Biogeochemical interfaces in soil: The interdisciplinary challenge for soil science

Abstract

Soil, the “Earth's thin skin” serves as the delicate interface between the biosphere, hydrosphere, atmosphere, and lithosphere. It is a dynamic and hierarchically organized system of various organic and inorganic constituents and organisms, the spatial structure of which defines a large, complex, and heterogeneous interface. Biogeochemical processes at soil interfaces are fundamental for the overall soil development, and they are the primary driving force for key ecosystem functions such as plant productivity and water quality. Ultimately, these processes control the fate and transport of contaminants and nutrients into the vadose zone and as such their biogeochemical cycling. The definite objective in biogeochemical‐interface research is to gain a mechanistic understanding of the architecture of these biogeochemical interfaces in soils and of the complex interplay and interdependencies of the physical, chemical, and biological processes acting at and within these dynamic interfaces in soil. The major challenges are (1) to identify the factors controlling the architecture of biogeochemical interfaces, (2) to link the processes operative at the individual molecular and/or organism scale to the phenomena active at the aggregate scale in a mechanistic way, and (3) to explain the behavior of organic chemicals in soil within a general mechanistic framework. To put this in action, integration of soil physical, chemical, and biological disciplines is mandatory. Indispensably, it requires the adaption and development of characterization and probing techniques adapted from the neighboring fields of molecular biology, analytical and computational chemistry as well as materials and nano‐sciences. To shape this field of fundamental soil research, the German Research Foundation (DFG) has granted the Priority Program “Biogeochemical Interfaces in Soil”, in which 22 individual research projects are involved.

Plant litter and soil type drive abundance, activity and community structure of alkB harbouring microbes in different soil compartments

“…However, to understand the functionality of soils in relation to the performance of microbial communities, the spatial resolution of analyses close to biogeochemical interfaces as they have been defined by Totsche et al (2010) have to be improved. These authors stated that 'linking the heterogeneous architecture of soil interfaces with the diverse structure of microbial communities in predictive ways in order to understand soil functions and the role for ecosystem services has yet to be seen as one of the grand decadal challenges in science'.…”

“…Such habitats are characterised by multidimensional interfaces at the mm to mm scale, and are the result of the interplay of soil microbiota with their physical and chemical environment (Totsche et al, 2010). As these structural elements are highly dynamic in response to the surrounding environmental conditions, they can be considered as hotspots for microbial activity and the basis of all ecosystem services provided by soils (Yaalon, 2000).…”

Inter-crown versus under-crown area: contribution of local configuration of trees to variation in topsoil morphology, pH and moisture in Abies alba Mill. forests

“…Environmental variability can occur over various spatial scales, ranging from micrometers, to small patches at the scale of individual plants to long gradients over hundreds of metres (Ehrenfeld et al 1997;Totsche et al 2010). In forested ecosystems, one important source of micro-site heterogeneity is the distribution of trees and their organs in the above-and belowground space.…”

Making big data smart—how to use metagenomics to understand soil quality

“…Soils are vertically and horizontally structured ecosystems, which are composed of a multitude of different microhabitats comprising diverse physical, chemical, and biological properties (Totsche et al 2010). The degree of heterogeneity strongly depends on (i) the sampled compartment, e.g., the rhizosphere is less heterogeneous compared to bulk soil (Hinsinger et al 2009), (ii) the soil texture, which strongly influences aggregate formation and also nucleic acid extraction efficiency, (iii) the above ground diversity and plant coverage, (iv) season, and (v) specific site characteristics like slope, shadowing, and groundwater table.…”

“…Since DNA extraction protocols vary in efficiency depending on the nature of the samples and in removing various inhibitors we recommend testing the workflow on a few non-essential samples first (Frostegård et al 1999). After a DNA extraction method has been selected, it should be used consistently given Gilbert et al 2014;Penton et al 2016;Prosser 2010;Salter et al 2014;Tatangelo et al 2014;Totsche et al 2010 Sequencing library preparation -Check for inhibitory effects -Avoid multiple displacement amplification (MDA) -Use your controls -Shear DNA for shotgun sequencing Salter et al 2014;Yilmaz et al 2010 Bioinformatic data analysis -Remove contaminants -Remove adapters -Quality & length filter -Estimate coverage -If possible, use mock community (defined mixture of microbial cells) to validate your workflow -Upload raw sequencing data to public server Bergkemper et al 2016;Darzi et al 2016;Del Fabbro et al 2013;Menzel et al 2016;Rodriguez-R and Konstantinidis 2014a;Sanchez-Flores et al 2015;Schmieder and Edwards 2011;Schubert et al 2016;Wood and Salzberg 2014 the inherent bias introduced throughout the whole project. Finally, depending on the aim of the study, one might also consider employing methods that separate extracellular DNA from intracellular DNA (Pietramellara et al 2009) which allow a discrimination between alive and dead microbes.…”