Talking about food chain. You can include bacteria to each and every food chain out there. They are the decomposers, they break down the complex organic matter found in the dead bodies of plants and animals. The digested material then provides a food source for other organisms. The decomposing process greatly increases the nutrient-load of an ecosystem which allows for greater biodiversity.
There is another concept “ Microbial Loop”. You can connect microorganisms to aquatic and soil ecosystems. The pathway starts with dissolved organic matter (DOM : DOM consists of molecules which were once parts of living organisms such as proteins, carbohydrates, lipids, and nucleic acids) which makes its way through various trophic levels via its incorporation into bacterial biomass, and then coupled with the classical food chain. The term microbial loop was coined by and et al (1983). The microbial loop is ecologically significant because it is directly involved in nutrient cycling and primary production of biomass ultimately effecting large-scale ecological functions.