Culture-independent methods for studying environmental microorganisms: methods, application, and perspective

Area of Science:

• Environmental microbiology
• Molecular ecology
• Microbial community analysis

Background:

• Culture-independent methods (CIMs) have advanced the study of microbial communities.
• Molecular techniques like PCR-based methods and non-PCR techniques have been developed over the past 20 years.
• Next-generation sequencing has propelled novel fields like metagenomics and single-cell genomics.

Purpose of the Study:

• To provide an updated review of various CIMs.
• To compare different CIMs and their applications.
• To focus on the analysis of microbial diversities and communities.

Main Methods:

• Review of established and novel molecular techniques.
• Comparison of PCR-based methods (e.g., DGGE, T-RFLP, qPCR) and non-PCR methods (e.g., microarray, FISH).
• Inclusion of advanced single-cell technologies (e.g., Raman microspectroscopy, nanoSIMS) and omics approaches (metagenomics, metatranscriptomics, metaproteomics).

Main Results:

• CIMs allow in situ analysis of microbial genes, transcripts, proteins, and metabolites.
• These methods reveal how microbial interactions impact distribution patterns.
• The review highlights the revolution in microbiology due to direct analysis of natural communities.

Conclusions:

• CIMs are essential for understanding microbial ecology and environmental microbiology.
• Comparative analysis of CIMs aids in selecting appropriate methods for specific research questions.
• The ongoing development of molecular technologies continues to expand the scope of microbial community studies.