Mass spectrometry-based microbial identification and profiling for environmental sciences

The identification of microorganisms in environmental science is a key component in the process of understanding community structure, function, and interactions. For the past two decades, this process has relied on the use of molecular profiling methods to sequence DNA and RNA. Although informative, this approach is limited in terms of functional understanding of microbial communities in environmental processes and systems. Mass spectrometry (MS) offers novel analytical approaches to both culture-dependent and culture-independent microbial identification and functional profiling, and holds potential to provide ever greater insight into microbial community structure and function in the environmental sciences. This chapter explores the requirement for microbial identification in the environmental sciences and MS methods for both culture-dependent and culture-independent identification. It goes on to discuss the role of MS in functional profiling of microbial communities in environmental science and combines MS with identification methods in several case studies. Finally, the chapter ends with a discussion of the future role and opportunities of MS in microbial research within the environmental sciences.