Microorganisms inhabit almost every imaginable environment and are important players in biogeochemical cycles.
With the development and improvement of molecular biology-based approaches,the functions and community composition of
microorganisms in ecosystems can be explored in more detail than ever before. Rapidly advancing molecular techniques have
been applied to questions regarding microbial diversity,biogeography,and responses to environmental changes. Studies of
microorganisms in the environment generally focus on three objectives—determining which microorganisms are present,what
their functions are,and which are active at a given time. Comprehending the range of techniques currently available can be
daunting. To facilitate the selection of the appropriate approach by researchers to study microbial communities in the
environment,we introduce molecular methods according to microbial diversity and function,such as the rapidly developing
high-throughput sequencing,meta-omics,and microbial single-cell approaches ( e. g.,nano-scale secondary ion mass
spectrometry-fluorescence in situ hybridization,NanoSIMS-FISH) ,and their applications in microbial ecology studies.
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