Allium cepa is one of the main spices in Indonesia which is used as the main ingredient in various types of dishes. Allium cepa has become a national strategic product since the consumption and export of this crop continues to grow annually . This commodity is popularly cultivated worldwide considering its high economic value and importance as a vegetable, condiment, and spice with medicinal benefits . Sun et al.  verified that Allium cepa has been found to have significant nutritional and bioactive properties, with great potential for antibiotic, hypolipidemic, anticancer, antioxidant, hypoglycaemic, kidney protective, and hepatoprotective properties.
To meet production needs, farmers use chemical fertilizers. The application of chemical fertilizers to crops has increased toxicity to plants while reducing soil quality in the future . This habit can increase soil salinity and heavy metal accumulation which leads to the deterioration of soil fertility . Heavy metals including Hg, Cd, As, Pb, Cu, Ni, and Cu; natural radionuclides like 238U, 232Th, and 210Po absorbed by plants can also enter the plant system and if the plant is consumed by humans, it will affect human health . The use of chemical fertilizer leaves residues in plant tissue, this is harmful since crops should have a top grade of food safety and security.
An alternative to reduce the effect of chemical fertilizers is the application of biofertilizers made from microbial consortiums. The addition of microbial consortium is widely used to increase the growth and yield of plants . The use of microbial consortiums in many countries has been encouraged as a substitute and/or replacement for chemical fertilizers . Moreover, the use of microbial consortium in the rhizosphere increases soil microbial diversity which is critical for the function and sustainability of the soil ecosystem to enhance healthy plant growth .
The diversity of microbes that interact with plants can be pathogens that cause disease, can be beneficial endophytic bacteria, and can also be resident microbes. These microbes build dynamic communities that affect the life and growth of a plant . Microbes inhabit all parts of the plant, including the rhizosphere . The rhizosphere is a dynamic and promising zone for the microbial community to grow and metabolize since it provides nutrients for both plants and microorganisms . Root-colonizing bacteria role in inhibiting the growth and activity of pathogens or inducing defense responses . Root exudates increase the metabolic activity of some bacteria, and root vicinities are abundant in bacteria and other microbes . To increase yield quality, several microbes were found to increase plant defense mechanisms against pathogens, for example, adding bacterial consortium to mulberry increases plant resistance to root rot . The utilization of a consortium of endophytic microbes has also been recognized for its capability to increase the grain yield and photosynthetic capacity of wheat durum . Studying the influence of biotic or abiotic factors on the organization of the rhizosphere microbial community is critical since rhizosphere microorganism have such a significant impact on plants .
Studying microbial diversity and its interaction in the environmental soil is still struggling since several microbes in the environment are unculturable at present laboratory conditions. To face this issue, the methodology to describe the microbial diversity present in the rhizosphere soil or any other environmental samples is available and developed using the metagenomic technique . With this technique, we can study the total DNA present in a particular environmental sample . Metagenomic is preferred since it helps to understand how to scale up methods and study the microbial richness and diversity, and then understand the plant-microbe interaction in the environment . The comparative metagenomics in which libraries are prepared from different sites or at different times can be compared to understanding the differences among environments or communities. The genomics of environmental DNA can lead to the discovery of important physiological processes in uncultured microorganisms. Some strong correlations between the presence of organisms and microbial processes or soil structure and function will assist in making a wise choice before making a major investment such as a sequencing project .
This study aimed to discover the effect of endophytic bacteria consortium inoculations in the bacterial community structure of Allium cepa rhizosphere and the interrelationship with ecosystem functions. This research can be used as a selection of endophytic microbes that are useful for the replacement of inorganic fertilizer, increasing Allium cepa productivity and resulting in a high selling value of Allium cepa which will help the welfare of farmers. Although many studies of microbial diversity have been done including one investigating soil rhizosphere microbial communities in organic farming of Allium cepa , studies on microbial diversity in Allium cepa grown under the application of endophytic bacteria consortium to replace inorganic fertilizer have never been studied. The metagenomic sequencing approach was chosen because it is a new and reliable method for investigating microbial diversity in the rhizosphere after applications of beneficial endophytic microbes. Furthermore, this study examines beneficial endophytic microbial interactions in increasing the growth of Allium cepa.