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Profiling In Situ Microbial Community Structure with an Amplification Microarray.

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Title: Profiling In Situ Microbial Community Structure with an Amplification Microarray.
Authors: Chandler, Darrell P.1 dchandler@akonni.com, Knickerbocker, Christopher1, Bryant, Lexi1, Golova, Julia1, Wiles, Cory1, Williams, Kenneth H.2, Peacock, Aaron D.3, Long, Philip E.2
Source: Applied & Environmental Microbiology. Feb2013, Vol. 79 Issue 3, p799-807. 9p.
Subjects: Alkalinity, Shewanella, Flexibacter, Microbiological assay, Polymerase chain reaction
Abstract: The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(Vl) mobility under conditions of various alkalinities (as HCO,) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consis- tent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO3, but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications. [ABSTRACT FROM AUTHOR]
Copyright of Applied & Environmental Microbiology is the property of American Society for Microbiology and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
Database: Engineering Source
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DbLabel: Engineering Source
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PubType: Academic Journal
PubTypeId: academicJournal
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  Data: Profiling In Situ Microbial Community Structure with an Amplification Microarray.
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  Data: <searchLink fieldCode="AR" term="%22Chandler%2C+Darrell+P%2E%22">Chandler, Darrell P.</searchLink><relatesTo>1</relatesTo><i> dchandler@akonni.com</i><br /><searchLink fieldCode="AR" term="%22Knickerbocker%2C+Christopher%22">Knickerbocker, Christopher</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Bryant%2C+Lexi%22">Bryant, Lexi</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Golova%2C+Julia%22">Golova, Julia</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Wiles%2C+Cory%22">Wiles, Cory</searchLink><relatesTo>1</relatesTo><br /><searchLink fieldCode="AR" term="%22Williams%2C+Kenneth+H%2E%22">Williams, Kenneth H.</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22Peacock%2C+Aaron+D%2E%22">Peacock, Aaron D.</searchLink><relatesTo>3</relatesTo><br /><searchLink fieldCode="AR" term="%22Long%2C+Philip+E%2E%22">Long, Philip E.</searchLink><relatesTo>2</relatesTo>
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  Data: <searchLink fieldCode="JN" term="%22Applied+%26+Environmental+Microbiology%22">Applied & Environmental Microbiology</searchLink>. Feb2013, Vol. 79 Issue 3, p799-807. 9p.
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  Data: <searchLink fieldCode="DE" term="%22Alkalinity%22">Alkalinity</searchLink><br /><searchLink fieldCode="DE" term="%22Shewanella%22">Shewanella</searchLink><br /><searchLink fieldCode="DE" term="%22Flexibacter%22">Flexibacter</searchLink><br /><searchLink fieldCode="DE" term="%22Microbiological+assay%22">Microbiological assay</searchLink><br /><searchLink fieldCode="DE" term="%22Polymerase+chain+reaction%22">Polymerase chain reaction</searchLink>
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  Data: The objectives of this study were to unify amplification, labeling, and microarray hybridization chemistries within a single, closed microfluidic chamber (an amplification microarray) and verify technology performance on a series of groundwater samples from an in situ field experiment designed to compare U(Vl) mobility under conditions of various alkalinities (as HCO,) during stimulated microbial activity accompanying acetate amendment. Analytical limits of detection were between 2 and 200 cell equivalents of purified DNA. Amplification microarray signatures were well correlated with 16S rRNA-targeted quantitative PCR results and hybridization microarray signatures. The succession of the microbial community was evident with and consis- tent between the two microarray platforms. Amplification microarray analysis of acetate-treated groundwater showed elevated levels of iron-reducing bacteria (Flexibacter, Geobacter, Rhodoferax, and Shewanella) relative to the average background profile, as expected. Identical molecular signatures were evident in the transect treated with acetate plus NaHCO3, but at much lower signal intensities and with a much more rapid decline (to nondetection). Azoarcus, Thaurea, and Methylobacterium were responsive in the acetate-only transect but not in the presence of bicarbonate. Observed differences in microbial community composition or response to bicarbonate amendment likely had an effect on measured rates of U reduction, with higher rates probable in the part of the field experiment that was amended with bicarbonate. The simplification in microarray-based work flow is a significant technological advance toward entirely closed-amplicon microarray-based tests and is generally extensible to any number of environmental monitoring applications. [ABSTRACT FROM AUTHOR]
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  Data: <i>Copyright of Applied & Environmental Microbiology is the property of American Society for Microbiology and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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        Value: 10.1128/AEM.02664-12
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        Text: English
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        PageCount: 9
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        Type: general
      – SubjectFull: Shewanella
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      – SubjectFull: Flexibacter
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      – SubjectFull: Microbiological assay
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      – SubjectFull: Polymerase chain reaction
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      – TitleFull: Profiling In Situ Microbial Community Structure with an Amplification Microarray.
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              Text: Feb2013
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              Y: 2013
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