Semester

Fall

Date of Graduation

2012

Document Type

Thesis

Degree Type

MS

College

Davis College of Agriculture, Natural Resources and Design

Department

Horticulture

Committee Chair

Alan J Sexstone

Committee Co-Chair

Gary K Bissonnette

Committee Member

Eugene E Felton

Abstract

Rumens harbor diverse groups of microorganisms. These microorganisms help ruminants in efficient digestion of a wide variety of feed materials. Most of these microorganisms are anaerobic and work symbiotically with the host. The amount of microbial diversity depends on the types of substrates present in the feed. Although some of these microorganisms have been cultured and characterized, the majority of them are unknown because they are unculturable. With the development of molecular techniques such as Denaturing Gradient Gel Electrophoresis (DGGE), Temperature Gradient Gel Electrophoresis (TGGE), Automated Ribosomal Intergenic Spacer Analysis (ARISA), Restriction Fragment Length Polymorphism (RFLP), Terminal Restriction Fragment Length Polymorphism (TRFLP) etc., now it is possible to quantify existing rumen microbial diversity, even if the microorganisms are not culturable. Previous studies on rumen ecosystems have shown that microbial populations generally vary with diet. A majority of these studies emphasized changes in bacterial communities in relation to grain diets, and less emphasis was given to traditional pasture diets which provide the main cattle food in several developing countries, and also on effect of changes in diets on archaeal communities in the rumen ecosystem. To understand bacterial and archaeal diversity associated with different pasture diets, I amplified bacterial and archaeal 16S rRNA genes from rumen samples using a universal FAM labeled forward primer and a non-labeled reverse primer, and then these products were digested with different tetrameric restriction enzymes. T-RFLP profiles obtained from Hha I and Rsa I digested fragments from open canopy (OC) and wooded canopy (WC) pasture diets suggested that bacterial and archaeal community structures were not significantly different in these pasture diets and that harvest time of these diets had no effect on bacterial and archaeal community structure. T-RFLP profiles obtained from Hha I, Rsa I, and Hae III digested fragments from naturalized pasture early cut (NPEC), naturalized pasture late cut (NPLC), teff, and triticale diets showed highest bacterial and archaeal diversities in triticale and nplc diets respectively. Diet pairs npec-teff and nplc-triticale shared more bacterial and archaeal community, and bacterial and archaeal communities associated with diet pairs npec-nplc, npec-triticale, nplc-teff, and teff-triticale were significantly different. This study will help in better understanding of the microbial diversity in cattle which in turn will help in optimal utilization of a wide variety of feeds.

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