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Critical evaluation of solid waste sample processing for DNA-based microbial community analysis

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dc.contributor.author Staley B.F.
dc.contributor.author Saikaly P.E.
dc.contributor.author de los Reyes III F.L.
dc.contributor.author Barlaz M.A.
dc.contributor.editor
dc.date 2011
dc.date.accessioned 2017-10-04T11:04:33Z
dc.date.available 2017-10-04T11:04:33Z
dc.date.issued 2011
dc.identifier 10.1007/s10532-010-9387-3
dc.identifier.issn 9239820
dc.identifier.uri http://hdl.handle.net/10938/13678
dc.description.abstract Landfills represent a unique microbial ecosystem and play a significant role in global biogeochemical processes. The study of complex ecosystems such as landfills using DNA-based techniques can be advantageous since they allow for analysis of uncultured organisms and offer higher resolution in measuring demographic and metabolic (functional) diversity. However, sample acquisition and processing from refuse is challenging due to material heterogeneity. Decomposed refuse was used to evaluate the effect of seven sample processing methods on Bacteria and Archaea community structure using T-RFLP. Bias was assessed using measured richness and by comparing community structure using multi-dimensional scaling (MDS). Generally, direct methods were found to be most biased while indirect methods (i. e., removal of cellular material from the refuse matrix before DNA extraction) were least biased. An indirect method using PO4 buffer gave consistently high bacterial and archaeal richness and also resulted in 28 and 34percent recovery of R. albus and M. formicicum spiked into refuse, respectively. However, the highest recovery of less abundant T-RFs was achieved using multiple processing methods. Results indicate differences in measured T-RF diversity from studies of landfill ecosystems could be caused by methodological (i. e., processing method) variation rather than refuse heterogeneity or true divergence in community structure. © 2010 Springer Science+Business Media B.V.
dc.format.extent
dc.format.extent Pages: (189-204)
dc.language English
dc.publisher NEW YORK
dc.relation.ispartof Publication Name: Biodegradation; Publication Year: 2011; Volume: 22; no. 1; Pages: (189-204);
dc.source Scopus
dc.title Critical evaluation of solid waste sample processing for DNA-based microbial community analysis
dc.type Article
dc.contributor.affiliation Staley, B.F., Environmental Research and Education Foundation, 3301 Benson Drive, Suite 301, Raleigh, NC 27609, United States
dc.contributor.affiliation Saikaly, P.E., Department of Civil and Environmental Engineering, American University of Beirut, Beirut, Lebanon
dc.contributor.affiliation de los Reyes III, F.L., Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC, United States
dc.contributor.affiliation Barlaz, M.A., Department of Civil, Construction, and Environmental Engineering, North Carolina State University, Raleigh, NC, United States
dc.contributor.authorAddress Staley, B. F.; Environmental Research and Education Foundation, 3301 Benson Drive, Suite 301, Raleigh, NC 27609, United States; email: bstaley@erefdn.org
dc.contributor.authorCorporate University: American University of Beirut; Faculty: Faculty of Engineering and Architecture; Department: Civil and Environmental Engineering;
dc.contributor.authorDepartment Civil and Environmental Engineering
dc.contributor.authorDivision
dc.contributor.authorEmail bstaley@erefdn.org
dc.contributor.authorFaculty Faculty of Engineering and Architecture
dc.contributor.authorInitials Staley, BF
dc.contributor.authorInitials Saikaly, PE
dc.contributor.authorInitials de los Reyes, FL
dc.contributor.authorInitials Barlaz, MA
dc.contributor.authorOrcidID
dc.contributor.authorReprintAddress Staley, BF (reprint author), Environm Res and Educ Fdn, 3301 Benson Dr,Suite 301, Raleigh, NC 27609 USA.
