We designed this review to describe a compilation of studies to enlighten the concepts of plant–microbe interactions, adopted protocols in smart crop farming, and biodiversity to reaffirm sustainable agriculture. The ever-increasing use of agrochemicals to boost crop production has created health hazards to humans and the environment. Microbes can bring up the hidden strength of plants, augmenting disease resistance and yield, hereafter, crops could be grown without chemicals by harnessing microbes that live in/on plants and soil. This review summarizes an understanding of the functions and importance of indigenous microbial communities; host–microbial and microbial–microbial interactions; simplified experimentally controlled synthetic flora used to perform targeted operations; maintaining the molecular mechanisms; and microbial agent application technology. It also analyzes existing problems and forecasts prospects. The real advancement of microbiome engineering requires a large number of cycles to obtain the necessary ecological principles, precise manipulation of the microbiome, and predictable results. To advance this approach, interdisciplinary collaboration in the areas of experimentation, computation, automation, and applications is required. The road to microbiome engineering seems to be long; however, research and biotechnology provide a promising approach for proceeding with microbial engineering and address persistent social and environmental issues.

In order to illustrate their tolerance mechanism, four leading cultivars of Brassica napus (Mianyou 15, Guohaoyou 8, Yiyou 21, and Mianyou 16) were investigated to study the effects of Clopyralid, Benazolin, and Clethodium on physio-chemical and ultrastructural attributes of Brassica napus at during seed germination stage, by various concentrations (0.0, 0.5, 0.7, 1.0, 1.3 μg/10 mL) of Clopyralid, Benazolin, and Clethodium to rape seedlings in terms of various physiological and biochemical measurements and microscopic analysis. The main results were as follows: low concentration (0.5 μg/10 ml) of Clopyralid, Benazolin, and Clethodium had no significant effect on Brassica napus CVS. It was found that with the increasing of treated concentrations, the growth of Brassica napus was inhibited more when the concentration of Clopyralid, Benazolin, and Clethodium was higher than 1.3 μg·L-1. It inhibited the net photosynthetic rate, chlorophyll content, chlorophyll fluorescence value, and anti-enzyme activities of Brassica napus. Moreover, it increased lipid peroxidation, accumulated reactive oxygen species, and damaged the ultrastructure of chloroplasts and mitochondria in mesophyll cells. In addition, the ability of resistance to the stress of Clopyralid, Benazolin, and Clethodium in all cultivars shows higher sensitivity which is more effective. Therefore, this study defined the effect of selected herbicides on Brassica napus, and the findings have great significance in extending the calculation by field application of those herbicides.