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In this opinion paper we review recent methodological developments underpinning the study of roots, the rhizosphere and interactions affecting soil functions, and explore new understanding resulting from these advances. We focus on methods that have improved our understanding of rhizodeposition, rhizosphere enzymatic processes and root growth, water and nutrient acquisition at several levels. Finally, we suggest that the future will require new methods that continue to overcome the difficulties posed by the opacity of soil, can scale results spatially and temporally, and integrate multiple aspects of rhizosphere processes simultaneously.

Aims Soil priming affects soil N transformation and plant N availability, but few studies have investigated these interactions to date. Methods To address this, we reviewed the literature for studies quantifying soil priming, soil N transformation and plant N uptake. Results Gross N mineralization was strongly controlled by soil priming in studies with plants, while abiotic factors had a minor influence on gross N mineralization. In contrast, soil priming was negatively related to gross N mineralization and had a low explanatory power in incubation studies where substrates are added as surrogates for root exudates. These results indicate that plants support increased N mineralization and that this is not adequately reflected in incubation studies. Additionally, we observed a positive relationship between soil priming and the % of Norg-derived N uptake as well as total N uptake, which demonstrates that priming enhances the availability of N that was previously organically bound and that at least part of the N mineralized during priming was available for plant uptake. Conclusion Our results show that the effect of roots and rhizodeposition leads to a number of processes supporting N mineralization and availability through priming that are not well reflected in incubation studies. To fully capture the interactions between plant roots and their associated microbiota, we recommend focusing research on systems with plants. Additionally, the strong correlation between C and N transformation should be considered in biogeochemical modelling.

Publication from the Healthy Soils project outlining soils research through the Scottish Government Rural and Environment Science and Analytical Services (RESAS) funded Strategic Research Programme. The Soil Sentinel will be published very 4 months throughout the project duration, 2022-2027.

Plant-soil interactions play an important role in regulating CO2 emissions and storage of carbon (C) as soil organic matter (SOM) creating the potential for crop selection to be a tool for sustainable agriculture. This is of particular importance in grassland soils which are known to be important stores of C. However, there is still a need to understand whether the selection of different grass species and varieties can control the rates and products of C cycling and if this is driven by the interaction with below ground microbial communities.

Here we describe and evaluate the success of a multi-institutional Centre for Doctoral Training (CDT), which was established to address a UK skills shortage in Soil Science. The government-funded ‘STARS’ (Soils Training And Research Studentships) CDT was established in 2015 across a range of universities and research institutes in the UK. It recruited 41 PhD students equitably split across the institutions under four core research themes identified as being central to the national need, namely, (1) Understanding the soil–root interface, (2) Soils and the delivery of ecosystem services, (3) Resilience and response of functions in soil systems and (4) Modelling the soil ecosystem at different spatial and temporal scales. In addition, the STARS CDT provided a diverse skills programme, including: Holistic training in soils, the promotion of collegiality and joint working, strategies to promote science and generate impact, internships with end users (e.g., policymakers, industry), personal wellbeing, and ways to generate a lasting soils training legacy. Overall, both supervisors and students have reported a positive experience of the CDT in comparison to the conventional doctoral training programmes, which have less discipline focus and little chance for students to scientifically interact with their cohorts or to undertake joint training activities. The STARS CDT also allowed students to freely access research infrastructure across the partner institutions (e.g., long-term field trials, specialised analytical facilities, high-performance computing), breaking down traditional institutional barriers and thus maximising the students' potential to undertake high-quality research. The success and legacy of the STARS CDT can be evidenced in many ways; however, it is exemplified by the large number and diversity of journal papers produced, the lasting collaborations, final career destinations, and creation of a web-based legacy portal including new and reflective video material. STARS CDT, Grant/Award Numbers: NE/V017667/1, NE/R010218/1, NE/M009106/1; UKRI

Climate change and soil fertility decline are major threats to smallholder farmers' food and nutrition security in southern Africa, and cropping systems that improve soil health are needed to address these challenges. Cropping systems that invest in soil organic matter, such as no-tillage (NT) with crop residue retention, have been proposed as potential solutions. However, a key challenge for assessing the sustainability of NT systems is that soil carbon (C) stocks develop over long timescales, and there is an urgent need to identify trajectory indicators of sustainability and crop productivity. Here we examined the effects of NT as compared with conventional tillage without residue retention on relationships between soil characteristics and maize (Zea mays L.) productivity in long-term on-farm and on-station trials in Zimbabwe. Our results show that relationships between soil characteristics and maize productivity, and the effects of management on these relationships, varied with soil type. Total soil nitrogen (N) and C were strong predictors of maize grain yield and above-ground biomass (i.e., stover) in the clayey soils, but not in the sandy soils, under both managements. This highlights context-specific benefits of management that fosters the accumulation of soil C and N stocks. Despite a strong effect of NT management on soil C and N in sandy soils, this accrual was not sufficient to support increased crop productivity in these soils. We suggest that sandy soils should be the priority target of NT with organic resource inputs interventions in southern Africa, as mineral fertilizer inputs alone will not halt the soil fertility decline. This will require a holistic management approach and input of C in various forms (e.g., biomass from cover crops and tree components, crop residues, in combination with mineral fertilizers). Clayey soils on the other hand have greater buffering capacity against detrimental effects of soil tillage and low C input.

