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Purpose <p>Methanogens-methanotrophs interactions regulate wetland methane fluxes, yet their community composition across ecosystems remains underexplored. This study employs three universal 16&#xa0;S rRNA prokaryotic primers and next-generation sequencing (NGS) to assess their diversity and habitat specificity in freshwater, brackish, and sewage-fed wetlands.</p> Materials and methods <p>Nine samples were collected from three wetland ecosystems—freshwater, brackish water, and sewage-fed. Three universal 16&#xa0;S prokaryotic primers were used to profile microbial communities. NGS was employed to identify the methanogen and methanotroph Amplicon Sequence Variants (ASVs). The diversity analysis of these microbial communities was done using Reny’s diversity profile, allowing for the ranking of microbial diversity across the three wetlands. Compositional diversity was investigated by community structural pattern, which was explored using Non-Metric Multidimensional Scaling.</p> Results and discussion <p>The study identified 299 methanogen and 65 methanotroph ASVs from nine samples across three wetlands. Freshwater ecosystems had the highest diversity and abundance of these communities, followed by sewage-fed and brackish water environments. Primers detected 4–49% of distinct ASVs, emphasizing the importance of primer selection in revealing unique taxa. Reny’s diversity profile ranked freshwater as the most diverse, followed by sewage-fed and brackish water wetland. In total, 11 methanogen and nine methanotroph genera were found, with primer-specific variation in their abundance. However, community compositions remained consistent across primers but varied across wetlands. Habitat-specific genera were identified in freshwater, brackish, and sewage-fed wetlands.</p> Conclusions <p>The study highlights the importance of primer selection for comprehensive microbial community profiling. It demonstrates that different wetland ecosystems harbour distinct methanogen and methanotroph communities, with freshwater habitats supporting the greatest diversity. These findings support the use of multiple primers for broad-spectrum microbial analysis across diverse ecosystems.</p>

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Assessment of three prokaryote primers for concurrent and comprehensive profiling of methanogen and methanotroph community and habitat specificity in three distinct wetland sediments

  • 期刊论文

  • 发表日期：

    2025年6月19日

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  • Kavita Kumari,
  • Malay Naskar,
  • Md. Aftabuddin,
  • Uttam Kumar Sarkar,
  • Subir Kumar Nag,
  • Bandana Das Ghosh,
  • Basanta Kumar Das

摘要

Purpose

Methanogens-methanotrophs interactions regulate wetland methane fluxes, yet their community composition across ecosystems remains underexplored. This study employs three universal 16 S rRNA prokaryotic primers and next-generation sequencing (NGS) to assess their diversity and habitat specificity in freshwater, brackish, and sewage-fed wetlands.

Materials and methods

Nine samples were collected from three wetland ecosystems—freshwater, brackish water, and sewage-fed. Three universal 16 S prokaryotic primers were used to profile microbial communities. NGS was employed to identify the methanogen and methanotroph Amplicon Sequence Variants (ASVs). The diversity analysis of these microbial communities was done using Reny’s diversity profile, allowing for the ranking of microbial diversity across the three wetlands. Compositional diversity was investigated by community structural pattern, which was explored using Non-Metric Multidimensional Scaling.

Results and discussion

The study identified 299 methanogen and 65 methanotroph ASVs from nine samples across three wetlands. Freshwater ecosystems had the highest diversity and abundance of these communities, followed by sewage-fed and brackish water environments. Primers detected 4–49% of distinct ASVs, emphasizing the importance of primer selection in revealing unique taxa. Reny’s diversity profile ranked freshwater as the most diverse, followed by sewage-fed and brackish water wetland. In total, 11 methanogen and nine methanotroph genera were found, with primer-specific variation in their abundance. However, community compositions remained consistent across primers but varied across wetlands. Habitat-specific genera were identified in freshwater, brackish, and sewage-fed wetlands.

Conclusions

The study highlights the importance of primer selection for comprehensive microbial community profiling. It demonstrates that different wetland ecosystems harbour distinct methanogen and methanotroph communities, with freshwater habitats supporting the greatest diversity. These findings support the use of multiple primers for broad-spectrum microbial analysis across diverse ecosystems.