Protein- and RNA-Enhanced Fermentation by Gut Microbiota of the Earthworm Lumbricus terrestris

Abstract

Earthworms are a dominant macrofauna in soil ecosystems and have determinative effects on soil fertility and plant growth. These invertebrates feed on ingested material, and gizzard-linked disruption of ingested fungal and bacterial cells is conceived to provide diverse biopolymers in the anoxic alimentary canals of earthworms. Fermentation in the gut is likely important to the utilization of ingested biopolymer-derived compounds by the earthworm. This study therefore examined the fermentative responses of gut content-associated microbes of the model earthworm Lumbricus terrestris to (i) microbial cell lysate (to simulate gizzard-disrupted cells) and (ii) dominant biopolymers of such biomass, protein, and RNA. The microbial cell lysate augmented the production of H2, CO2, and diverse fatty acids (e.g., formate, acetate, propionate, succinate, and butyrate) in anoxic gut content microcosms, indicating that the cell lysate triggered diverse fermentations. Protein and RNA also augmented diverse fermentations in anoxic microcosms of gut contents, each yielding a distinct product profile (e.g., RNA yielded H2 and succinate, whereas protein did not). The combined product profile of protein and RNA treatments was similar to that of cell lysate treatments, and 16S rRNA-based analyses indicated that many taxa that responded to cell lysate were similar to taxa that responded to protein or RNA. In particular, protein stimulated Peptostreptococcaceae, Clostridiaceae, and Fusobacteriaceae, whereas RNA stimulated Aeromonadaceae. These findings demonstrate the capacity of gut-associated obligate anaerobes and facultative aerobes to catalyze biopolymer-driven fermentations and highlight the potential importance of protein and RNA as substrates linked to the overall turnover dynamics of organic carbon in the alimentary canal of the earthworm.IMPORTANCE The subsurface lifestyle of earthworms makes them an unnoticed component of the terrestrial biosphere. However, the propensity of these invertebrates to consume their home, i.e., soil and litter, has long-term impacts on soil fertility, plant growth, and the cycling of elements. The alimentary canals of earthworms can contain up to 500 ml anoxic gut content per square meter of soil, and ingested soil may contain 109 or more microbial cells per gram dry weight, considerations that illustrate that enormous numbers of soil microbes are subject to anoxia during gut passage. Feeding introduces diverse sources of biopolymers to the gut, and the gut fermentation of biopolymers could be important to the transformation of matter by the earthworm and its capacity to utilize fermentation-derived fatty acids. Thus, this study examined the capacity of microbes in earthworm gut contents to ferment protein and RNA, dominant biopolymers of cells that become disrupted during gut passage.

Dietary polysaccharides: fermentation potentials of a primitive gut ecosystem

“…4). This finding is consistent with other studies that have indicated that this taxon is not responsive during gut content fermentation (Meier et al, 2018;Zeibich et al, 2018). This finding is consistent with other studies that have indicated that this taxon is not responsive during gut content fermentation (Meier et al, 2018;Zeibich et al, 2018).…”

“…S2A and Table S5). S3A) corroborated previous findings that revealed a positive response of these taxa to anoxia and endogenous gut nutrients (Zeibich et al, 2018(Zeibich et al, , 2019. S3A) corroborated previous findings that revealed a positive response of these taxa to anoxia and endogenous gut nutrients (Zeibich et al, 2018(Zeibich et al, , 2019.…”

“…In support of the hypothetical model (Fig. amino acid-driven fermentation is not integrated into the model (Zeibich et al, 2018)]. The experimental design did not simulate all in situ parameters of the gut, and the model (Fig.…”

“…Panel A. phylotypes that might have increased in abundance initially but returned to low abundance at the end of the incubation (Zeibich et al, 2018)] would have not been detected. Phylotypes are based on a sequence similarity cut-off of 97% and were considered to be stimulated when a phylotype in at least one of the supplemented treatments displayed a ≥ 4% higher relative abundance than in the control treatment at the end of incubation.…”

“…Gut contents were extracted as described (Zeibich et al, 2018). Three replicate microcosms per treatment were prepared in an O 2 -free chamber (100% N 2 [Mecaplex, Grenchen, Switzerland]).…”