There is a lack of field methods for measuring plant and soil processes controlling soil organic matter (SOM) turnover over diurnal, seasonal, and longer time-scales with which to develop datasets for modelling. We describe an automated field system for measuring plant and soil carbon fluxes over such time-scales using stable isotope methods, and we assess its performance. The system comprises 24 large (1-m deep, 0.8-m diameter) cylindrical lysimeters connected to gas-flux chambers and instruments. The lysimeters contain intact, naturally-structured C3 soil planted with a C4 grass. Fluxes of CO2 and their 13C isotope composition are measured 3-times daily in each lysimeter, and the isotope composition is used to partition the fluxes between plant and soil sources. We investigate the following potential sources of error in the measurement system and show they do not significantly affect the measured CO2 fluxes or isotope signatures: gas leaks; the rate of gas flow through sampling loops; instrument precision and drift; the concentration-dependence of isotope measurements; and the linearity of CO2 accumulation in the chambers and associated isotope fractionation resulting from different rates of 13CO2 and 12CO2 diffusion from the soil. For the loamy grassland soil and US prairie grass (Bouteloua dactyloides) tested, the precision of CO2 flux measurements was ± 0.04 % and that of the flux partitioning ± 0.40 %. We give examples of diurnal and seasonal patterns of plant and soil C fluxes and soil temperature and moisture. We discuss the limitations of the isotope methodology for partitioning fluxes as applied in our system. We conclude the system is suitable for measuring net ecosystem respiration fluxes and their plant and soil components with sufficient precision to resolve diurnal and seasonal patterns

Background The microbiota thriving in the rhizosphere, the thin layer of soil surrounding plant roots, plays a critical role in plant’s adaptation to the environment. Domestication and breeding selection have progressively differentiated the microbiota of modern crops from the ones of their wild ancestors. However, the impact of eco-geographical constraints faced by domesticated plants and crop wild relatives on recruitment and maintenance of the rhizosphere microbiota remains to be fully elucidated. Methods We grew twenty wild barley ( Hordeum vulgare ssp. spontaneum ) genotypes representing five distinct ecogeographic areas in the Israeli region, one of the sites of barley domestication, alongside four ’Elite’ varieties ( H. vulgare ssp. vulgare ) in a previously characterised agricultural soil under greenhouse conditions. At early stem elongation, rhizosphere samples were collected, and stem and root dry weight measured. In parallel, we generated high-resolution 16S rRNA gene profiles of the rhizosphere and unplanted soil samples. Ecological indices and multivariate statistical analyses allowed us to identify ‘host signatures’ for the composition of the rhizosphere microbiota. Finally, we capitalised on single nucleotide polymorphisms (SNPs) of the barley genome to investigate the relationships between microbiota diversity and host genetic diversity. Results Elite material outperformed the wild genotypes in aboveground biomass while, almost invariably, wild genotypes allocated more resources to belowground growth. These differential growth responses were associated with a differential microbial recruitment in the rhizosphere. The selective enrichment of individual bacterial members of microbiota mirrored the distinct ecogeographical constraints faced by the wild and domesticated plants. Unexpectedly, Elite varieties exerted a stronger genotype effect on the rhizosphere microbiota when compared with wild barley genotypes adapted to desert environments and this effect had a bias for Actinobacteria . Finally, in wild barley genotypes, we discovered a limited, but significant, correlation between microbiota diversity and host genomic diversity. Conclusions Our results revealed a footprint of the host’s adaptation to the environment on the assembly of the bacteria thriving at the root-soil interface. This recruitment cue layered atop of the distinct evolutionary trajectories of wild and domesticated plants and, at least in part, is encoded by the barley genome. This knowledge will be critical to further dissect microbiota contribution to plant’s adaptation to the environment and to devise strategies for climate-smart agriculture.

Both plant species and CO₂ concentration can potentially affect rhizodeposition and consequently soil microbial activity and community composition. However, the effect differs based on plant developmental stage. We focused on the effect of three plant species (forbs, grasses, and N₂‐fixers) at an early stage of development on root C deposition and fate, soil organic matter (SOM) mineralization and soil microbial community composition at ambient (aCO₂) and elevated (eCO₂) CO₂ levels. Plants were grown from seed, under continuous ¹³C‐labelling atmospheres (400 and 800 µmol mol⁻¹ CO₂), in grassland soil for three weeks. At the end of the growth period, soil respiration, dissolved organic C (DOC) and phospholipid fatty acid (PLFA) profiles were quantified and isotopically partitioned into root‐ and soil‐derived components. Root‐derived DOC (0.53 ± 0.34 and 0.26 ± 0.29 µg mL soil solution⁻¹) and soil‐derived CO₂ (6.14 ± 0.55 and 5.04 ± 0.44 µg CO₂‐C h⁻¹) were on average two times and 22% higher at eCO₂ than at aCO₂, respectively. Plant species differed in exudate production at aCO₂ (0.11 ± 0.11, 0.10 ± 0.18, and 0.58 ± 0.58 µg mL soil solution⁻¹ for Plantago, Festuca, and Lotus, respectively) but not at eCO₂ (0.20 ± 0.28, 0.66 ± 0.32, and 0.75 ± 0.15 µg mL soil solution⁻¹ for Plantago, Festuca, and Lotus, respectively). However, no differences among plant species or CO₂ levels were apparent when DOC was expressed per gram of roots. Relative abundance of PLFAs did not differ between the two CO₂ levels. A higher abundance of actinobacteria and G‐positive bacteria occurred in unplanted (8.07 ± 0.48 and 24.36 ± 1.18 mol%) and Festuca‐affected (7.63 ± 0.31 and 23.62 ± 0.69 mol%) soil than in Plantago‐ (7.04 ± 0.36 and 23.41 ± 1.13 mol%) and Lotus‐affected (7.24 ± 0.17 and 23.13 ± 0.52 mol%) soil. In conclusion, the differences in root exudate production and soil respiration are mainly caused by differences in root biomass at an early stage of development. However, plant species evidently produce root exudates of varying quality affecting associated microbial community composition.

