Temporal dynamics of fibrolytic and methanogenic rumen microorganisms during in situ incubation of switchgrass determined by 16S rRNA gene profiling

Abstract

The rumen microbial ecosystem is known for its biomass-degrading and methane-producing phenotype. Fermentation of recalcitrant plant material, comprised of a multitude of interwoven fibers, necessitates the synergistic activity of diverse microbial taxonomic groups that inhabit the anaerobic rumen ecosystem. Although interspecies hydrogen (H2) transfer, a process during which bacterially generated H2 is transferred to methanogenic Archaea, has obtained significant attention over the last decades, the temporal variation of the different taxa involved in in situ biomass-degradation, H2 transfer and the methanogenesis process remains to be established. Here we investigated the temporal succession of microbial taxa and its effect on fiber composition during rumen incubation using 16S rRNA amplicon sequencing. Switchgrass filled nylon bags were placed in the rumen of a cannulated cow and collected at nine time points for DNA extraction and 16S pyrotag profiling. The microbial community colonizing the air-dried and non-incubated (0 h) switchgrass was dominated by members of the Bacilli (recruiting 63% of the pyrotag reads). During in situ incubation of the switchgrass, two major shifts in the community composition were observed: Bacilli were replaced within 30 min by members belonging to the Bacteroidia and Clostridia, which recruited 34 and 25% of the 16S rRNA reads generated, respectively. A second significant shift was observed after 16 h of rumen incubation, when members of the Spirochaetes and Fibrobacteria classes became more abundant in the fiber-adherent community. During the first 30 min of rumen incubation ~13% of the switchgrass dry matter was degraded, whereas little biomass degradation appeared to have occurred between 30 min and 4 h after the switchgrass was placed in the rumen. Interestingly, methanogenic members of the Euryarchaeota (i.e., Methanobacteria) increased up to 3-fold during this period of reduced biomass-degradation, with peak abundance just before rates of dry matter degradation increased again. We hypothesize that during this period microbial-mediated fibrolysis was temporarily inhibited until H2 was metabolized into CH4 by methanogens. Collectively, our results demonstrate the importance of inter-species interactions for the biomass-degrading and methane-producing phenotype of the rumen microbiome—both microbially facilitated processes with global significance.

Effect of dietary crude protein and forage contents on enteric methane emissions and nitrogen excretion from dairy cows simultaneously

“…However, it has been shown that, rather than the number, it is the distribution of different archaea species that drives the formation of CH 4 in the rumen (Morgavi et al 2010;Abecia et al 2012). The distribution of rumen bacteria and archaea species can be rapidly adapted according to the dynamics of rumen microorganisms determined by gene profiling (Piao et al 2014). In the present study, the enteric CH 4 emission measurements (416 AE 49 g/day; mean AE s.d.)…”

Live yeasts enhance fibre degradation in the cow rumen through an increase in plant substrate colonization by fibrolytic bacteria and fungi

“…In addition, from their in sacco data with switchgrass, Piao et al . () have suggested that early fermentation of soluble carbohydrates was likely to increase the H 2 partial pressure that may affect the activity of fibrolytic organisms. Moreover, the formation of multispecies consortia between fibrolytic and nonfibrolytic species may enhance degradation later in time (Shinkai et al .…”

“…Koike et al (2003) have suggested that it could be due to consumption of soluble carbohydrates by fibrolytic bacteria at the earliest phases of incubation, which could facilitate their growth, rather than rapid production of fibrolytic enzymes necessary for NDF digestion. In addition, from their in sacco data with switchgrass, Piao et al (2014) have suggested that early fermentation of soluble carbohydrates was likely to increase the H 2 partial pressure that may affect the activity of fibrolytic organisms. Moreover, the formation of multispecies consortia between fibrolytic and nonfibrolytic species may enhance degradation later in time (Shinkai et al 2010).…”

Invited review: Application of meta-omics to understand the dynamic nature of the rumen microbiome and how it responds to diet in ruminants

“…Bacteria preferentially attach to damaged sites on the plant surface, whereas fungi are able to physically disrupt the ingested material via rhizoidal growth. Microbial attachment is absolutely essential for the development of the complex microbial populations required for feed digestion in the rumen and occurs via a multistep process: (1) displacement of the epiphytic microbiome by rumen microbes (time <1 h), (2) establishment of a primary colonizing community of generalist microbes that primarily metabolize accessible carbohydrates (time 1 h to 4 h), (3) loss of some primary colonizers and selection of secondary colonizers specialized in digesting hemicellulose and cellulose (time > 4 h; Figure 2) (Piao et al, 2014;Huws et al, 2016;Mayorga et al, 2016). Within this community are taxa including Butyrivibrio, Fibrobacter, Olsenella and Prevotella that do not change significantly in abundance during primary and secondary colonization Liu et al, 2016).…”