Pea plant shapes its rhizosphere microbiome for nutrient uptake and combating stress

-By Kranti Karande

Legume crops like Pea are used as rotation crops along with rice cultivation in long term conservation agriculture experiments in the acidic soils of the North East region of India. Rhizosphere microbiomes present in the soil have significant influence on plant growth and productivity. The study aims at understanding the bacterial composition of microbiomes present in bulk soil as compared to the rhizosphere. It also aims to understand how the pea plant influences the bacterial communities present in soil and the rhizosphere microbiome in order to improve nutrient uptake and stress improvement. Pea cultivation is a practice used in conservation agriculture which strives to preserve and enrich the environmental resources to sustain and improve crop productivity. The study conducted will help devise future strategies to expand pea cultivation and improve soil health in the region. 

Crop rotation is an important and effective strategy as part of conservation agriculture practices. The North East region of India is a fragile, marginal, inaccessible and diverse ecosystem. Generally a mono-cropping system of rice is followed in this region.  Zero tillage (without disturbing the soil) cultivation of pea (Pisum sativum L.) has been considered beneficial to enhance the cropping intensity in the region. The majority of soils in North-East India are acidic in nature. The pH of soil among many other environmental factors has a significant influence on the type of nutrients and microorganisms present in the soil which in turn have an influence on the productivity of crops. Similarly, nutrient and residue management practices like the application of chemical fertilizers often influence the endogenous microbial communities. 

Sample collection for the study was done from experimental fields of the ICAR Research Complex for NEH Region, Umiam, Meghalaya, located in Eastern Himalayan region. Different tillage and residue management treatments were maintained in these fields for the last eight years by alternatively cultivating rice followed by pea cultivation. For microbial community analysis, bulk soil and pea rhizosphere samples were collected from each treatment plot. All the samples were processed for community DNA extraction. Analysis of the chemical properties of the soil samples was done using available methods. Rhizosphere soils were harvested from roots of pea plants. 

Soil pH (1:2.5) was found to be influenced by tillage and nutrient management practices at depth  0-15 cm. The combined effect of tillage and nutrient management practices on available N, P and K content and SOC,TOC of soil were significant. The rhizosphere showed higher diversity indices in comparison to the bulk soil samples. A total of 71 bacterial phyla were detected in the bulk soil and rhizosphere samples. A higher abundance of Firmicutes was recorded in bulk soil (~41.7%) in comparison to the rhizosphere (~17.8%). On the contrary, Proteobacteria were highly abundant in the rhizosphere (~43.9%) in comparison to bulk soil (~18.6%) samples. Significantly higher abundance of Proteobacteria and Bacteroidetes was observed in pea rhizosphere samples in comparison to bulk soil. 

Impact of residue management practices on abundance of specific microbial communities was observed across both rhizosphere and bulk soil samples. The impact of tillage history was also observed on the enrichment of specific OTUs in the bulk soil and rhizospheric soil. Differences in the abundance of 11 genera were recorded in the rhizosphere sample across the history of different tillage treatment. All these genera showed higher abundance in the conventional tillage fields. The correlation between soil properties and microbial community structure was also studied as part of the study. Significant correlations were observed between relative abundance of few bacterial phyla & genera and soil properties in both bulk soil and rhizospheric soil samples. However, the number of significant correlations was low in rhizosphere samples, in comparison to bulk soil samples. 

The study was designed to investigate the effect of long-term exposure to various tillage and residue management practices on the bacterial community structures of the bulk soils and how pea plant (a rotation crop) shapes the rhizosphere communities. A higher species diversity and evenness was observed in rhizospheric samples. There was no significant difference in bacterial richness and evenness among different tillage and residue management treatments in both rhizospheric and bulk soil samples. This is an indication that the plant rhizosphere effect (a plant’s ability to alter microbial communities in rhizospheric soil) is the key driver of alpha diversity. Plants can alter the microbial communities by secreting a variety of nutrients and bioactive molecules into the rhizosphere. Enrichment of specific OYUs in the Pea rhizosphere were also confirmed which can be attributed to the selection pressure of the Pea root. The results of the Pea rhizosphere and bulk soils were consistent with the fact that the majority of members of microbial communities in the host plant are horizontally acquired from the surrounding environment, and the soil is the main reservoir of a plant rhizosphere microbiome. The genus Nitrobacter was at higher abundance in pea rhizosphere samples than bulk soils, suggesting its enrichment by the host plant as Nitrobacter converts nitrite to nitrate making nitrogen more readily available to the host plant. Higher abundance of genes related to nitrogen fixation, phytohormone and siderophore production, phosphate solubilization in the rhizosphere soil substantiate the conclusion that the selection of bacterial communities is always based on plant growth promoting potential in the rhizosphere. 

The study concluded that pea plant is the most dominating selection factor shaping the microbial communities under diverse residue management and tillage treatments. The rhizospheric soil was found to be enriched with bacterial taxa known for plant growth promotion which indicates that the plant plays a role in selecting the rhizospheric communities to meet its requirement of nutrient uptake and combating stress.


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