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Related Concept Videos

Methods to Assess Microbial Communities01:19

Methods to Assess Microbial Communities

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Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Updated: May 3, 2026

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Quantitative microbial metatranscriptomics.

Scott Gifford1, Brandon Satinsky, Mary Ann Moran

  • 1Department of Marine Sciences, University of Georgia, Athens, GA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|February 12, 2014
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Summary
This summary is machine-generated.

Environmental RNA sequencing reveals microbial community activity. This protocol details sample collection, RNA processing, and bioinformatic analysis for accurate transcript quantification and ecological comparisons.

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Area of Science:

  • Microbiology
  • Environmental Science
  • Molecular Biology

Background:

  • Direct retrieval and sequencing of environmental RNA (eRNA) offers insights into microbial community functions.
  • Understanding in situ microbial activities is crucial for ecological and biogeochemical studies.

Purpose of the Study:

  • To present a comprehensive metatranscriptomic protocol for analyzing environmental RNA.
  • To enable the quantification of microbial gene expression in environmental samples.

Main Methods:

  • Detailed steps for environmental sample collection and processing.
  • Methods for ribosomal RNA (rRNA) depletion and messenger RNA (mRNA) amplification.
  • Techniques for complementary DNA (cDNA) synthesis and bioinformatic analysis.
  • Preparation and use of internal RNA standards for absolute transcript quantification.

Main Results:

  • The protocol facilitates the direct retrieval and sequencing of eRNA.
  • It allows for the accurate measurement of absolute transcript abundances.
  • Enables robust comparisons with biogeochemical and ecological data.

Conclusions:

  • This metatranscriptomic protocol provides a standardized approach for studying microbial activities.
  • Absolute quantification of transcripts enhances the ecological relevance of metatranscriptomic data.
  • The method supports a deeper understanding of microbial community functions in their natural environments.