Comparative Analysis of Metagenomics and Metataxonomics for the Characterization of Vermicompost Microbiomes

Abstract

The study of microbial communities or microbiotas in animals and environments is important because of their impact in a broad range of industrial applications, diseases and ecological roles. High throughput sequencing (HTS) is the best strategy to characterize microbial composition and function. Microbial profiles can be obtained either by shotgun sequencing of genomes, or through amplicon sequencing of target genes (e.g., 16S rRNA for bacteria and ITS for fungi). Here, we compared both HTS approaches at assessing taxonomic and functional diversity of bacterial and fungal communities during vermicomposting of white grape marc. We applied specific HTS workflows to the same 12 microcosms, with and without earthworms, sampled at two distinct phases of the vermicomposting process occurring at 21 and 63 days. Metataxonomic profiles were inferred in DADA2, with bacterial metabolic pathways predicted via PICRUSt2. Metagenomic taxonomic profiles were inferred in PathoScope, while bacterial functional profiles were inferred in Humann2. Microbial profiles inferred by metagenomics and metataxonomics showed similarities and differences in composition, structure, and metabolic function at different taxonomic levels. Microbial composition and abundance estimated by both HTS approaches agreed reasonably well at the phylum level, but larger discrepancies were observed at lower taxonomic ranks. Shotgun HTS identified ~1.8 times more bacterial genera than 16S rRNA HTS, while ITS HTS identified two times more fungal genera than shotgun HTS. This is mainly a consequence of the difference in resolution and reference richness between amplicon and genome sequencing approaches and databases, respectively. Our study also revealed great differences and even opposite trends in alpha- and beta-diversity between amplicon and shotgun HTS. Interestingly, amplicon PICRUSt2-imputed functional repertoires overlapped ~50% with shotgun Humann2 profiles. Finally, both approaches indicated that although bacteria and fungi are the main drivers of biochemical decomposition, earthworms also play a key role in plant vermicomposting. In summary, our study highlights the strengths and weaknesses of metagenomics and metataxonomics and provides new insights on the vermicomposting of white grape marc. Since both approaches may target different biological aspects of the communities, combining them will provide a better understanding of the microbiotas under study.

Role of Vermicomposting Microorganisms in the Conversion of Biomass Ash to Bio-Based Fertilizers

“…X-axis represents biological replica samples for each species, which are K, T0, T1, T2, and T3. Y-axis represents the taxon abundan Some studies have suggested that worms may form a microbial bac subpopulation that reflects the composition of ingested food [26,40,41]. The dom bacterial phylum Bacterioids, Proteobacteria and Planctomycetota in samples T0, T1, T2 a were similar in non-worm-digested sample K. A decreasing trend was found i proportion of Bacterioids when comparing the pre-fermented treatment K and samp with T0, T2 and T3.…”

“…The fact that the g Flavomacterium, which is called an opportunistic pathogen in the Bacteriodata family prominent in treatment K and in sample T1 among all samples was throught to be a of the high temperature during composting and the inability to resist the alkalin value of BA for the pre-fermented treatment K. It can also be concluded that the a BA ratio for T1 is ideal to ensure P transformation during vermicomposting. It has reported that Chryseolinea bacteria play significant roles in nitrogen fixation as impo remineralizers that convert organic materials into micronutrients due to the re abundance of Chyophagales, which is determined as the dominant genus belonging Some studies have suggested that worms may form a microbial bacterial subpopulation that reflects the composition of ingested food [26,40,41]. The dominant bacterial phylum Bacterioids, Proteobacteria and Planctomycetota in samples T 0 , T 1 , T 2 and T 3 were similar in non-worm-digested sample K. A decreasing trend was found in the proportion of Bacterioids when comparing the pre-fermented treatment K and sample T 1 with T 0 , T 2 and T 3 .…”

Vermicomposting as a Valorization Solution to the Winery Sector By-Products

“…A compilation of the literature's findings, regarding vermicomposting studies on by-products from the vine and wine industry, is depicted in Table 2. While fungi and bacteria are the main agents behind biochemical decomposition, earthworms are essential to the process of plant vermicomposting [114] Spent grape marc Eisenia fetida (1000 individuals); 3 mos; One wood box Chemical analysis C:N ratio was higher in GMC than GMV; the pH was close to neutrality for both; the total Mg and P concentrations were similar; K concentration was higher for GMC, and the Ca concentration was higher for GMV [115] Nogales et al [25] conducted a study to evaluate the capacity of the earthworm species E. andrei to compost different winery wastes, including a mix between vine shoots and lees cake, into valuable agricultural products. After a 16-week study, the resulting vermicompost exhibited a lower C:N ratio, electrical conductivity, and phytotoxicity compared to initial substrates.…”

“…The work of Kolbe et al [108] reached similar results, obtaining a vermicompost from white grape marc after 91 days, rich in a stable bacterial community with functional properties beneficial for plant growth. Pérez-Losada et al [114] assessed the taxonomic and functional diversity of bacterial and fungal communities during the vermicomposting of white grape marc. The authors concluded that, although bacteria and fungi are the main agents behind biochemical decomposition, earthworms play an essential role in vermicomposting, as evidenced by their ability to accelerate decomposition and significantly modify the physical and microbiological properties of the substrate [114].…”

“…Pérez-Losada et al [114] assessed the taxonomic and functional diversity of bacterial and fungal communities during the vermicomposting of white grape marc. The authors concluded that, although bacteria and fungi are the main agents behind biochemical decomposition, earthworms play an essential role in vermicomposting, as evidenced by their ability to accelerate decomposition and significantly modify the physical and microbiological properties of the substrate [114]. Furthermore, Gómez Brandón et al [117] treated distilled grape marc through vermicomposting over 42 days, and the results showed significant changes in the bacterial community, accompanied by a two-fold increase in bacterial richness and diversity, both taxonomically and phylogenetically.…”