GENOMIC APPROACHES FOR MONITORING WETLAND AND LAKE MICROBIOMES
DOI:
https://doi.org/10.32782/1998-6475.2026.60.6Keywords:
environmental DNA, freshwater, wetlands, bacterioplankton, long-read sequencing, Oxford Nanopore, 16S rRNA, environmental monitoringAbstract
Environmental metagenomics is changing how we monitor water bodies (lakes, reservoirs, rivers) and wetlands by analyzing DNA and RNA directly from water and sediments. Microorganisms (algae, bacteria, fungi) respond quickly to environmental, hydrological, and limnological changes (water flow, level fluctuation, inorganic nutrients and organic matter accumulation, temperature shifts, etc.), allowing them to provide early signals of ecosystem change. This review focuses on practical freshwater metagenomics of bacterioplankton, especially how portable long-read nanopore sequencing can support real monitoring in the field. This review summarizes practical options for freshwater monitoring, with an emphasis on portable long-read Oxford Nanopore sequencing (ONT), which can support near-real-time, field-based workflows and full-length 16S rRNA profiling for improved taxonomic resolution. We contrast two complementary strategies: routine amplicon profiling (cost-effective for frequent sampling) and shotgun metagenomics (more resource-intensive but informative for functional inference). A pragmatic monitoring model uses amplicons for baseline surveillance and escalates to shotgun or targeted functional assays when samples deviate from baseline. We frame interpretation at three levels: (1) community composition, (2) functional potential, and (3) process understanding and forecasting. We also emphasize that reliable inference depends on sampling designs aligned with hydrologic connectivity and habitat structure, with replication across space and time. Because 16S tables are typically compositional, we discuss statistical practices that reduce false signals (e.g., avoiding routine rarefaction and using composition-aware methods), and we highlight the value of adding an absolute scale when feasible. Finally, using the Balaton–Kis-Balaton wetland–lake hydrological continuum as an applied example, we outline candidate indicators that separate stable “core” states from local transitions and provide a reporting checklist that supports reproducibility and long-term reuse.
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