dc.contributor.authorResearcherID Saikaly, Pascal-G-7958-2014
dc.contributor.authorUniversity American University of Beirut
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dc.description.citedCount 4
dc.description.citedTotWOSCount 3
dc.description.citedWOSCount 3
dc.format.extentCount 16
dc.identifier.articleNo
dc.identifier.coden BIODE
dc.identifier.pubmedID 20652623
dc.identifier.scopusID 78650523052
dc.publisher.address 233 SPRING ST, NEW YORK, NY 10013 USA
dc.relation.ispartOfISOAbbr Biodegradation
dc.relation.ispartOfIssue 1
dc.relation.ispartofPubTitle Biodegradation
dc.relation.ispartofPubTitleAbbr Biodegradation
dc.relation.ispartOfVolume 22
dc.source.ID WOS:000286504100018
dc.type.publication Journal
dc.subject.otherAuthKeyword Bias
dc.subject.otherAuthKeyword Landfill
dc.subject.otherAuthKeyword Refuse
dc.subject.otherAuthKeyword Sample processing
dc.subject.otherAuthKeyword Solid waste
dc.subject.otherAuthKeyword T-RFLP
dc.subject.otherChemCAS DNA, Archaeal
dc.subject.otherChemCAS DNA, Bacterial
dc.subject.otherIndex Archaea
dc.subject.otherIndex Archaeal
dc.subject.otherIndex Bias
dc.subject.otherIndex Biogeochemical process
dc.subject.otherIndex Cellular material
dc.subject.otherIndex Community structures
dc.subject.otherIndex Critical evaluation
dc.subject.otherIndex Direct method
dc.subject.otherIndex DNA extraction
dc.subject.otherIndex Higher resolution
dc.subject.otherIndex Indirect methods
dc.subject.otherIndex Material heterogeneity
dc.subject.otherIndex matrix
dc.subject.otherIndex Microbial community analysis
dc.subject.otherIndex Microbial eco system
dc.subject.otherIndex Multi-dimensional scaling
dc.subject.otherIndex Multiple processing
dc.subject.otherIndex Processing method
dc.subject.otherIndex Refuse
dc.subject.otherIndex Sample processing
dc.subject.otherIndex T-RFLP
dc.subject.otherIndex Waste samples
dc.subject.otherIndex Analytical geochemistry
dc.subject.otherIndex Bacteriology
dc.subject.otherIndex DNA
dc.subject.otherIndex Ecosystems
dc.subject.otherIndex Processing
dc.subject.otherIndex Social sciences
dc.subject.otherIndex Solid wastes
dc.subject.otherIndex Waste disposal
dc.subject.otherIndex Land fill
dc.subject.otherIndex archaeal DNA
dc.subject.otherIndex bacterial DNA
dc.subject.otherIndex bacterium
dc.subject.otherIndex community structure
dc.subject.otherIndex heterogeneity
dc.subject.otherIndex landfill
dc.subject.otherIndex microbial community
dc.subject.otherIndex polymorphism
dc.subject.otherIndex sampling
dc.subject.otherIndex solid waste
dc.subject.otherIndex species diversity
dc.subject.otherIndex archaebacterium
dc.subject.otherIndex article
dc.subject.otherIndex bacterium
dc.subject.otherIndex bioremediation
dc.subject.otherIndex evaluation
dc.subject.otherIndex genetics
dc.subject.otherIndex isolation and purification
dc.subject.otherIndex metabolism
dc.subject.otherIndex methodology
dc.subject.otherIndex restriction fragment length polymorphism
dc.subject.otherIndex waste disposal
dc.subject.otherIndex Archaea
dc.subject.otherIndex Bacteria
dc.subject.otherIndex Biodegradation, Environmental
dc.subject.otherIndex DNA, Archaeal
dc.subject.otherIndex DNA, Bacterial
dc.subject.otherIndex Polymorphism, Restriction Fragment Length
dc.subject.otherIndex Refuse Disposal
dc.subject.otherIndex Archaea
dc.subject.otherIndex Bacteria (microorganisms)
dc.subject.otherKeywordPlus FRAGMENT-LENGTH-POLYMORPHISMS
dc.subject.otherKeywordPlus IN-SITU HYBRIDIZATION
dc.subject.otherKeywordPlus RIBOSOMAL-RNA GENES
dc.subject.otherKeywordPlus BACTERIAL COMMUNITIES
dc.subject.otherKeywordPlus RUMINAL DIGESTA
dc.subject.otherKeywordPlus RUMEN BACTERIA
dc.subject.otherKeywordPlus BOVINE RUMEN
dc.subject.otherKeywordPlus METHANOGENIC ARCHAEA
dc.subject.otherKeywordPlus CHEMICAL-COMPOSITION
dc.subject.otherKeywordPlus PURIFICATION METHODS
dc.subject.otherWOS Biotechnology and Applied Microbiology
dc.identifier.doi http://dx.doi.org/10.1007/s10532-010-9387-3


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