Microbial diversity in rumen ecosystem of lactating cows grazing different levels of highly digestible persian clover

Abstract

16S rDNA clone libraries were analysed to investigate the microbial diversity in rumen contents taken at 6.30 a.m. and 7.00 p.m. from two lactating cows grazing either medium (MA) or high (HA) levels of highly digestible Persian clover. Ruminal pH was 6.4 and 5.7 for the MA cow and 6.4 and 5.2 for the HA cow at 6.30 a.m. and 7.00 p.m. respectively. Total genomic DNA was extracted from samples of ruminal content, and used for Amplified Ribosomal DNA Restriction Analysis (ARDRA) to examine the microbial diversity present in each sample. No less than 36 different ARDRA profiles were obtained from 120 clones from 4 libraries. However, only 2 of these ARDRA profiles were found to occur in all samples (designated A and B, with 49 clones). Clones obtained from HA cow had the diversity of 0.40 and 0.43 at 6.30 a.m. and 7.00 p.m. respectively and appeared to be lower than that of the clones obtained from MA cow which were 0.56 and 0.60 at 6.30 a.m. and 7.00 p.m. respectively. Distinct differences in microbial community structure were found in all samples of two cows. Using a Dice similarity coefficient of 0.60, the ARDRA profiles can be separated into 2 major clusters. The first cluster includes the ARDRA profiles A and B, representing about 63.3% and 36.6% of the total clones analysed at 6.30 a.m. and 7.00 p.m. respectively, in HA cow; and 33.3% and 29.9% at 6.30 a.m. and 7.00 p.m. respectively, in the MA cow. The second cluster is comprised mainly of single clones representing a unique ARDRA profile, and the profiles obtained are distinctly different between low and high pH samples from both cows. Further work needs to be done on clones selected from the dendrogram distribution to sequence the rDNA and determine their phylogenetic affiliation.