Soil microbial biomass elemental composition and stoichiometry beyond carbon, nitrogen, and phosphorus

This work offers a first glimpse into the microbial biomass ionome beyond the elements carbon, nitrogen, and phosphorus by application of an adapted extraction procedure after chloroform-fumigation. It was hypothesised that the extractant and the soil to extractant ratio would be greatly influential on the amounts of elements extracted from soil and the resulting microbial biomass element fractions. Furthermore, the effects of mineral fertilisation treatments and different agricultural management systems on the soil microbial ionome and stoichiometry were investigated. It was hypothesised that differences in organic matter and fertiliser inputs affect microbial biomass carbon and other microbial biomass element concentrations, which may also affect the soil microbial stoichiometry, and which may be associated with differences in the microbial community composition. Initially, using six different soils, the chloroform-fumigation-extraction method was adapted to the extraction of elements beyond carbon, nitrogen, and phosphorus. Furthermore, long-term field trials were used to investigate how mineral fertilisation treatments and agricultural management systems affect the microbial ionome and stoichiometry. The field trial in Askov (Denmark) included mineral nitrogen, phosphorus, and potassium treatments either in single, double or triple combinations. The DOK field trial in Switzerland included different management strategies such as conventional, organic and biodynamic agriculture, including farmyard manure fertilisation, either at full or half application rate. The 16S rRNA and ITS1 gene abundances were used to quantify the abundance of bacteria, archaea and fungi. The chloroform-fumigation-extraction method was most successfully applied to potassium, magnesium, manganese, and zinc using the extractant calcium chloride (0.01 M) at a soil to extractant ratio of 1:20 and extraction time of one hour. Higher availability of phosphorus due to mineral fertilisation increased the microbial biomass phosphorus concentration and reduced the microbial biomass carbon to phosphorus ratio, in Askov and DOK. However, the microbial biomass reacted more homeostatically to increased potassium availability. In the DOK trial it was observed that farmyard manure application increased the availability of magnesium, which resulted in an increased microbial biomass magnesium concentration and in a reduced microbial biomass carbon to magnesium ratio. In both trials, Askov and DOK, an increased availability of manganese, as affected by a decreasing pH, increased the microbial biomass manganese concentration and reduced the microbial biomass carbon to manganese ratio. This increased sequestration of manganese within the microbial biomass was associated with a relative increase in fungal abundance. Currently it is difficult to distinguish if the fungal abundance and manganese availability are both increased independently from pH-reduction or if it is an indirect association between manganese availability and fungal abundance. In the DOK trial, manure application lead to a relative increase in bacterial abundance. Associated with this increased relative abundance of bacteria was an increased magnesium concentration within the microbial biomass and a reduced microbial biomass carbon to magnesium ratio, as well as a higher pH and soil organic carbon concentration. Moving forward in the field of soil ionomics necessitates the disentanglement of direct and indirect effects, which pH and element availability have on community composition and microbial biomass element concentration and stoichiometry. Furthermore, combining the chloroform-fumigation-extraction approach with a better understanding of the functional relevance of elements on a (sub)-cellular level, with gene expression and with isotope labelling experiments will provide the most comprehensive understanding of the soil microbial ionome and stoichiometry and its functional importance. Thus far it has emerged that the elemental stoichiometry, at least in the case of phosphorus, magnesium and manganese, might be manipulated by agricultural management such as fertilisation and liming. A micronutrient fertilisation strategy aimed at a community, which is functionally adapted to the pH conditions, may provide a good opportunity for soil organic carbon sequestration via microbial growth and activity.