Abstract
Many microbes in complex competitive environments share genes for acquiring and utilising nutrients, questioning whether niche specialisation exists and if so, how it is maintained. We investigated the genomic signatures of niche specialisation in the rumen microbiome, a highly competitive, anaerobic environment, with limited nutrient availability determined by the biomass consumed by the host. We generated individual metagenomic libraries from 14 cows fed an ad libitum diet of grass silage and calculated functional isoform diversity for each microbial gene identified. The animal replicates were used to calculate confidence intervals to test for differences in diversity of functional isoforms between microbes that may drive niche specialisation. We identified 153 genes with significant differences in functional isoform diversity between the two most abundant bacterial genera in the rumen (Prevotella and Clostridium). We found Prevotella possesses a more diverse range of isoforms capable of degrading hemicellulose, whereas Clostridium for cellulose. Furthermore, significant differences were observed in key metabolic processes indicating that isoform diversity plays an important role in maintaining their niche specialisation. The methods presented represent a novel approach for untangling complex interactions between microorganisms in natural environments and have resulted in an expanded catalogue of gene targets central to rumen cellulosic biomass degradation.
Highlights
Recent metagenomic sequencing of natural environments has revealed that microbial communities act in different trophic levels (Lauro et al, 2009), exhibit successional change (Koenig et al, 2011; Teeling et al, 2012; Huws et al, 2016) and engage in fierce competition when resources are limited (Weckx et al, 2011)
Significant differences were observed in key metabolic processes indicating that isoform diversity plays an important role in maintaining their niche specialisation
Metabolic adaptations in Prevotella We found that Prevotella possess more diverse functional isoforms than Clostridium in genes involved in specific metabolic processes
Summary
Recent metagenomic sequencing of natural environments has revealed that microbial communities act in different trophic levels (Lauro et al, 2009), exhibit successional change (Koenig et al, 2011; Teeling et al, 2012; Huws et al, 2016) and engage in fierce competition when resources are limited (Weckx et al, 2011). This suggests that adaptation to specific niches must occur in microbial communities, demonstrating this in natural communities remains a challenge (Marco, 2008). Samples of enzymatic activity (Stewart, 1976; Nevo, 2001)
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