While rhizosphere priming effects are well-documented under laboratory and controlled-environment conditions, their significance in undisturbed systems under field conditions is less clear. This is in part because it is impracticable to measure rates of rhizodeposition in the field with high resolution over a substantial period. We propose that photosynthesis, closely linked to rhizodeposition, can be used as a proxy for plant root activity.We have used a field system containing 24 0.8-m diameter, 1-m deep lysimeters holding naturally-structured soil monoliths from two contrasting C3 soils sown with a C4 grass (Bouteloua dactyloides) to measure carbon (C) fluxes at a high temporal resolution, exploiting isotopic differences to allow partitioning of plant and soil fluxes. These fluxes are coupled to high-resolution measurements of soil temperature and moisture, alongside atmospheric temperature and solar radiation. This system has allowed measurement of both ecosystem resolution and net ecosystem exchange, and the partitioning of respiration between plant and soil sources using stable isotope methods. Using this system we have generated a dataset of measured and modelled respiration and photosynthesis fluxes over two years.Our dataset has revealed clear seasonal and diurnal patterns in plant and soil fluxes. We have assessed the relationship between diurnal patterns in soil respiration and potential drivers, and examined whether model estimates of soil respiration are improved by the inclusion of photosynthesis as an explanatory variable alongside soil moisture and temperature. We found a significant positive relationship between photosynthesis and soil respiration, and inclusion of photosynthesis improves models of soil respiration. This is best explained by rhizosphere priming enhancing soil C turnover.

Purpose Rhizodeposition shapes soil microbial communities that perform important processes such as soil C mineralization, but we have limited understanding of the plant genetic regions influencing soil microbes. Here, barley chromosome regions affecting soil microbial biomass-C (MBC), dissolved organic-C (DOC) and root biomass were characterised. Methods A quantitative trait loci analysis approach was applied to identify barley chromosome regions affecting soil MBC, soil DOC and root biomass. This was done using barley Recombinant Chromosome Substitution Lines (RCSLs) developed with a wild accession (Caesarea 26-24) as a donor parent and an elite cultivar (Harrington) as recipient parent. Results Significant differences in root-derived MBC and DOC and root biomass among these RCSLs were observed. Analysis of variance using single nucleotide polymorphisms genotype classes revealed 16 chromosome regions influencing root-derived MBC and DOC. Of these chromosome regions, five on chromosomes 2H, 3H and 7H were highly significant and two on chromosome 3H influenced both root-derived MBC and DOC. Potential candidate genes influencing root-derived MBC and DOC concentrations in soil were identified. Conclusion The present findings provide new insights into the barley genetic influence on soil microbial communities. Further work to verify these barley chromosome regions and candidate genes could promote marker assisted selection and breeding of barley varieties that are able to more effectively shape soil microbes and soil processes via rhizodeposition, supporting sustainable crop production systems.

Protein hotspots in soil, such as those associated with decaying soil fauna or plant litter, may produce ephemeral patches of disproportionately high soil nutrients. These hotspots may occur at the macro- and microscale in close proximity to plant roots, however, the likely concentration of soluble products produced in these hotspots remains poorly understood. To address this, we buried two contrasting biomass residues in soil, namely earthworm (Lumbricus terrestris) and clover (Trifolium repens). Their transformation to amino acids, NH4+ and NO3− were monitored continually over 6 days using microdialysis. All treatments showed greater soluble nitrogen (N) concentrations compared to the unamended controls. The highest concentrations of both amino acids (12.9 mM after 12 h) and NH4+ (45.3 mM after 6 h) were generated in the vicinity of decomposing earthworm. In comparison, dried clover residues yielded 2.7 mM of amino acids at 6 h. After 12 h, amino acid and NH4+ concentrations in both earthworm and dried clover treatments showed a steep decline, returning close to background levels (

Summary • This study examined morphological and topological responses of nodal root axes to defoliation in a fast- and a slow-growing grass species. • Vegetative tillers of both Lolium perenne and Festuca ovina were grown on slant boards and either left intact or subjected to repeated defoliation, under both a high nitrogen (N) and a low N supply. Root length, diameter and branching characteristics were measured on individual nodal root axes. • The total axis root length of F. ovina was less when plants had been defoliated. Root axis weight, primary root axis length and primary root diameter were also less with defoliation than an undefoliated control, under high N. Under low N conditions the root axes of F. ovina had a more randomly branched topology without defoliation. For L. perenne under low N conditions, the length of the primary root axis was longer with defoliation than in an undefoliated control, while the primary root axis diameter decreased. By contrast to F. ovina, the root axes of L. perenne had a more randomly branched topology without defoliation only when supplied with high N. • The greatest plasticity in branching caused by defoliation was observed under high N for L. perenne and under low N for F. ovina. Although grass root axis topology has, in general, a herringbone in structure, the nodal root system can alter root axis structure in response to defoliation.

SummaryAgricultural management practices that increase soil organic matter (SOM), such as no-tillage (NT) with crop residue retention, together with crop varieties best able to source nutrients from SOM may help reverse soil degradation and improve soil nutrient supply and uptake by plants in low-input environments of tropical and sub-tropical areas.Here, we screened germplasm representing genetic diversity within tropical maize breeding programs in relation to shaping SOM mineralisation. Then we assessed effects of contrasting genotypes on nitrification rates, and genotype by management history interactions on these rates.SOM-C mineralisation and gross nitrification rates varied under different maize genotypes. Cumulative SOM-C mineralisation increased with root diameter but decreased with increasing root length. Strong influences of management history and interaction of maize genotype by management history on nitrification were observed. Overall, nitrification rates were higher in NT soil with residue retention.We propose that there is potential to exploit genotypic variation in traits associated with SOM mineralisation and nitrification within breeding programs. Root diameter and length could be used as proxies for root-soil interactions driving these processes. Development of maize varieties with enhanced ability to mineralize SOM combined with NT and residue retention to build/replenish SOM could be key to sustainable production.

