Article Figures & Data
Figures
- FIG 1
Simplified schematic of soil horizon and soil macro- and microaggregates. Important properties include local chemistry, surface area, pore sizes within and between aggregates, surface roughness, and connectivity. POM, particulate organic matter.
- FIG 2
Conceptual drawing of isolated micro- and macroaggregates during (left) dry conditions and (right) wet conditions. Wet conditions would allow for nutritional, microbial, viral and metabolite dispersal.
- FIG 3
Microfluidic approaches can recreate soil features for lab-based studies. (A) A heterogeneous porous medium design replicates the natural shape and distribution of sand particles. (B) Within these pore spaces, bacteria grow (green) and decay (red) under the influence of pressure-driven flow (scale bar = 100 μm). (C) A consistent particle layout between replicates allows the pore space hydrodynamics to be computationally simulated. (D) This system showed that a soil bacteria initially clogs pores with high shear rates (scale bar = 100 μm). (E) A random pore network generated from Voronoi tessellations was used to study two-phase flow underground. (F) A microfluidic design created by a particle-generating algorithm was used to study the influence of microbial extracellular polysaccharides on pore space water retention. For more information regarding the associated techniques, see references 124 (A to D), 125 (E), and 126 (F).
Tables
- TABLE 1
Length scales relevant for interactions between soil particles and microbes
Size (μm) Biological relevance Soil relevance Interaction <1 Viral particle sizes,a E. coli cells deform (300 nm)b Particle surface roughness promotes selective adhesion of specific bacterial species (10–100 nm)c Lysogeny and gene transfer,d bacterial shape deformation,b surface attachmentc 1–2 Bacterial cell sizeb Pores within soil microaggregatese Nitrogen fixationf 1–15 Fungal hyphal diam,g bacterial biofilm thickness in (0.12-mm-diameter) sandh Fungal mycelia reinforce aggregate tensile strength,i bacterial biofilm EPS production binds soil particles togetherj 10–30 Distance at which majority of bacterial cell interactions occur (<20 μm)k Pores between soil microaggregates, can retain water against gravity for multiple dayse Denitrification,l quorum-sensing bacteria exhibit inhibited cell divisionm ↵a Williamson et al. (134).
↵b Männik et al. (137).
↵c Hol and Dekker (127).
↵d Canchaya et al. (64).
↵e Watt et al. (36).
↵f Chotte et al. (44).
↵g Friese and Allen (138).
↵h Or et al. (139).
↵i Rillig et al. (140).
↵j Alami et al. (141).
↵k Raynaud and Nunan (35).
↵l Lensi et al. (43).
↵m Boedicker et al. (142).
- TABLE 2
Advanced analytical techniques used to determine the physicochemical characteristics of aggregatesa
Method Sample size Resolution Limitations Information collected Reference(s) SANS 150-μm-thick sections 1 nm to 0.8 μm Technique relies on the contrasting agent (D2O/H2O), diffusion of contrasting agent to estimate pore connectivity, requires a long time to collect data, and pore geometry is assumed for when analyzing natural samples Particle size distribution, pore vol, surface roughness, surface area, and interconnected porosity 143 USANS 150-μm-thick sections 60 nm to 20 μm FIB-T 10 μm3 10 nm to 0.1 μm Small sample volume used in analysis, and the technique is destructive, which limits reproducibility Pore vol, porosity, pore size statistics, and connected and unconnected pore network; also, data can be correlated to elemental composition using EDS 144, 145 ET 100-nm needle <1 nm to 0.05 μm Small sample volume, fixed-needle geometry, and technique relies on image analysis and 3D reconstruction Pore geometry and connectivity; pore data can be cross-correlated with elemental composition using EDS 146 BSEM Thin sections 100 nm to ∼500 μm 2D analysis of a 3D geometry requires sample prep, and technique relies on image analysis to distinguish intra- and intergrain porosity Pore geometry and connectivity; pore data can be cross-correlated with elemental composition using EDS 145 XCT 1 mm by 5-mm cylinders to 10-cm-diam cores 300 nm to 100 μmb Technique relies on image analysis and 3D reconstruction Results allow for full reconstruction of pore network 147 MIP 3.38 cm3 2 nm to 500 μm Technique only measures connected porosity and assumes pore geometry Results provide details on pore vol, pore size distribution, and surface area 148 PGA Powder samples 0.5 nm to 0.2 μm Technique only measures connected porosity and assumes pore geometry Results provide details on pore vol, pore size distribution, and surface area 149 ↵a SANS, small-angle neutron scattering; USANS, ultrasmall-angle neutron scattering; FIB-T, focused ion beam tomography; ET, electron tomography; BSEM, backscattered scanning electron microscopy; XCT, X-ray computed tomography; MIP, mercury intrusion porosimetry; PGA, physical gas adsorption; EDS, energy dispersive spectroscopy. Table adapted from Zachara et al. (89).
↵b Actual detectable pore size resolution will vary depending upon X-ray source, optics, and material.
- Top
- Article
- ABSTRACT
- INTRODUCTION
- OVERVIEW OF SOIL AGGREGATES
- IMPACTS OF AGGREGATE STRUCTURE ON SOIL COMMUNITIES
- VIRUSES IN SOIL AGGREGATES
- STUDIES SUPPORTING AGGREGATES AS THE FUNCTIONAL UNIT OF SOIL ECOSYSTEMS
- APPROACHES FOR ISOLATING AGGREGATE COMMUNITIES FROM NATURAL ENVIRONMENTS
- NANOSCALE TECHNIQUES TO CHARACTERIZE AGGREGATE SCALE COMMUNITIES
- ARTIFICIAL AGGREGATES FOR LAB-BASED COMMUNITY STUDIES
- FUTURE DIRECTIONS
- CONCLUSION
- ACKNOWLEDGMENTS
- REFERENCES
- Figures & Data
- Info & Metrics