Abstract
Strategic enrichment of microcosms derived from wood foragers can facilitate the discovery of key microbes that produce enzymes for the bioconversion of plant fiber (i.e., lignocellulose) into valuable chemicals and energy. In this study, lignocellulose-degrading microorganisms from the digestive systems of Canadian beaver (Castor canadensis) and North American moose (Alces americanus) were enriched under methanogenic conditions for over 3 years using various wood-derived substrates, including (i) cellulose (C), (ii) cellulose + lignosulphonate (CL), (iii) cellulose + tannic acid (CT), and (iv) poplar hydrolysate (PH). Substantial improvement in the conversion of amended organic substrates into biogas was observed in both beaver dropping and moose rumen enrichment cultures over the enrichment phases (up to 0.36–0.68 ml biogas/mg COD added), except for enrichments amended with tannic acid where conversion was approximately 0.15 ml biogas/mg COD added. Multiplex-pyrosequencing of 16S rRNA genes revealed systematic shifts in the population of Firmicutes, Bacteroidetes, Chlorobi, Spirochaetes, Chloroflexi, and Elusimicrobia in response to the enrichment. These shifts were predominantly substrate driven, not inoculum driven, as revealed by both UPGMA clustering pattern and OTU distribution. Additionally, the relative abundance of multiple OTUs from poorly defined taxonomic lineages increased from less than 1% to 25–50% in microcosms amended with lignocellulosic substrates, including OTUs from classes SJA-28, Endomicrobia, orders Bacteroidales, OPB54, and family Lachnospiraceae. This study provides the first direct comparison of shifts in microbial communities that occurred in different environmental samples in response to multiple relevant lignocellulosic carbon sources, and demonstrates the potential of enrichment to increase the abundance of key lignocellulolytic microorganisms and encoded activities.
Highlights
Lignocellulose in agricultural and forest residues, as well as energy crops, is considered as an important renewable resource for the production of bioenergy, liquid biofuels, and specialty chemicals
Anaerobic enrichments were established and methanogenic activity was sustained over 10 feedings for 3 years on four different lignocellulosic substrate mixes (Supplementary Table S2)
The average volumes of biogas produced per amount of COD added decreased initially and increased by the ninth growth phase, suggesting acclimatization to each lignocellulosic carbon source by 154– 171 weeks of enrichment (Figure 1, Supplementary Table S3)
Summary
Lignocellulose in agricultural and forest residues, as well as energy crops, is considered as an important renewable resource for the production of bioenergy, liquid biofuels, and specialty chemicals. Metagenomic analysis of microbial communities that degrade lignocellulose has been motivated by decreasing DNA sequencing costs, along with the rich repertoire of CAZymes encoded by gut microflora. We directly compared shifts in microbial profiles that result from long-term enrichment (>3 years) of digestive microflora from the Canadian beaver and North American moose, on four lignocellulosic carbon sources: C, CT, CL, and PH. These amendments represented increasingly complex and potentially inhibitory carbon sources. Aside from monitoring metabolic activities through biogas yield from each enrichment, pyrotag sequencing was performed to characterize shifts in microbial communities that would suggest specialization and expression of distinct lignocellulolytic activities
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