Biochar alters the soil microbiome and soil function: results of next‐generation amplicon sequencing across Europe

Abstract

Wide-scale application of biochar to soil has been suggested as a mechanism to offset increases in CO 2 emissions through the long-term sequestration of a carbon rich and inert substance to the soil, but the implications of this for soil diversity and function remain to be determined. Biochar is capable of inducing changes in soil bacterial communities, but the exact impacts of its application are poorly understood. Using three European sites [UK SRC, short rotation coppice, French grassland (FR) and Italian SRF, short rotation forestry (IT)] treated with identical biochar applications, we undertook 16S and ITS amplicon DNA sequencing. In addition, we carried out assessments of community change over time and N and P mobilization in the UK. Significant changes in bacterial and community structure occurred due to treatment, although the nature of the changes varied by site. STAMP differential abundance analysis showed enrichment of Gemmatimonadete and Acidobacteria in UK biochar plots 1 year after application, whilst control plots exhibited enriched Gemmataceae, Isosphaeraceae and Koribacteraceae. Increased mobility of ammonium and phosphates was also detected after 1 year, coupled with a shift from acid to alkaline phosphomonoesterase activity, which may suggest an ecological and functional shift towards a more copiotrophic ecology. Italy also exhibited enrichments, in both the Proteobacteria (driven by an increase in the order Rhizobiales) and the Gemmatimonadetes. No significant change in the abundance of individual taxa was noted in FR, although a small significant change in unweighted UNIFRAC occurred, indicating variation in the identities of taxa present due to treatment. Fungal b diversity was affected by treatment in IT and FR, but was unaffected in UK samples. The effects of time and site were greater than that of biochar application in UK samples. Overall, this report gives a tantalizing view of the soil microbiome at several sites across Europe and suggests that although application of biochar has significant effects on microbial communities, these may be small compared with the highly variable soil microbiome that is found in different soils and changes with time.

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential after 2 Years of Biochar Amendment in a Tropical Oxisol

“…Consistent with previous studies based on 16S rRNA gene amplicons, we showed that Proteobacteria and Bacteroidetes relative abundances significantly increased in biochar-amended samples and that the relative abundance of Acidobacteria decreased (22,24,35,44). Overall, all classes of Proteobacteria were more abundant in the biochar-amended samples, consistent with our previous study (22) in which we observed that biochar increased Proteobacteria abundance in the oxisol as early as 1 month and up to 1 year after the initial amendment.…”

“…While previous studies have used a single phylogenetic marker to investigate the effects of biochar on the soil microbial community (18,24,32,33,35), to date, only one has utilized shotgun metagenomics to examine the effects of biochar on the microbial community (42). Our results from the biochar-amended soil metagenomes showed some similarities to those of this previous study of biochar metagenomes (42).…”

“…As part of a sustainable management practice, biochar addition induces changes in the soil physical and chemical properties and shifts in the soil microbiome. However, the microbial response to biochar addition depends strongly on the soil type and cropping system as well as the properties of the biochar being added (21)(22)(23)(24)(25)(26)(27). The observed effects of biochar on microbial processes are varied.…”

“…The effects of biochar on microbial community composition have also been reported with some contradictory findings. Several studies have observed increases in Actinobacteria, Proteobacteria, Bacteroidetes, and Gemmatimonadetes (32)(33)(34)(35) and decreases in Acidobacteria in biochar-amended soils (22,24), while others have reported decreases in Proteobacteria and Bacteroidetes (33,35,36). Shifts in the microbiome composition and function influenced by biochar addition have the potential to impact GHG emissions, alter nutrient mineralization, and influence plant growth promotion.…”

Comparative Evaluation of Four Bacteria-Specific Primer Pairs for 16S rRNA Gene Surveys

“…In some studies, it is even more desirable to focus on bacteria alone to centralize the effort and expenses to optimally address the research question. For example, in the field of bioremediation, several reports focus on re-structuring bacterial communities to improve the efficiency of organic contaminant degradation (Bell et al, 2013a,b; Thijs et al, 2016), monitor bacterial community structure in response to pollution (Truyens et al, 2013; Bell et al, 2015), or in response to agricultural management (Jenkins et al, 2016), plant genetic modification (Beckers et al, 2016), and to study the connections between plant-associated bacteria and human/animal microflora (Berg et al, 2015; Mahnert et al, 2015). For all these studies, next to universal prokaryotic primers, adequate bacteria-specific primers that are carefully selected in terms of coverage, reproducibility, exclusion of the amplification of host-organelles, and comparability between studies is needed.…”