Table 1 Analysis of recent literatures on crop plants and their studies associated with rhizosphere

1

[106]

Wheat

To characterize the rhizospheric microbiome of high Zinc (HZn) and Low Zinc (LZn) wheat; (2) To determine microbes that can mobilize zinc. And (3) Identify the abundance of microbes

1.Bowtie 2 v2.2.7

2.MEGAHIT v1.1.3

3.Prodigal v2.6.3

4.MMseqs2 Linclust kaiju v1.7.3

Novel microbial species with zinc mobilizing potential were identified as Massilia and Pseudomonas species, which may have a functional module to accelerate soil zinc mobilization. Around 30 novel bacteria were isolated using high throughput targeted culturomics

Involved in zinc mobilization in the given environment and their role in altering the concentration of grain zinc among the cultivars

eggNOG-Mapper v2.0.1

These isolates having strong potential to increase the availability of Zn in soil could be used as a synthetic community to improve the nutrition and growth of cereal plants

2

[107]

Legumes

To analyze the rhizospheric microbiota assembly of two lentil cultivars under the effect of rice fallow ecology to identify the diversity of the microbial population

1.WINRHIZO software package

2.MeV tool

3.Parallel-metatool

The two cultivars Farmer-2 and Moitree show cased insignificant differences in the diversity and role of microbiomes concerning Nitrogen metabolism in their rhizosphere

3

[108]

Legumes

To determine the effect of strigolactones on the recruitment of microbes to the rhizosphere

1.LefSe software

2. Mothur software

Altering the strigolactone signaling and biosynthesis pathway alters the rhizosphere

bacteria community

4

[109]

Wheat and chickpea

To understand the microbiome, present in the detritus sphere and the effects it shows due to agricultural management that involves soil tillage and crop rotations

1. 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. The species Pseudomonas was never before reported to be associated with the said plant

9

[114]

Rice

To investigate the factors involved in chemotaxis systems that have been affected by the selection at the time of domestication of rice species

–-

Genes involved in bacterial chemotaxis showed a greater richness in the rhizospheres of wild rice as compared to cultivated rice, and the two types of rice showed significant variation in the compositional makeup of their respective chemotaxis genes

10

[115]

Rice

Root tissues of the rice (Oryza sativa L.) is habited by Bacillus paralicheniformis strain KMS 80 (MTCC No. 12704) that is known to display plant growth promoting abilities along with nitrogen fixation. Whole genome sequencing is performed on the DNA of this bacterium to evaluate its functional gene profile

–

Whole genome sequencing of the Bacillus species results were predicted as: 21 genes took part in Nitrogen Metabolism pathway and two main genes glnR and tnrA (transcriptional factors) were involved in regulating nitrogen fixation in the Bacillus strain KMS 80. This will help to understand the enhanced endophytic nitrogen fixation and other beneficial role of B. paralicheniformis in rice

11

[116]

Rice

To determine the potential effect of Nitrogen fertilizer and the Azospirillium product on growth and development of rice and its yield and on diversity of its bacterial community with respect to both the rice roots and the rhizosphere

Silva database, QIIME (version 1.7.0)

Greater Nitrogenase activity (533–634 nmol C2H4/plant/h compared to the control) was observed when the Azospirillum product (A was applied with less than 1 dose of the nitrogen fertilizer. The grain yield was (6,001.3– 6,480.6 kg/ha) which is same as adding 100% of nitrogen fertilizer. The richness of bacterial community of the soil rhizosphere was higher as compared to the rice roots as predicted by metagenomic analysis

12

[117]

Wheat

1.Trimmomatic v 0.36

2.Pear v 0.9.6

3.VSEARCH v 2.7.1

4. QIIME 2 v 2019.4

The analysis showed that application of P fertilization for a long term affected the soil Carbon and Phosphorus significantly and phoD-harboring bacterial community compositions in rhizosphere of wheat soil. This high application of P fertilizers decreased the total Bacterial OTUs along with diversity and their connections potentially affecting the biogeochemical cycles of the soil

13

[118]

Legume

The soil bacterial community was assessed due to addition of P fertilizer on the soil to determine the difference in the diversity and structure of the clover rhizosphere microbial community along with the nitrogen fixing bacterial communities of the soils in the presence of different Hg contamination levels

Quantitative Insights into Microbial Ecology

High levels of Hg in the soil decreased bacterial diversity and community abundance along with increased in the richness and diversity of nitrogen-fixing bacteria. High Hg level soils had the presence of Rhizobium which was a biomarker. Other important factors affecting structure and abundance of the microbial community was: soil total nitrogen (TN), soil organic matter (SOM), nitrate nitrogen (NO3 − N) and available molybdenum (Mo)

14

[119]

Cowpea, sorghum, maize

To determine the mineral nutrient concentrations, activity of P- enzyme and the differences in the rhizospheres of intra-hole planted cowpea (cvs. TVu 546 and PAN 311), maize (cv. ZM 521), and sorghum (cv. M48) with their sole cropped

QIIME, UCLUST

Modifications in the rhizosphere bacterial community structure were observed because of intra-hole cropping. The soil was dominated by Proteobacteria, Actinobacteria, Verrucomicrobia, Acidobacteria, Firmicutes, Bacteroidetes and Planctomycetes which together consisted more than 95% of the sequence. Absent for the soil were pathogens like like Ralsotonia and Agrobacterium