Molecular Tools in Environmental Microbiology

Dear Colleagues,

Environmental microbiology continues to face significant technical and analytical challenges. One of the primary obstacles is the extraction of high-quality genomic DNA from complex and inhibitor-rich environmental samples such as soil, feces, sediments, wastewater, and biological fluids. These matrices often contain humic substances, polysaccharides, and other PCR inhibitors that compromise downstream molecular analyses. Another major limitation is the low abundance of target microorganisms within a given environmental sample. This presents difficulties in both the enrichment and specific detection of species of interest, especially in cases where the microbial signal is overwhelmed by a high background of non-target DNA. The advent of next-generation sequencing (NGS) technologies has revolutionized the field, yet several critical limitations remain. These include the scarcity of reference genome sequences for many environmental microbes, the incompleteness and inconsistency of current taxonomic databases, and the challenge of selecting appropriate genetic markers for accurate species-level identification and functional analysis.

The goal of this Special Issue is to present recent advances in molecular methods for studying microorganisms in complex environmental samples. It focuses on overcoming challenges in DNA extraction, PCR inhibition, detection of low-abundance species, and limitations of current sequencing tools and databases. The issue aims to provide practical solutions and highlight innovative tools for accurate microbial identification and functional analysis in environmental microbiology.

We invite microbiologists, molecular ecologists, and environmental scientists to contribute their insights in the following areas and related topics:

• Experimental Methods and Technical Challenges (improvement methods for DNA/RNA extraction from environmental matrices; strategies to overcome PCR inhibition; novel approaches for microbial enrichment and target-specific amplification; advances in primer design and genetic marker selection; and so on).
• Sequencing Technologies and Applications (applications of metagenomics, metatranscriptomics, and single-cell sequencing in environmental microbiology).
• Applications and Case Studies (case studies using molecular tools to monitor microbial communities; standardization and reproducibility in environmental microbiology).
• Bioinformatics and Database Development (bioinformatics tools and pipelines for environmental microbial analysis; challenges and solutions in microbial reference database development).

Dr. Živilė Strazdaitė-Žielienė
Dr. Juliana Lukša
Guest Editors

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