Protein represents a major input of organic matter to soil and is an important source of carbon (C) and nitrogen (N) for microorganisms. Therefore, determining which soil properties influence protein mineralisation in soil is key to understanding and modelling soil C and N cycling. However, the effect of different soil properties on protein mineralisation, and especially the interactions between soil properties, are poorly understood. We investigated how topsoil and subsoil properties affect protein mineralisation along a grassland altitudinal (catena) sequence that contained a gradient in soil type and primary productivity. We devised a schematic diagram to test the key edaphic factors that may influence protein mineralisation in soil (e.g. pH, microbial biomass, inorganic and organic N availability, enzyme activity and sorption). We then measured the mineralisation rate of 14C-labelled soluble plant-derived protein and amino acids in soil over a two-month period. Correlation analysis was used to determine the associations between rates of protein mineralisation and soil properties. Contrary to expectation, we found that protein mineralisation rate was nearly as fast as for amino acid turnover. We ascribe this rapid protein turnover to the low levels of protein used here, its soluble nature, a high degree of functional redundancy in the microbial community and microbial enzyme adaptation to their ecological niche. Unlike other key soil N processes (e.g. nitrification, denitrification), protease activity was not regulated by a small range of factors, but rather appeared to be affected by a wide range of interacting factors whose importance was dependent on altitude and soil depth [e.g. above-ground net primary productivity (NPP), soil pH, nitrate, cation exchange capacity (CEC), C:N ratio]. Based on our results, we hypothesise that differences in soil N cycling and the generation of ammonium are more related to the rate of protein supply rather than limitations in protease activity and protein turnover per se.

Aims The capacity of plant roots to directly acquire organic nitrogen (N) in the form of oligopeptides and amino acids from soil is well established. However, plants have poor access to protein, the central reservoir of soil organic N. Our question is: do plants actively secrete proteases to enhance the breakdown of soil protein or are they functionally reliant on soil microorganisms to undertake this role? Methods Growing maize and wheat under sterile hydroponic conditions with and without inorganic N, we measured protease activity on the root surface (root-bound proteases) or exogenously in the solution (free proteases). We compared root protease activities to the rhizosphere microbial community to estimate the ecological significance of root-derived proteases. Results We found little evidence for the secretion of free proteases, with almost all protease activity associated with the root surface. Root protease activity was not stimulated under N deficiency. Our findings suggest that cereal roots contribute one-fifth of rhizosphere protease activity. Conclusions Our results indicate that plant N uptake is only functionally significant when soil protein is in direct contact with root surfaces. The lack of protease upregulation under N deficiency suggests that root protease activity is unrelated to enhanced soil N capture.

Plant roots have both direct and indirect effects on nutrient availabilities and fluxes in rhizosphere soil. Direct effects include impacts that are a consequence of root growth, water/nutrient uptake and secretion of compounds that promote solubility of poorly available elements such as phosphorus and iron. Indirect effects are largely a consequence of plant–microbe interactions, mediated by the release of organic compounds from roots that both shape rhizosphere microbial community structure and promote microbial nutrient cycling activity. In recent years, significant advances have been made in the quantification of root-mediated impacts on soil biogeochemical processes, demonstrating the importance of these interactions for nutrient cycling to support plant productivity and as a critical control point for the response of soils to environmental change. This is now supplemented with an appreciation that there is a strong element of regulation, both plant and microbial, in how the underlying interactions are established and maintained. This raises the exciting possibility that management of root–microbiota interactions could be a realistic means of improving plant health and productivity, while potentially also mitigating environmental impacts. This chapter discusses progress in quantifying root impacts on soil processes and parallel advances in characterising the specificity of the plant-driven selection of associated microbiota. A clear opportunity for future research is to combine these approaches, functional -omics technologies and bioinformatics to guide next-generation crop breeding that targets both the plant and its associated microbiota (i.e. the holobiont), for productivity and resilience in sustainable agricultural systems.

