Distribution and diversity of members of the bacterial phylum Fibrobacteres in environments where cellulose degradation occurs

Abstract

The Fibrobacteres phylum contains two described species, Fibrobacter succinogenes and Fibrobacter intestinalis, both of which are prolific degraders of cellulosic plant biomass in the herbivore gut. However, recent 16S rRNA gene sequencing studies have identified novel Fibrobacteres in landfill sites, freshwater lakes and the termite hindgut, suggesting that members of the Fibrobacteres occupy a broader ecological range than previously appreciated. In this study, the ecology and diversity of Fibrobacteres was evaluated in 64 samples from contrasting environments where cellulose degradation occurred. Fibrobacters were detected in 23 of the 64 samples using Fibrobacter genus-specific 16S rRNA gene PCR, which provided their first targeted detection in marine and estuarine sediments, cryoconite from Arctic glaciers, as well as a broader range of environmental samples. To determine the phylogenetic diversity of the Fibrobacteres phylum, Fibrobacter-specific 16S rRNA gene clone libraries derived from 17 samples were sequenced (384 clones) and compared with all available Fibrobacteres sequences in the Ribosomal Database Project repository. Phylogenetic analysis revealed 63 lineages of Fibrobacteres (95% OTUs), with many representing as yet unclassified species. Of these, 24 OTUs were exclusively comprised of fibrobacters derived from environmental (non-gut) samples, 17 were exclusive to the mammalian gut, 15 to the termite hindgut, and 7 comprised both environmental and mammalian strains, thus establishing Fibrobacter spp. as indigenous members of microbial communities beyond the gut ecosystem. The data highlighted significant taxonomic and ecological diversity within the Fibrobacteres, a phylum circumscribed by potent cellulolytic activity, suggesting considerable functional importance in the conversion of lignocellulosic biomass in the biosphere.

Characteristics and Functions of the Rumen Microbial Community of Cattle-Yak at Different Ages

“…Some studies have reported that F. succinogenes is the most highly represented of these species [17,30], while others have shown that R. albus is more abundant [31,32]. F. succinogenes functions in the degradation of plant cellulose [33][34][35]; we found here that F. succinogenes was the predominant species in the rumen of adult cattle-yaks whereas R. albus was the least abundant, which may be related to the grazing state of cattle-yaks in the plateau and long-term natural foraging behavior.…”

Fibrobacter communities in the gastrointestinal tracts of diverse hindgut‐fermenting herbivores are distinct from those of the rumen

“…Although the first isolates of Fibrobacter were reported over 65 years ago (Hungate, 1950), cultured representatives for much of the apparent phylogenetic diversity of this group are lacking (Amann et al, 1992;Jewell et al, 2013;Ransom-Jones et al, 2014). As a result, knowledge regarding their ecology and physiology is limited.…”

“…Currently, there are only two formally described species for the genus Fibrobacter: F. succinogenes and F. intestinalis (Amann et al, 1992;Ransom-Jones et al, 2012). Phylogenetic analysis based on full-length 16S rRNA gene sequences of all of the available isolates from these two species groups indicates that there are at least four distinct phylogenetic lineages of F. succinogenes (Amann et al, 1992;Shinkai et al, 2009), but culture-independent analyses suggest that this represents only a fraction of the true diversity in the F. succinogenes group (Jewell et al, 2013;Ransom-Jones et al, 2014). Similarly, poor cultural representation almost certainly exists for F. intestinalis, since fewer representative isolates have been described.…”

Molecular investigation of Australian termites and their gut symbionts

“…Members of the Fibrobacteres are best known for their ability to hydrolyse plant polymers in anoxic habitats such as the bovine rumen (Suen et al, 2011;Jewell et al, 2013;Ransom-Jones et al, 2014) and termite gut (Warnecke et al, 2007;. Therefore, we began by identifying genes encoding glycoside hydrolases (GHs) classified according to the CAZy database .…”

“…Fibrobacter currently comprises two species, F. succinogenes isolated from a cow rumen (Hungate, 1950) and F. intestinalis isolated from a rat cecum (Montgomery and Macy, 1982), of which the former has a publicly available genome sequence (Suen et al, 2011). Both species are primary degraders of cellulosic plant biomass in herbivore guts (Hungate, 1950;Montgomery et al, 1988), which has prompted the suggestion that cellulose degradation may be a unifying feature of the phylum (Ransom- Jones et al, 2012;Ransom-Jones et al, 2014). This is supported by culture-independent 16S rRNA-based environmental surveys identifying relatively high numbers of diverse members of the Fibrobacteres in cellulolytic ecosystems (Ransom-Jones et al, 2012;Ransom-Jones et al, 2014).…”