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Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics

Analyzing Gene Expression from Marine Microbial Communities using Environmental Transcriptomics

Published on: February 18, 2009

Optimization of whole-transcriptome amplification from low cell density deep-sea microbial samples for

Jieying Wu¹, Weimin Gao, Weiwen Zhang

¹Center for Biosignatures Discovery Automation, The Biodesign Institute, Arizona State University, Tempe, AZ 85287-6501, USA.

Journal of Microbiological Methods

|November 4, 2010

Summary

This study developed a robust protocol for whole-transcriptome amplification of challenging deep-sea microbial samples. The optimized method enables accurate analysis of microbial gene expression and community function in extreme environments.

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Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Purifying the Impure: Sequencing Metagenomes and Metatranscriptomes from Complex Animal-associated Samples

Published on: December 22, 2014

Area of Science:

Microbiology
Molecular Biology
Bioinformatics

Background:

Metatranscriptomics is crucial for understanding microbial communities but limited by sample quality and quantity.
Deep-sea microbes present unique challenges due to low cell density and high impurity.

Purpose of the Study:

To evaluate and identify the best whole-transcriptome amplification method for deep-sea microbial samples.
To develop a comprehensive protocol for isolating and amplifying RNA from these challenging environments.

Main Methods:

A modified RNA isolation combining Trizol and RNeasy methods.
Whole-transcriptome amplification using WT-Ovation™ Pico RNA Amplification System.
Conversion to double-strand DNA with WT-Ovation™ Exon Module.
Sequencing via random clone libraries and Roche GS FLX Titanium.

Main Results:

The developed protocol successfully amplified RNA from low-biomass, high-impurity deep-sea samples.
Sequencing confirmed the dominance of marine-based sequences, aligning with sample origin.
Preliminary metatranscriptomic data exhibited good sequencing quality.

Conclusions:

The established protocol is effective for deep-sea microbial metatranscriptomics.
This method is adaptable for studying microbial communities in other extreme environments.