Our understanding of soil carbon (C) dynamics is limited; field measurements necessarily conflate fluxes from plant and soil sources and we therefore lack long-term field-scale data on soil C fluxes to use to test and improve soil C models. Furthermore, it is often unclear whether findings from lab-based studies, such as the presence of rhizosphere priming, apply to soil systems in the field. It is particularly important that we are able to understand the roles of soil temperature and moisture, and plant C inputs, as drivers of soil C dynamics in order to predict how changing climate and plant productivity may affect the net C balance of soils. We have developed a field laboratory with which to generate much-needed long-term C flux data under field conditions, giving near-continuous measurements of plant and soil C fluxes and their drivers.The laboratory contains 24 0.8-m diameter, 1-m deep, naturally-structured soil monoliths of two contrasting C3 soils (a clay-loam and a sandy soil) in lysimeters. These are sown with a C4 grass (Bouteloua dactyloides), providing a large difference in C isotope signature between C4 plant respiration and C3-origin soil organic matter (SOM) decomposition, which enables clear partitioning of the net C flux. This species is used as a pasture grass in the United States, and regular trimming through the growing season simulates low-intensity grazing. The soil monoliths are fitted with gas flux chambers and connected via an automated sampling loop to a cavity ring-down spectrometer, which measures the concentration and 12C:13C isotopic ratio of CO2 during flux chamber closure. Depth-resolved measurements of soil temperature and moisture in each monolith are made near-continuously, along with measurements of incoming solar radiation, rainfall, and air temperature a the field site. The gas flux chambers are fitted with removable reflective backout covers allowing flux measurements both incorporating, and in the absence of, photosynthesis.We have collected net ecosystem respiration data, measurements of photosynthesis, and recorded potential drivers of respiration over two growing seasons through 2018 and 2019. Through partitioning fluxes between plant respiration and SOM mineralisation we have revealed clear diurnal trends in both plant and soil C fluxes, along with overarching seasonal trends which modify both the magnitude of fluxes and their diurnal patterns. Rates of photosynthesis have been interpolated between measurement periods using machine learning to generate a predictive model, which has allowed us to investigate the effect of plant productivity on SOM mineralisation and assess whether rhizosphere priming can be detected in our system. Through regression analyses and linear mixed effects modelling we have evaluated the roles of soil temperature, soil moisture, and soil N content as drivers of variation in plant and soil respiration in our two contrasting soils. This has shown soil temperature to be the most important control on SOM mineralisation, with soil moisture content playing only a minor role. We have also used our empirical models to suggest how the carbon balance of pasture and grassland soils may respond to warming temperatures.

Temporal dynamism of plant resource capture, and its impacts on plant–plant interactions, can have important regulatory roles in multispecies communities. For example, by modifying resource acquisition timing, plants might reduce competition and promote their coexistence. However, despite the potential wide ecological relevance of this topic, short-term (within growing season) temporal dynamism has been overlooked. This is partially a consequence of historic reliance on measures made at single points in time. We propose that with current technological advances this is a golden opportunity to study within growing season temporal dynamism of resource capture by plants in highly informative ways. We set out here an agenda for future developments in this research field, and explore how new technologies can deliver this agenda.

We hypothesized that the rhizosphere priming effect (RPE) of soil organic matter by mutant barley lacking root hairs is dependant on a large network of symbiotic arbuscular mycorrhizal fungi (AMF). We thus predicted that fertilizing with phosphate-P would reduce AMF abundance and, in turn, reduce RPE of mutant barley. We packed microcosms with a P-responsive soil in which we grew mutant barley lacking root hairs as well as wild type barley and narrowleaf plantain, each possessing root hairs. One set of microcosms was fertilized with phosphate-P while another set was not fertilized. The plants were grown in a labelling chamber with 13C-depleted CO2. Soil respiration and δ13C of headspace CO2 were measured after 3, 4 and 5 weeks and RPE was calculated using an isotope mass balance approach. Root hair length was measured and soils were analyzed for the 16:1ω5 neutral lipid fatty acid (i.e. AMF biomarker). AMF abundance was greater, whereas RPE was lower, in mutant barley soil under low-P than under high-P conditions. In the other two plant-types, P had no effect on AMF or on RPE. As our results contradict our prediction, we propose an alternative explanation based on plant N demand under high-P.

Maize root traits associated with soil organic matter (SOM) mineralization were demonstrated to have a heritable genetic basis. We show root length, root diameter and cumulative root-derived C mineralization to be strong predictors of SOM-C mineralization and identify two candidate genes associated with enhanced SOM-C mineralization rates. There is potential to target these genes to enhance release of nutrients from SOM to support crop nutrition within sustainable maize cropping systems.

Septic tank effluent (STE) contributes to catchment nutrient and pollutant loads. To assess the role of STE discharges in impairment of surface water, it is essential to identify the sources of pollution by tracing contaminants in watercourses. We examined tracers that were present in STE to establish their potential for identifying STE contamination in two stream systems (low and high dilution levels) against the background of upstream sources. The studied tracers were microbial, organic matter fluorescence, caffeine, artificial sweeteners and effluent chemical concentrations. The results revealed that tracer concentration ratios Cl/EC, Cl/NH4-N, Cl/TN, Cl/TSS, Cl/turbidity, Cl/total coliforms, Cl/sucralose, Cl/saccharin and Cl/Zn had potential as tracers in the stream with low dilution level (P

Mechanisms controlling carbon stabilisation in soil and its feedback to climate change are of considerable importance. Microbial substrate-use efficiency is an important property during decomposition of soil organic matter. It determines the allocation of substrate towards biosynthetic stabilisation of carbon and for respiratory losses into the atmosphere. Previously, it was observed that substrate-use efficiency declines with an increase in temperature and that it varies across organic substrates. Yet, our mechanistic understanding of processes causing the temperature sensitivity of substrate-use efficiency is limited. Changes in substrate-use efficiency could be triggered by (i) shifts in the active components of microbial communities, (ii) changes in microbial physiology within the same community, or (iii) a combination of both. In the present study, we evaluated the link between microbial community composition and substrate-use efficiency, combining measurements of carbon mineralisation and microbial energetics. We found only minor shifts in microbial community composition, despite large differences in substrate-use efficiencies across incubation temperatures and substrate additions. We conclude that short-term changes in substrate-use efficiency were mainly caused by changes in microbial physiology, but emphasize that future studies should focus on resolving long-term trade-offs between physiological and community influences on substrate-use efficiency.

