Biochar selectively enriches farm specific microbial species and supports niche differentiation in chicken manure across housing and feeding systems

Abstract Biochar is increasingly considered for treating chicken manure before residues are returned to farmland. It remains unclear whether biochar changes the whole manure-derived community or selectively enriches bacteria on its surface. This study investigated microbial community changes during 35 days of anaerobic incubation of manure from four broiler farms representing a 2 × 2 combination of feeding (probiotic or commercial feed) and housing (deep-litter or high-rise). Incubation was conducted with or without 10% (w/v) manure-derived biochar. Full-length Nanopore 16S rRNA gene sequencing characterised communities in fresh manure, post-incubation without biochar, and in biochar-liquid and biochar-solid fractions. Deep-litter manures were dominated by poultry lactobacilli (63.3–88.8%), whereas high-rise manures were rich in Proteobacteria (63.9–66.6%). During incubation, the liquid communities shifted towards Escherichia coli in three farms and Alcaligenes faecalis in the fourth. The mean between-farm Bray–Curtis dissimilarity fell from 0.86 to 0.61. Across all farms, the biochar-solid had lower relative abundance of E. coli and higher Shannon diversity than the adjacent liquid. One or two species were less abundant (≤3.5%) in that biochar-liquid but reached 14–51% on the biochar-solid. These dominant species varied among farms, and more than 98% of each biochar-solid community came from species detected in the same farm, including 18.5–58.8% from species present in its fresh manure. As each production system was represented by one farm, housing and feeding effects remain descriptive. Overall, biochar acted as a selective filter on farm-specific manure microbiomes. Recovered biochar therefore carries a farm-specific, manure-derived community and should be screened before land application.