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ARS Home » Midwest Area » Ames, Iowa » National Animal Disease Center » Food Safety and Enteric Pathogens Research » Research » Publications at this Location » Publication #211903
Title: IDENTIFYING MICROORGANISMS INVOLVED IN SPECIFIC IN SITU FUNCTIONS: EXPERIMENTAL DESIGN CONSIDERATIONS FOR RRNA GENE-BASED POPULATION STUDIES AND SEQUENCE-SELECTIVE PCR ASSAYS

Author
item BORNEMAN, JAMES - UNIV. OF CA-RIVERSIDE
item BECKER, J - UNIV. OF CA-RIVERSIDE
item BENT, ELIZABETH - UNIV. OF CA-RIVERSIDE
item LANOIL, BRIAN - UNIV. OF CA-RIVERSIDE
item GARDENER, BRIAN - OHIO STATE UNIV.
item OLATINWO, RABIU - UNIV. OF CA-RIVERSIDE
item PRESLEY, LAURA - UNIV. OF CA-RIVERSIDE
item Scupham, Alexandra
item VALINSKY, LEA - CENTRAL LAB, ISRAEL
item YIN, BEI - UNIV. OF CA-RIVERSIDE

Submitted to: Manual of Environmental Microbiology
Publication Type: Book / Chapter
Publication Acceptance Date: 1/17/2006
Publication Date: 5/16/2007
Citation: Borneman, J., Becker, J.O., Bent, E., Lanoil, B., Gardener, B.M., Olatinwo, R., Presley, L., Scupham, A.J., Valinsky, L., Yin, B. 2007. Identifying microorganisms involved in specific in situ functions: experimental design considerations for rRNA gene-based population studies and sequence-selective PCR assays. In: Hurst, C.J. editor. Manual of Environmental Microbiology. 3rd edition. Washington, D.C.: ASM Press. p.748-757.

Interpretive Summary: Ecological studies have three general purposes: to identify the constituents in a population, determine individual species roles in the ecosystem and examine interspecies interactions. The field of microbial ecology has benefited greatly from recent development of molecular methods such as 16S ribosomal sequencing for phylogenetic studies and microarrays. Most microbial ecology studies to date, however, have focused primarily on community descriptions and examination of the physiology of cultured species. Understanding the roles of individual microbial species and how species interactions affect microbial community functions is an area that is only recently being investigated, but is essential for studies in health, agriculture and bioengineering. This chapter discusses methods and experimental design considerations for in situ microbial functionality studies.

Technical Abstract: This chapter examines experimental design considerations for a population-based approach for identifying microorganisms involved in specific in situ functions. Here, the term function is used in its broadest sense, and may refer to any number of defined biochemical, physiological or ecological phenomena. Although this chapter focuses on a particular population-based approach, many of the experimental design considerations apply to a wide range of rRNA gene-based population studies and sequence-selective PCR assays.