"Microbes" is a somewhat imprecise term as it can refer mainly to bacteria, fungi, and algae. Generally, multiple species of algae, bacteria, and fungi are known to metabolize organic pollutants; this process is known as biotic degradation. For example, OECD 301 and 310 procedures (https://www.oecd-ilibrary.org/environment/test-no-301-ready-biodegradability_9789264070349-en, https://www.oecd-ilibrary.org/environment/test-no-310-ready-biodegradability-co2-in-sealed-vessels-headspace-test_9789264224506-en) use activated sludge or sewage effluent which contains multiple microorganisms to assess the biodegradability of organic compounds (you can find some examples in my work: Article Ecotoxicity studies reveal that organic cations in dicamba-d...
). Multiple example of fungi for bioremediation can be find there:
Article Diverse Metabolic Capacities of Fungi for Bioremediation
.
For soil fertility, it is crucial to supply nitrogen compound, which can be done directly from atmosphere by nitrogen-fixing bacteria capable of transforming nitrogen gas from the atmosphere into nitrogen compounds, that are usable by plants. (more about it: Article The microbial nitrogen-cycling network