Livestock Manure Type Affects Microbial Community Composition and Assembly During Composting

Abstract

Composting is an environmentally friendly way to turn plant and animal wastes into organic fertilizers. However, it is unclear to what extent the source of animal waste products (such as manure) affects the physicochemical and microbiological properties of compost. Here, we experimentally tested how the type of livestock manure of herbivores (sheep and cattle) and omnivores (pig and chicken) influences the bacterial and fungal communities and physicochemical properties of compost. Higher pH, NO₃-N, Total carbon (TC) content and C/N were found in sheep and cattle manure composts, while higher EC, NH₄-N, Total nitrogen (TN) and total phosphorus (TP) content were measured in pig and chicken manure composts. Paired clustering between herbivore and omnivore manure compost metataxonomy composition was also observed at both initial and final phases of composting. Despite this clear clustering, all communities changed drastically during the composting leading to reduced bacterial and fungal diversity and large shifts in community composition and species dominance. While Proteobacteria and Chloroflexi were the major phyla in sheep and cattle manure composts, Firmicutes dominated in pig and chicken manure composts. Together, our results indicate that feeding habits of livestock can determine the biochemical and biological properties of manures, having predictable effects on microbial community composition and assembly during composting. Manure metataxonomy profiles could thus potentially be used to steer and manage composting processes.

Keywords: composting; feeding habit; livestock manures; microbial community; physicochemical properties.

FIGURE 1

Principal component analysis of the physicochemical compost properties at the initial (open symbols) and final (filled symbols) phases of composting. In panel (A), colors correspond to different types of manure used for composting. Panel (B) shows the contribution of each physiochemical property on the first two principal components in panel A that explained 81.3% of the total variation (54.8 and 26.5% for PC1 and PC2, respectively). Red dashed lines in panel (B) indicate the theoretical contribution of physicochemical properties. N = 3 for each type of manure compost.

FIGURE 2

Effect of composting on manure compost metataxonomy diversity and composition. Shannon diversity of bacterial (A) and fungal (B) communities. Bacterial (C) and fungal (D) community composition based on the principal coordinate analysis of unweighted UniFrac distance matrix. Colors correspond to different types of manure composts, and open and closed symbols represented initial and final phases of composting, respectively. N = 3 for each type of manure composts.

FIGURE 3

Effect of composting on manure compost metataxonomy at phyla and genera levels. The relative abundance of the dominant bacterial (A) and fungal (B) taxa at the phyla level in all manure compost treatments at the initial and final phases of the composting (based on OTUs of top 9 phyla). The relative abundance of the dominant bacterial (C) and fungal (D) taxa at the genera level (top 20 genera included). In all panels, colors correspond to relative abundance of different phyla or genera. N = 3 for each type of manure compost.

FIGURE 4

Correlations between physiochemical compost properties and microbial abundances based on redundancy analysis (RDA). Panels (A,B) show the relationship between bacterial and fungal genera with physicochemical composting properties (pH, EC, NH₄-N, NO₃-N, TC, TN, C/N, and TP) at the initial and final phases of composting. Panels (C,D) show the same relationship between fungal genera and physicochemical compost properties. In panels (A–D), red vectors show the genera with >2% relative abundance, while blue vectors show compost physicochemical properties. Panel (E) shows Spearman correlation analysis between bacterial and fungal genera and compost physicochemical properties, where r > 0 denotes for positive correlations (red) and r < 0 for negative correlation s (blue); *, **, and *** denote for P values lower than 0.05, 0.01, and 0.001, respectively. N = 3 for each type of manure compost.