The intrinsic nitrogen (N) supply capacity of soil is central to understanding the productivity of natural plant communities, and essential in the context of determining optimal fertilization rates for agricultural soils. However, it is largely unknown how nutrient availability affects plant mediated priming effects driving soil organic matter mineralisation and associated N-fluxes. We applied continuous, steady-state 13C–CO2 labelling to Lolium perenne grown in high and low productivity grassland soils to allow quantification of SOM- and root-derived soil CO2 efflux. Nutrient treatments (N, P and K) were applied as repeated additions to soils, and impacts on source partitioned soil CO2 efflux were assessed relative to unamended planted and fallow soils. Plants were clipped to uniform height at weekly intervals. Increasing nutrient availability in both soils resulted in a reduction in plant-mediated SOM mineralisation and clipping of plants greatly lowered root-derived respiration but increased SOM mineralisation. Nutrient addition to fallow systems had no effect on SOM mineralisation in either soil. Plant growth stimulated SOM priming, concurrent mobilisation of N from SOM and subsequent plant N uptake in the high productivity soil. Priming was not observed in the low productivity soil due to its greater inherent organic matter stability, resulting in lowered plant-mediated and basal SOM mineralisation. That addition of nutrients reduced SOM mineralisation in planted systems but had no effect in fallow systems is indicative of nutrient availability specifically altering plant-mediated priming of SOM mineralisation. We suggest that plant-soil interactions mediating priming effects are an important determinant of productivity and that the magnitudes of these effects are modified by nutrient availability and soil-specific controls.

Contaminants in septic tank effluent (STE) are expected to be removed by the soil system before discharging to the environment. However, potential contaminants such as phosphorus (P), caffeine and artificial sweeteners do find their way to watercourses impacting aquatic eco systems. In this study, the attenuation of STE P, caffeine and saccharin were investigated in untreated soil and in soil with reduced microbial activity, in aqueous solutions and in the complex matrix of STE. Time series sorption and desorption experiments using batch equilibrium and a column experiment of STE P attenuation were conducted. The results revealed that the soil distribution coefficients (Kd) were: P 81.57 > caffeine 22.16 > saccharin 5.98 cm3/g, suggesting greater soil affinity to P adsorption. The data revealed that 80% of saccharin and 33% of caffeine attenuation was associated with microbial activities rather than adsorption processes. However, a complete removal of saccharin and caffeine did not occur during the equilibration period, suggesting their leaching potential. The dominant mechanism of P attenuation was adsorption (chemical and physical), yielding P retention of >73% and 35% for P in aqueous solution and in STE matrix, respectively, for batch equilibrium. The soil in the column acted as effluent P sink retaining 125 μg P/g soil of effluent P. The attenuation of P, caffeine and saccharin in the aqueous solution was greater than in STE, suggesting that the complex composition of STE reduced soil adsorption ability, and that other substances present in STE may be competing for soil binding sites. The data revealed that caffeine and P had similarities in the interaction with soils and thus caffeine may be considered as a STE tracer of anthropogenic source of P in receiving waters.

Herbivory is one of the most globally distributed disturbances affecting carbon (C)-cycling in trees, yet our understanding of how it alters tree C-allocation to different functions such as storage, growth or rhizodeposition is still limited. Prioritized C-allocation to storage replenishment vs growth could explain the fast recovery of C-storage pools frequently observed in growth-reduced defoliated trees. We performed continuous 13C-labeling coupled to clipping to quantify the effects of simulated browsing on the growth, leaf morphology and relative allocation of stored vs recently assimilated C to the growth (bulk biomass) and non-structural carbohydrate (NSC) stores (soluble sugars and starch) of the different organs of two tree species: diffuse-porous (Betula pubescens Ehrh.) and ring-porous (Quercus petraea [Matt.] Liebl.). Carbon-transfers from plants to bulk and rhizosphere soil were also evaluated. Clipped birch and oak trees shifted their C-allocation patterns above-ground as a means to recover from defoliation. However, such increased allocation to current-year stems and leaves did not entail reductions in the allocation to the rhizosphere, which remained unchanged between clipped and control trees of both species. Betula pubescens and Q. petraea showed differences in their vulnerability and recovery strategies to clipping, the ring-porous species being less affected in terms of growth and architecture by clipping than the diffuse-porous. These contrasting patterns could be partly explained by differences in their C cycling after clipping. Defoliated oaks showed a faster recovery of their canopy biomass, which was supported by increased allocation of new C, but associated with large decreases in their fine root biomass. Following clipping, both species recovered NSC pools to a larger extent than growth, but the allocation of 13C-labeled photo-assimilates into storage compounds was not increased as compared with controls. Despite their different response to clipping, our results indicate no preventative allocation into storage occurred during the first year after clipping in either of the species.

Root-derived compounds can change rates of soil organic matter decomposition (rhizosphere priming effects) through microbial production of extracellular enzymes. Such soil priming can be affected by plant identity and soil nutrient status. However, the effect of plant-plant competition on the temporal dynamics of soil organic matter turnover processes is not well understood. This study used zymography to detect the spatial and temporal pattern of cellulase and leucine aminopeptidase activity, two enzyme classes involved in soil organic matter turnover. The effect of plant-plant competition on enzyme activity was examined using barley (Hordeum vulgare) plants grown in i) isolation, ii) intra- and iii) inter-cultivar competition. The enzyme activities of leucine aminopeptidase and cellulase were measured from portions of the root system at 18, 25 and 33 days after planting, both along the root axis and in the root associated area with detectable enzyme activity. The activities of cellulase and leucine aminopeptidase were both strongly associated with plant roots, and increased over time. An increase in the area of cellulase activity around roots was delayed when plants were in competition compared to in isolation. A similar response was found for leucine aminopeptidase activity, but only when in intra-cultivar competition, and not when in inter-cultivar competition. Therefore, plant-plant competition had a differential effect on enzyme classes, which was potentially mediated through root exudate composition. This study demonstrates the influence of plant-plant competition on soil microbial activity and provides a potential mechanism by which temporal dynamism in plant resource capture can be mediated.

