BER launches Environmental System Science Program. Visit our new website under construction!

U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights


Sequencing FISH-Separated Microbes from Environmental Samples
Published: July 05, 2010
Posted: July 28, 2010

Most microbes found in environmental samples cannot be cultured in the laboratory making them very hard (or impossible) to study in detail and limiting their exploitation for DOE mission needs in energy, environmental remediation, and carbon cycling. One approach to overcoming this obstacle is to separate individual microbial cells from complex environmental samples using Fluorescence in situ Hybridization (FISH) and to study those with desired characteristics. The standard FISH protocol involved “fixing” cells with paraformaldehyde which complicated subsequent DNA sequencing. Researchers at DOE’s Joint Genome Institute have developed a new protocol that avoids the fixation step. Susan Yilmaz and her colleagues successfully used a variety of fluorescence probes to study freshly-collected, unfixed microbial samples from bioreactor sludge and the termite hind gut. These promising results constitute a significant technical advance for gaining access to otherwise hard to study microbes. The authors conclude: “This approach should facilitate subsequent genomic sequencing and analysis of targeted populations as DNA is not compromised by crosslinking during fixation”.

Reference: Yilmaz et al, The ISME Journal (27 May 2010)doi:10.1038/ismej.2010.73

Contact: Dan Drell, SC-23.2, (301) 903-4742
Topic Areas:

  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Microbes and Communities
  • Research Area: Sustainable Biofuels and Bioproducts
  • Research Area: DOE Joint Genome Institute (JGI)
  • Research Area: Research Technologies and Methodologies

Division: SC-33.2 Biological Systems Science Division, BER

 

BER supports basic research and scientific user facilities to advance DOE missions in energy and environment. More about BER

Recent Highlights

Jan 11, 2022
No Honor Among Copper Thieves
Findings provide a novel means to manipulate methanotrophs for a variety of environmental and in [more...]

Dec 06, 2021
New Genome Editing Tools Can Edit Within Microbial Communities
Two new technologies allow scientists to edit specific species and genes within complex laborato [more...]

Oct 27, 2021
Fungal Recyclers: Fungi Reuse Fire-Altered Organic Matter
Degrading pyrogenic (fire-affected) organic matter is an important ecosystem function of fungi i [more...]

Oct 19, 2021
Microbes Offer a Glimpse into the Future of Climate Change
Scientists identify key features in microbes that predict how warming affects carbon dioxide emi [more...]

Aug 25, 2021
Assessing the Production Cost and Carbon Footprint of a Promising Aviation Biofuel
Biomass-derived DMCO has the potential to serve as a low-carbon, high-performance jet fuel blend [more...]

List all highlights (possible long download time)