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Activity-Informed Network Analysis Reveals Keystone Microbes Shaping Freshwater Ecosystem Function.

Qiyao Yang1,2,3, Rosa Aghdam1, Patricia Q Tran4

  • 1Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, Wisconsin, USA.

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Summary
This summary is machine-generated.

Freshwater microbial communities show that abundance doesn't equal activity. Combining genomic and transcriptomic data reveals context-dependent keystone species, highlighting the importance of both abundance and transcriptional activity for ecological relevance.

Keywords:
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Area of Science:

  • Microbial ecology
  • Freshwater ecosystem dynamics
  • Metagenomics and metatranscriptomics

Background:

  • Freshwater lakes exhibit dynamic oxygen conditions influencing microbial communities.
  • Abundance metrics alone are insufficient for identifying ecologically active keystone species.
  • Previous studies have not analyzed microbial network activity in relation to oxygen gradients across depths.

Purpose of the Study:

  • To investigate how shifting oxygen conditions affect microbial community structure and activity at the network level.
  • To identify keystone taxa in freshwater ecosystems by integrating metagenomic and metatranscriptomic data.
  • To assess the reliability of ecological centrality metrics for keystone species identification.

Main Methods:

  • Leveraged metagenome-assembled genomes and metatranscriptomic data.
  • Employed SPIEC-EASI and CARlasso for mapping microbial associations.
  • Utilized permutation-based analyses to validate keystone identification robustness.

Main Results:

  • Ecological centrality of taxa is context-dependent.
  • Many species abundant but not transcriptionally active were misidentified as keystone.
  • Members of Bacteroidota and other lineages were confirmed as keystone taxa when considering both abundance and activity.

Conclusions:

  • Integrating metagenomic and metatranscriptomic approaches is crucial for accurate keystone species identification.
  • Abundance-based identification can be misleading; transcriptional activity provides functional relevance.
  • This study provides a framework for future microbial ecology research in freshwater environments.