There are many applications of micro-organisms in oil/petroleum industry especially for microbial degradation of oil contaminants and enhanced oil recovery process. Following references may be useful:
The application of enzymes in petroleum and oil refining industries is for environmental protection. Enzymes are efficient in the waste water treatment and soil bio-remediation activities. Perry's Chemical Engineers Handbook and other books on environmental protection can direct you on the procedures. There are so many work and good results in the area.
Enzymes are used in drilling and recovery of oil from the reservoir. Mitra commented on enhanced oil recovery. This is an aspect of optimizing the yield of oil/gas throughput from the reservoir. for details consult experts in the area.