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Changes of rumen methanogen diversity associated with different types of forage and protein in diets
The objective of this study was to compare the methanogenic community and number in the rumen of dairy cows fed with different types of forage and protein in diet. Forty-eight healthy Chinese Holstein dairy cows were randomly assigned into three groups according to milk yield and day in milking. The diets in three treatments were as follows: MF (alfalfa and corn silage, soybean meal), CSA (corn stover, soybean meal), CSB (corn stover, cottonseed and rapeseed meal). The cows were fed with different diets (MF, CSA, CSB) for 91 days. Rumen fluid samples were collected before and after feeding using stomach-tube on d 91. Mothur software was used to assign clones to operational taxonomic units (OTUs) based on a 94% sequence identity cutoff. The results showed that the copy number of total methanogen of CSA was greater than that of CSB (P=0.049). However, there was no difference between CSA and MF (P=0.67). A total of 739 clones isolated from six methanogen mcrA gene clone libraries (samples from MF, CSA and CSB groups before or after feeding) were assigned to 25 species-level OTUs. The average OTU coverage of clone libraries was 96% (from 95% to 97.6%). Libshuff analysis showed methanogenic community of CSA and CSB, MF and CSA were different ( P=0.03 and P=0.04, respectively ). MF (2.08) and CSB (2.24) had lower diversity of methanogen based on Shannon index, compared with CSA (2.31). Additionally, Rumen cluster C (RCC, 73.2%) and Methanobacteriales (26.3%) were the predominant methanogenic archaea in the rumen. However, OTU10 were only found in CSA and CSB, and OTU20 only in MF. Meanwhile, OTU11 was only found in CSA and MF, while OTU21 only in CSB. Taxonomy analysis showed that OTU10, OTU20, OTU11 and OTU21 were closely related to Candidatus Methanomethylophilus alvus Mx1201 (83%), Thermoplasmatales archaeon BRNA (100%), Methanobrevibacter ruminantium M1 (94%) and Methanomassiliicoccus Luminyensis B10 (78%), respectively. In conclusion, soybean diet could promote the number of total methanogen and increase the diversity of methanogen compared with rapeseed diet in rumen, and the diet with corn straw had higher diversity than the alfalfa and corn silage diet.
Keywords: methanogen; forage; protein