%, improved N2 fixation and uptake of fertilizer 15N and nutrients from soil, and increased concentrations of water-soluble nutrients in the rhizosphere. The structure of rhizospheric microbial communities varied to a greater extent depending on the plant genotype, as compared to soil conditions and inoculation. Thus, this study highlights the important role of symbiotic microorganisms and the plant genotype in complex interactions between the components of the soil-microorganism-plant continuum subjected to Al toxicity.

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“…During this process of increased microbial activity in plant rhizosphere, the selection of some specific microorganisms has been observed, leading to the buildup of plant-specific community in the rhizosphere (Hu et al, 2018). A recent study suggested that enrichment of members of bacterial families known for P-solubilizing, such as Rhizobiacea, Enterobacteriaceae, Pseudomonadaceae, and Burkholderiaceae, has been observed in the pea rhizosphere (Harkes et al, 2020). In comparison to cereals, legumes pose a much stronger influence on the selection of rhizosphere microbiome (Hamel et al, 2018;Harkes et al, 2019Harkes et al, , 2020.…”

Section: Introductionmentioning

confidence: 99%

Pea (Pisum sativum l.) Plant Shapes Its Rhizosphere Microbiome for Nutrient Uptake and Stress Amelioration in Acidic Soils of the North-East Region of India

et al. 2020

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Rhizosphere microbiome significantly influences plant growth and productivity. Legume crops such as pea have often been used as a rotation crop along with rice cultivation in long-term conservation agriculture experiments in the acidic soils of the northeast region of India. It is essential to understand how the pea plant influences the soil communities and shapes its rhizosphere microbiome. It is also expected that the longterm application of nutrients and tillage practices may also have a lasting effect on the rhizosphere and soil communities. In this study, we estimated the bacterial communities by 16S rRNA gene amplicon sequencing of pea rhizosphere and bulk soils from a longterm experiment with multiple nutrient management practices and different tillage history. We also used Tax4Fun to predict the functions of bacterial communities. Quantitative polymerase chain reaction (qPCR) was used to estimate the abundance of total bacterial and members of Firmicutes in the rhizosphere and bulk soils. The results showed that bacterial diversity was significantly higher in the rhizosphere in comparison to bulk soils. A higher abundance of Proteobacteria was recorded in the rhizosphere, whereas the bulk soils have higher proportions of Firmicutes. At the genus level, proportions of Rhizobium, Pseudomonas, Pantoea, Nitrobacter, Enterobacter, and Sphingomonas were significantly higher in the rhizosphere. At the same time, Massilia, Paenibacillus, and Planomicrobium were more abundant in the bulk soils. Higher abundance of genes reported for plant growth promotion and several other genes, including iron complex outer membrane receptor, cobalt-zinc-cadmium resistance, sigma-70 factor, and ribonuclease E, was predicted in the rhizosphere samples in comparison to bulk soils, indicating that the pea plants shape their rhizosphere microbiome, plausibly to meet its requirements for nutrient uptake and stress amelioration.

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Shifts in the Active Rhizobiome Paralleling Low Meloidogyne chitwoodi Densities in Fields Under Prolonged Organic Soil Management

Cited by 29 publications

References 61 publications

Bacterial Community Structure Dynamics in Meloidogyne incognita -Infected Roots and Its Role in Worm-Microbiome Interactions

Bacterial Community Structure Dynamics in Meloidogyne incognita -Infected Roots and Its Role in Worm-Microbiome Interactions

The Role of Symbiotic Microorganisms, Nutrient Uptake and Rhizosphere Bacterial Community in Response of Pea (Pisum sativum L.) Genotypes to Elevated Al Concentrations in Soil

Pea (Pisum sativum l.) Plant Shapes Its Rhizosphere Microbiome for Nutrient Uptake and Stress Amelioration in Acidic Soils of the North-East Region of India

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