Characterization and assembly dynamics of the microbiome associated with swine anaerobic lagoon manure treated with biochar

Authors: Frazier, Anthony; Willis, William; Robbe, Heather; Ortiz, Anna; Koziel, Jacek

Submitted to: Microorganisms
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/24/2025
Publication Date: 3/27/2025
Citation: Frazier, A.N., Willis, W.M., Robbe, H.A., Ortiz, A.C., Koziel, J.A. 2025. Characterization and assembly dynamics of the microbiome associated with swine anaerobic lagoon manure treated with biochar. Microorganisms. 13(4):758. https://doi.org/10.3390/microorganisms13040758.
DOI: https://doi.org/10.3390/microorganisms13040758

Interpretive Summary: The interest in the use of biochar in livestock and crop agriculture continues to grow. Biochar can reduce greenhouse gas and ammonia emissions from stored manure. While studies have investigated the effects of physicochemical properties of biochars on emissions mitigation, there has been little attention to how biochar treatment impacts the microbiome in manure. Herein, the scientists at ARS Bushland, Texas investigate the relationship between reduction in gaseous emissions and the microbial ecologies of swine manure treated with biochar. Results indicate temporal shifts in microbial diversity in treated and untreated manure. Further, we demonstrate that unique bacterial and archaeal features are enriched or depleted based on biochar treatment type. The results suggest that biochar treatment alters microbial ecology. The groundwork was laid for future studies in elucidating the mechanisms controlling microbial shifts due to biochar treatment and its subsequent role in mitigating greenhouse gas emissions and nutrient loss from stored manure.

Technical Abstract: Biochar (BC) has significant potential in the livestock and crop agriculture. Specifically, BC application presents a unique opportunity in reducing greenhouse gas (GHG) emissions and nutrient loss from stored manure. Importantly, the interactions between BC and manure microbiomes could hold important clues into the mechanisms of emission reduction. Therefore, a pilot study was designed to investigate the effect of BC application onto the surface of swine manure and the associated microbial communities. Samples were collected from four different treatment groups: control (n = 4), coarse BC (n = 4), fine BC (n = 4), and ultra fine BC (n = 4). Pooled samples were also collected for each treatment group (n = 4). Additionally, aged manure in bulk (AMB) was collected (n = 4) for a control comparison group. Samples were then subjected to 16S rRNA amplicon sequencing. Taxonomy and diversity analyses were conducted to characterize the microbiomes between the four BC treatments. Alpha diversity was significantly different between AMB samples and all treatment groups (Kruskal-Wallis; p < 0.05). Additionally, distinct community compositions were seen using both weighted and unweighted UniFrac distance matrices (PERMANOVA; p < 0.01). Multivariate dispersion analysis revealed non-significant differences (PERMANOVA; p > 0.05), indicating that observed differences were not due to within-group variability caused by dispersion. Thus, true community differences were seen between treatment groups and AMB. Differential abundance analysis (ANCOM-BC) revealed four distinct features within all treatment groups that were enriched (q < 0.001): Idiomarina spp., Geovibrio thiophilus, Parapusillimonas granuli, and an uncultured Gammaproteobacteria species. Similarly, Comamonas spp. and Brumimicrobium aurantiacum (q-value < 0.001) were significantly depleted by all the treatments. An uncultured Archaeal species was also significantly depleted by both the fine and ultra-fine treatments. The results of our study suggest distinct microbial ecologies between BC-treated manure and untreated groups. These results warrant further mechanistic investigation, especially into the release of main C- and N-containing gases of environmental concern.