Discharges from the widely distributed small point sources of pollutants such as septic tanks contribute to microbial and nutrient loading of streams and can pose risks to human health and stream ecology, especially during periods of ecological sensitivity. Here we present the first comprehensive data on the compositional variability of septic tank effluents (STE) as a potential source of water pollution during different seasons and the associated links to their influence on stream waters. To determine STE parameters and nutrient variations, the biological and physicochemical properties of effluents sampled quarterly from 12 septic tank systems were investigated with concurrent analyses of upstream and downstream receiving waters. The study revealed that during the warmer dryer months of spring and summer, effluents were similar in composition, as were the colder wetter months of autumn and winter. However, spring/summer effluents differed significantly (P

Arbuscular mycorrhizal (AM) hyphae represent an important route for input of plant-derived C to soil, but impacts of these inputs on microbial communities and processes are poorly understood. In this study we characterised pathways of C-flow through microbial communities associated with AM hyphae and quantified impacts on mineralisation of native SOM. Continuous, steady-state 13CO2 labelling was applied throughout the growth period (60 d) of Lolium perenne. Exclusion meshes were used to control access of roots and AM hyphae to soil, and plant-derived C was quantified within microbial PLFA and NLFA, and soil CO2 efflux was partitioned into plant- and soil organic matter (SOM) derived components. Pathways of C-flow through hyphosphere and mycorrhizosphere communities were distinct, as was the fate of plant-derived C from AM hyphae accessing soil through 37 and 1 μm meshes. Mineralisation of native SOM was increased in all treatments, relative to unplanted controls, and this priming effect was largest for AM hyphae accessing soil through the 1 μm mesh size. We demonstrated that AM hyphae can strongly increase mineralisation of native SOM and identified distinct pathways of C-flow through hyphosphere communities. Our results suggest that, in addition to affecting rates of litter decomposition, AM hyphae may have a significant influence on turnover of native SOM.

Rhizodeposition is an important source of substrate for microbial communities, supporting activities including soil organic matter (SOM) and nutrient cycling. Therefore, it is a potential trait of interest for crop plants, particularly in the context of variety selection for sustainable production systems. However, we do not have a good understanding of (i) whether there is significant variation in root-C deposition between varieties of important agricultural crops and (ii) whether variation in C deposition between varieties leads to major differences in C cycling in soil. In two experiments, we assessed variations in C deposition amongst barley genotypes and their respective impacts on microbial activity and SOM dynamics. In experiment 1, we applied 13C–CO2 labelling to selected barley recombinant chromosome substitution lines (RCSLs) and traced root-derived C in surface soil CO2 efflux, soil microbial biomass-C (MBC), soil solution, and soil particle-size fractions. In experiment 2, we conducted MicroResp analysis using 15 ecologically relevant C substrates to assess the impacts of barley genotypes on microbial activity. Soil respiration measurements (partitioned into plant- and SOM-derived components) revealed genotype-specific effects on plant-derived C, SOM-derived C and total C respired as CO2. For particle-size fractionation, we found that incorporation of plant-derived C to the silt-and-clay fraction varied between genotypes, indicating differences in relative stabilization of root-derived C as a result of barley genotype. Our data did not indicate genotype effects on total MBC size or dissolved organic-C (DOC) in soil solutions, but significant differences in plant-derived MBC and DOC were observed. MicroResp analysis showed differential utilization of 7 substrates (glucose, trehalose, lignin, arabinose, alanine, aminobutyric acid and lysine) revealing variation in community level physiological profiles (CLPPs) of soil microbes as impacted by barley genotypes. Furthermore, we found significant clustering of microbial CLPPs as a function of RCSLs and parent lines (Caesarea 26-24 and Harrington) suggesting a strong plant genetic control of the barley microbiome, and that this genetic control is heritable. Our results demonstrate barley genotype-specific effects on soil processes, revealing the potential for germplasm selection and variety improvement in barley to support sustainable production systems.

Small point sources of pollutants such as septic tanks are recognised as significant contributors to streams' pathogen and nutrient loadings, however there is little data in the UK on which to judge the potential risks that septic tank effluents (STEs) pose to water quality and human health. We present the first comprehensive analysis of STE to help assess multi-pollutant characteristics, management-related risk factors and potential tracers that might be used to identify STE sources. Thirty-two septic tank effluents from residential households located in North East of Scotland were sampled along with adjacent stream waters. Biological, physical, chemical and fluorescence characterisation was coupled with information on system age, design, type of tank, tank management and number of users. Biological characterisation revealed that total coliforms and Escherichia coli (E. coli) concentration ranges were: 10(3)-10(8) and 10(3)-10(7)MPN/100 mL, respectively. Physical parameters such as electrical conductivity, turbidity and alkalinity ranged 160-1730 μS/cm, 8-916 NTU and 15-698 mg/L, respectively. Effluent total phosphorus (TP), soluble reactive P (SRP), total nitrogen (TN) and ammonium-N (NH4-N) concentrations ranged 1-32,1-26, 11-146 and 2-144 mg/L, respectively. Positive correlations were obtained between phosphorus, sodium, potassium, barium, copper and aluminium. Domestic STE may pose pollution risks particularly for NH4-N, dissolved P, SRP, copper, dissolved N, and potassium since enrichment factors were1651, 213, 176, 63, 14 and 8 times that of stream waters, respectively. Fluorescence characterisation revealed the presence of tryptophan peak in the effluent and downstream waters but not detected upstream from the source. Tank condition, management and number of users had influenced effluent quality that can pose a direct risk to stream waters as multiple points of pollutants.

