Inorganic Chemical Fertilizer Application to Wheat Reduces the Abundance of Putative Plant Growth-Promoting Rhizobacteria

Abstract

The profound negative effect of inorganic chemical fertilizer application on rhizobacterial diversity has been well documented using 16S rRNA gene amplicon sequencing and predictive metagenomics. We aimed to measure the function and relative abundance of readily culturable putative plant growth-promoting rhizobacterial (PGPR) isolates from wheat root soil samples under contrasting inorganic fertilization regimes. We hypothesized that putative PGPR abundance will be reduced in fertilized relative to unfertilized samples. Triticum aestivum cv. Cadenza seeds were sown in a nutrient depleted agricultural soil in pots treated with and without Osmocote® fertilizer containing nitrogen-phosphorous-potassium (NPK). Rhizosphere and rhizoplane samples were collected at flowering stage (10 weeks) and analyzed by culture-independent (CI) amplicon sequence variant (ASV) analysis of rhizobacterial DNA as well as culture-dependent (CD) techniques. Rhizosphere and rhizoplane derived microbiota culture collections were tested for plant growth-promoting traits using functional bioassays. In general, fertilizer addition decreased the proportion of nutrient-solubilizing bacteria (nitrate, phosphate, potassium, iron, and zinc) isolated from rhizocompartments in wheat whereas salt tolerant bacteria were not affected. A “PGPR” database was created from isolate 16S rRNA gene sequences against which total amplified 16S rRNA soil DNA was searched, identifying 1.52% of total community ASVs as culturable PGPR isolates. Bioassays identified a higher proportion of PGPR in non-fertilized samples [rhizosphere (49%) and rhizoplane (91%)] compared to fertilized samples [rhizosphere (21%) and rhizoplane (19%)] which constituted approximately 1.95 and 1.25% in non-fertilized and fertilized total community DNA, respectively. The analyses of 16S rRNA genes and deduced functional profiles provide an in-depth understanding of the responses of bacterial communities to fertilizer; our study suggests that rhizobacteria that potentially benefit plants by mobilizing insoluble nutrients in soil are reduced by chemical fertilizer addition. This knowledge will benefit the development of more targeted biofertilization strategies.

The Impacts of Field Management on Soil and Tea Root Microbiomes

“…Interestingly, in the roots from organic farms, we found an increased abundance of Bradyrhizobium, Streptomyces, Burkholderia-Caballeronia-Paraburkholderia, and Sphingomonas, all of which are genera enriched by well-known plant growth-promoting bacteria [47][48][49][50]. This result is consistent with a recent report by Reid et al [43] showing a reduction in the population of plant growth-promoting bacteria in the rhizosphere after applying chemical fertilizers. Through both previous studies and this present study, we can see the benefit of organic cropping systems on microbial composition, which might increase crop growth and resilience to environmental stresses.…”

“…Previous studies showed that Acidothermus and Rhodanobacter preferred saline and acidic environments, respectively [35,41]. It is known that the long-term application of chemical fertilizers affects soil pH and salt content, and has a great impact on microbial community composition in the rhizosphere [42,43]. Further studies will be required to examine the seasonal change in soil fertility, plant nutrition status and microbiome to reveal the association between microbiomes and other environmental factors.…”

Competition, Nodule Occupancy, and Persistence of Inoculant Strains: Key Factors in the Rhizobium-Legume Symbioses

“…The addition of chemical fertilizers has a negative impact on the soil microbiome, as plants no longer need to interact with beneficial bacteria to access the nutrients that are being externally supplied and, therefore, the diversity of the microbial community in the root environment is reduced ( Zhu et al, 2016 ; Kavamura et al, 2018 ). A study performed in wheat has shown that chemical fertilizers reduce the number of bacteria associated with the roots that solubilise nutrients such as nitrogen, potassium, phosphorous, iron, and zinc ( Reid et al, 2021 ). Strikingly, the number of growth-promoting bacteria living on the roots fell from 91% of total bacteria for unfertilized plants, to just 19% for those that received the fertilizer dose.…”

Analysis and Interpretation of metagenomics data: an approach

“…SoapAligner software 2.MetaGeneMark software 3. CD-HIT software 4.BLAST software When the rhizosphere and detrituspheric microbiomes collaborate in the presence of decaying roots, it is observed that the rhizospheric microbiome degrades the plant root exudates, and the specific genes corresponding to membrane transporters, amino acid, and carbohydrate metabolism enhance their expression 5 [ 110 ] Wheat To study the response of chemical fertilizers on putative PGPR richness present in the commercial Cadenza, the wheat variety is grown in a low input agricultural soil exhausted in most nutrients. Under such conditions, the beneficial microbes are known to have a key role in sustaining the crop growth and production CASAVA data analysis software (Illumina) The rhizobacteria present in the soil is beneficial to plants as it is involved in insoluble nutrients mobilization in soil but in the presence of chemical fertilizers, its population is decreased considerably 6 [ 111 ] Wheat To study the collective response of eCO2 and nitrate levels on the function and structure of the bacterial community attached to the root surface 1.StepOne software v2.3 (Applied Biosystems) 2.CD-HIT-EST v4.8.1 3.MEGAN v6.15.2 4.Trinity mapping v2.8.4 5.Cytoscape v.3.7.2 The combined effect of CO2 and nitrate levels are responsible for plant growth and development and is also benefit the growth and function of the root surfaceassociated bacterial population which is involved in the fitness of root and root colonization 7 [ 112 ] Chickpea To analyze endophytic bacterial communities for their functionality and diversity present in internal root tissues of native legumes species growing into different locations of south Portugal further assess its potential to accelerate plant development and growth Tree of Life (iTOL) v4 The association of rhizobia and specific non –rhizobial endophytic bacteria elevates the growth of chickpea majorly via increasing the nodulation and nitrogen fixation capacity shown by mesorhizobial strains 8 [ 113 ] Sorghum To determine the time dependent change in the microbial complexity in the rhizospheres of field-grown sorghum USEARCH software suite An OUT of bacterial origin from the genus Pseudomonas was identified in the microbiome of the rhizosphere of Sorghum bicolor.…”