Exploring the methanogen and bacterial communities of rumen environments: solid adherent, fluid and epimural

Abstract

The rumen microbiome occupies a central role in animal health and productivity. A better understanding of the rumen ecosystem is essential to increase productivity or decrease methane production. Samples were collected from the three main rumen environments: the solid-adherent fraction, the liquid fraction and the epithelium. For the liquid and solid fraction, two alternative sample processing protocols were compared, resulting in a total of five sample types: crude solids (S), the eluted solid-adherent fraction (Ad), free-living species in the crude rumen liquid (CRL), strained liquid samples (Lq) and epimural scrapings (Ep). The bacterial and methanogen communities of these sample types were analysed using 16S metabarcoding and qPCR. The results indicate that the liquid and solid-adherent environments are distinguished mainly by the differential abundance of specific taxonomic groups. Cellulolytic bacteria that pioneer biofilm formation, together with secondary colonisers are prevalent in solid-adherent samples, while dominant species in the fluid samples are primarily identified as consumers of soluble nutrients. Also, methanogen species are found to have a preference for either a solid-adherent or free-living occurrence. The epimural environment is characterised by a different microbial profile. Ten bacterial families and two methanogen genera are almost exclusively found in this environment.

Changes in the Solid-, Liquid-, and Epithelium-Associated Bacterial Communities in the Rumen of Hu Lambs in Response to Dietary Urea Supplementation

“…In addition, we found that Prevotella was the most abundant genus in the three fractions (Figures 2B, 3B, 4B). This result is consistent with findings regarding the rumen solid and liquid fractions of dairy cattle fed ryegrass or white clover (Bowen et al, 2018) and a TMR (forage:concentrate = 70:30, forage = prewilted grass and maize silage) (De Mulder et al, 2017) and the rumen contents and epithelium of dairy cattle fed a TMR (forage:concentrate = 55:45, forage = corn silage and corn stover) (Liu et al, 2016). Prevotella represents one of the most abundant genera in the rumen; this genus exhibits genetic and metabolic diversity (Bekele et al, 2010) and plays roles in carbohydrate utilization (Dehority, 1966;Cotta, 1992;Gardner et al, 1995;Kabel et al, 2011), nitrogen metabolism (Kim et al, 2017), and fiber degradation (Mayorga et al, 2016).…”

“…Desulfobulbus spp. participate in the reduction of sulfur compounds (Schären et al, 2017) and oxygen consumption (De Mulder et al, 2017), which are affected by the concentration of propionate (John Parkes and Graham Calder, 1985); these observations are consistent with the increased rumen concentration of propionate observed in the UC and LU treatments. These results indicate that the ureolytic and sulfur-reducing abilities of rumen bacteria may be affected when the nitrogen content is increased.…”

“…At the genus level, the present study found that the unclassified bacteria within the families Muribaculaceae and Lachnospiraceae, Christensenellaceae R7, Ruminococcaceae NK4A214, Lachnospiraceae NK3A20, Ruminococcaceae UCG 014, and Ruminococcus 2 were abundant in the solid and liquid fractions ( Table 4). These bacteria have also been observed in the solid and liquid fractions of dairy cattle (De Mulder et al, 2017;Schären et al, 2017) and yak (Ren et al, 2019). The bacteria within the family Muribaculaceae encode enzymes that degrade plant glycans (hemicellulose and pectin) and host-derived glycans; they also exhibit specificity in nitrogen utilization and harbor a specific urease (Ormerod et al, 2016;Lagkouvardos et al, 2019).…”

“…Recent studies indicate that the rumen microbial ecosystem is composed of three communities associated with different microenvironments: a solid-, a liquid-, and an epitheliumassociated bacterial community (Cho et al, 2006;Sadet et al, 2007;Liu et al, 2016;De Mulder et al, 2017;Schären et al, 2017). The solid-adherent bacteria play key roles in fiber digestion (McAllister et al, 1994).…”

“…The solid-adherent bacteria play key roles in fiber digestion (McAllister et al, 1994). The liquid-associated bacteria transmit bacteria from the solid-adherent biofilms to newly ingested feed (De Mulder et al, 2017). The epithelial community is diverse and distinct from the solid-and liquid-associated bacterial communities; it is associated with volatile fatty acid (VFA) fermentation, oxygen consumption, urea hydrolysis, and recycling of nitrogen and tissue Wallace et al, 1979).…”