Use of functional gene arrays for elucidating in situ biodegradation

Nostrand, Joy D.  Van; He, Zhili; Zhou, Jizhong

doi:10.3389/fmicb.2012.00339

Use of functional gene arrays for elucidating in situ biodegradation

Journal Article · Sat Dec 31 23:00:00 EST 2011 · Frontiers in Microbiology

DOI:https://doi.org/10.3389/fmicb.2012.00339· OSTI ID:1628069

Nostrand, Joy D. Van ^[1]; He, Zhili ^[2]; Zhou, Jizhong ^[2]

Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics; Univ. of Oklahoma, Norman, OK (United States). Dept. of Microbiology and Plant Biology; DOE/OSTI
Univ. of Oklahoma, Norman, OK (United States). Inst. for Environmental Genomics; Univ. of Oklahoma, Norman, OK (United States). Dept. of Microbiology and Plant Biology

Microarrays have revolutionized the study of microbiology by providing a high-throughput method for examining thousands of genes with a single test and overcome the limitations of many culture-independent approaches. Functional gene arrays (FGA) probe a wide range of genes involved in a variety of functions of interest to microbial ecology (e.g., carbon degradation, N fixation, metal resistance) from many different microorganisms, cultured and uncultured. The most comprehensive FGA to date is the GeoChip array, which targets tens of thousands of genes involved in the geochemical cycling of carbon, nitrogen, phosphorus, and sulfur, metal resistance and reduction, energy processing, antibiotic resistance and contaminant degradation as well as phylogenetic information (gyrB). Since the development of GeoChips, many studies have been performed using this FGA and have shown it to be a powerful tool for rapid, sensitive, and specific examination of microbial communities in a high-throughput manner. As such, the GeoChip is well-suited for linking geochemical processes with microbial community function and structure. This technology has been used successfully to examine microbial communities before, during, and after in situ bioremediation at a variety of contaminated sites. These studies have expanded our understanding of biodegradation and bioremediation processes and the associated microorganisms and environmental conditions responsible. This review provides an overview of FGA development with a focus on the GeoChip and highlights specific GeoChip studies involving in situ bioremediation.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1628069

Journal Information:: Frontiers in Microbiology, Journal Name: Frontiers in Microbiology Vol. 3; ISSN 1664-302X

Publisher:: Frontiers Research FoundationCopyright Statement

Country of Publication:: United States

Language:: English

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Research and Technological Advances Regarding the Study of the Spread of Antimicrobial Resistance Genes and Antimicrobial-Resistant Bacteria Related to Animal Husbandry Li, Na; Liu, Chong; Zhang, Zhiguo International Journal of Environmental Research and Public Health, Vol. 16, Issue 24 https://doi.org/10.3390/ijerph16244896	journal	December 2019

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59 BASIC BIOLOGICAL SCIENCES
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