Comparison of Rumen and Manure Microbiomes and Implications for the Inoculation of Anaerobic Digesters

Abstract

Cattle manure is frequently used as an inoculum for the start-up of agricultural biogas plants or as a co-substrate in the anaerobic digestion of lignocellulosic feedstock. Ruminal microbiota are considered to be effective plant fiber degraders, but the microbes contained in manure do not necessarily reflect the rumen microbiome. The aim of this study was to compare the microbial community composition of cow rumen and manure with respect to plant fiber-digesting microbes. Bacterial and methanogenic communities of rumen and manure samples were examined by 454 amplicon sequencing of bacterial 16S rRNA genes and mcrA genes, respectively. Rumen fluid samples were dominated by Prevotellaceae (29%), whereas Ruminococcaceae was the most abundant family in the manure samples (31%). Fibrobacteraceae (12%) and Bacteroidaceae (13%) were the second most abundant families in rumen fluid and manure, respectively. The high abundances of fiber-degrading bacteria belonging to Prevotellaceae and Fibrobacteraceae might explain the better performance of anaerobic digesters inoculated with rumen fluid. Members of the genus Methanobrevibacter were the predominant methanogens in the rumen fluid, whereas methanogenic communities of the manure samples were dominated by the candidate genus Methanoplasma. Our results suggest that inoculation or bioaugmentation with fiber-digesting rumen microbiota can enhance the anaerobic digestion of lignocellulosic biomass.

Increase of Silica Recovery by Lignocellulose-degrading Enzyme Complex from Cow Rumen Fluid in a Reactive Extraction of Oryza sativa L. Husk

“…This results also implied that the rumen fluid had specialized enzymes secreted by the indigenous microorganisms for lignocellulose degradation, the presence of this microbial community have been detected through several modern molecular techniques [29]. Several investigations in the potential microorganism of rumen fluid were carried out, a significant reduction in content was achieved on cellulose in 72 h treatment as much as 23%, and it was found that the dominated microorganism was Firmicutes, and this particular group of bacteria are the potential cellulase producer [30], [31].…”

Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community

“…The four bacteria families (Bacteroidaceae, Prevotellaceae, Ruminococcaceae, and Clostridiaceae) dominated in the yak fecal microbiome have also been detected as the main producers for CAZymes in the cattle rumen microbiome [26]. However, the Fibrobacteres bacteria, which are important degraders of cellulose and are often highly abundant in the bovine rumen [31,32], were found to be lowly abundant in the yak fecal microbiome (Additional le 3). Besides, Paenibacillaceae within the class Bacilli was the third abundant population among all microbial producers contributing to the PL-encoding genes in the fecal microbiome of yak.…”

Metagenomic insights into the diversity of carbohydrate-degrading enzymes in the yak fecal microbial community

“…The four bacteria families (Bacteroidaceae, Prevotellaceae, Ruminococcaceae, and Clostridiaceae) dominated in the yak fecal microbiome have also been detected as the main producers for CAZymes in the cattle rumen microbiome [26]. However, the Fibrobacteres bacteria, which are important degraders of cellulose and are often highly abundant in the bovine rumen [31,32], were found to be lowly abundant in the yak fecal microbiome (Additional le 3). Besides, Paenibacillaceae within the class Bacilli was the third abundant population among all microbial producers contributing to the PLencoding genes in the fecal microbiome of yak.…”