Congratulations, Dr Joe Jenkins!

Congratulations to Joe Jenkins, who successfully defended his PhD on 12th May and was awarded his doctorate following his viva, with Professor Gary Bending as external examiner. It’s been a busy week for Joe, with the main paper from his PhD out this week too!

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

Jenkins JR, Viger M, Arnold EC, Harris ZM, Ventura M, Miglietta F, Girardin C, Edwards RJ, Rumpel C, Fornasier F, Zavalloni C, Tonon G, Alberti G & Taylor G (2016): Biochar alters the soil microbiome and soil function: results of next generation amplicon sequencing across Europe. GCB Bioenergy Adv. Access DOI: 10.1111/gcbb.12371

Abstract

Wide scale application of biochar to soil has been suggested as a mechanism to offset increases in CO2 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 mobilisation 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 one year after application, whilst control plots exhibited enriched Gemmataceae, Isosphaeraceae and Koribacteraceae. Increased mobility of ammonium and phosphates were also detected after one year, coupled with a shift from acid to alkaline phophomonoesterase 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 were noted in FR, although a small significant change in unweighted UNIFRAC occurred, indicating variation in the identities of taxa present due to treatment. Fungal β 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 tantalising 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.

iOES Poster: Using metagenomics to assess soil microbial diversity under future climate scenarios

Joseph Jenkins, Prof. Gail Taylor, Dr. Rich Edwards.

1st International Environmental Omics Synthesis (iEOS) Conference, Cardiff, UK (Sept 11-13, 2013). Poster CE-3.

Abstract:

Soil microbes are responsible for the function of biogeochemical cycles, which are essential to maintain soil quality. Anthropogenic climate change is resulting in variation of the soil habitat, through alteration of a multitude of soil variables. In particular, prevalence of drought and use of geoengineering methods to sequester carbon (such as biochar) are expected to increase.

To test the implications of drought and biochar amendment in soil habitats, soil samples were collected from two long term experimental sites, and shotgun metagenomic sequencing undertaken to determine changes in soil microbial diversity. Furthermore, analysis of the method itself will be undertaken to determine potential issues with the technique, and to improve the methodology for future studies.

Future work will attempt to compare results of shotgun and amplicon metagenomic methods, and sequencing of additional biochar treated samples from a range of European sites undertaken. This will provide a means to compare changes in microbial diversity after biochar incorporation under a variety of field conditions, providing insight into its likely effects for soil microbial ecology.