Proteins play a crucial role in many soil processes, however, standardised methods to extract soluble protein from soil are lacking. The aim of this study was to compare the ability of different extractants to quantify the recovery of soluble proteins from three soil types (Cambisol, Ferralsol and Histosol) with contrasting clay and organic matter contents. Known amounts of plant-derived 14C-labelled soluble proteins were incubated with soil and then extracted with solutions of contrasting pH, concentration and polarity. Protein recovery proved highly solvent and soil dependent (Histosol > Cambisol > Ferralsol) and no single extractant was capable of complete protein recovery. In comparison to deionised water (10–60% of the total protein recovered), maximal recovery was observed with NaOH (0.1 M; 61–80%) and Na-pyrophosphate (0.05 M, pH 7.0; 45–75% recovery). We conclude that the dependence of protein recovery on both extractant and soil type prevents direct comparison of studies using different recovery methods, particularly if no extraction controls are used. We present recommendations for a standard protein extraction protocol.

Soil organic matter (SOM) is the dominant store of nutrients required for plant growth, but the availability of these nutrients is dependent on transformations mediated by the microbial biomass. The addition of labile C to soil is known to alter SOM turnover (priming effect, PE), but understanding of this is limited, particularly with respect to impact on gross nitrogen (N) fluxes. Here we examined relationships between C and N fluxes from SOM under primed and non-primed conditions in two soils. Stable isotopes (13C and 15N) were used to measure gross C and N fluxes from SOM and to differentiate between SOM mineralised due to priming and that from basal mineralisation. 13C-glucose was added daily to simulate the effect of addition of labile C on SOM-C and –N mineralisation within the rhizosphere. Addition of glucose increased both gross N and C mineralisation from SOM. However, the C-to-N ratio of the mineralised flux from ‘primed’ SOM was 5:1, whereas the C-to-N ratio of the basal mineralised flux was 20:1 indicating that priming acted on specific organic matter pools. This result is consistent with the concept that priming is a distinct N-mining response of the microbial biomass, as opposed to an acceleration of the basal flux. Our data suggest that C and N fluxes are not directly linked through their gross stoichiometry in SOM. This is due to the heterogeneity and overall passiveness of OM relative to the dynamic nature of mineralisation fluxes and source pools, and in primed systems the mineralisation of N-rich compounds.

Fluxes of rhizodeposit carbon (C) to soil stimulate microbial activity affecting soil organic matter (SOM) decomposition and, in turn, nutrient fluxes in soil. In agricultural soils, residues from previous crops also have major impacts on SOM and nutrient cycling, and their turnover by microbes is likely to be indirectly impacted by rhizodeposition. However, the combined effects of rhizodeposit C and inputs of C from dead plant materials in soil on native SOM decomposition are unclear. In this study, we assessed (i) the individual and combined effects of barley rhizodeposition and ryegrass root residue inputs (as a model for residue input from previous crop) on SOM mineralization, (ii) the intraspecies variation within barley in impacting residue mineralization, and (iii) whether genotypes that stimulate high mineralization rates of plant residues in soil also directly benefit through increased nutrient uptake from these residues. We continuously applied 13C depleted CO2 to selected barley recombinant chromosome substitution lines (RCSLs) to trace the flow of barley root-derived C in surface soil CO2 efflux, soil microbial biomass and soil particle-size fractions. In addition, 13C and 15N enriched ryegrass root residues were mixed into soil to trace the mineralization of residue-derived C and the residue-derived nitrogen (N) uptake by plants. Our results show (i) genotype-specific variation in impacting total soil CO2 efflux and its component sources: SOM-derived C, barley root-derived C and/or ryegrass residue-derived C, (ii) residue effects on total C and SOM-derived C respired as CO2, (iii) genotype-residue combined effects on SOM primed C, that were very similar to the sum of primed C caused by planting or residue addition alone (except for the last sampling date), and (iv) that plant uptake of residue released N between genotypes was linked to genotype impacts on residue mineralization. These results suggest that impacts of plant rhizodeposition and residue inputs had additive effects on SOM priming. Furthermore, these results demonstrate, for the first time, genotype differences in impacting the mineralization of recent plant-derived organic materials in soil, and reveal that this process directly contributes to plant nutrition.

Phospholipid fatty acid (PLFA) analysis is an effective non-culture-based technique for providing information on the living soil microbial community. The coupling of 13C tracers with PLFA analysis can indicate the response of microbial populations to environmental change and has been widely used to trace C flux in soil-plant systems. Based on studies applying 13C PLFA analysis, the current technological status, current applications and future opportunities are discussed and evaluated. First we describe some aspects of the labelling and analytical methodology. The approaches to study the incorporation of 13C substrate and rhizodeposition C into soil microbial communities are compared. We continue with the application of 13C-labelling to study soil microbial communities, including the utilization of soil mineralisation products, the C flux from plants into the soil microbial pool, the biodegradation of pollutants and on the application to a specific microbial group, i.e. methanotrophs. Additionally, some perspectives on the limitations of the 13C PLFA method and future research avenues are noted. Although including some limitations and complications, the 13C PLFA method provides an excellent tool for understanding the relationship between microbial populations and soil biogeochemical cycling, thus providing a key to open the soil microbial black box.

Soil organic matter (SOM) is the largest store of organic carbon (C) in the biosphere, but the turnover of SOM is still incompletely understood and not well described in global C cycle models. Here we use the Community Land Model (CLM) and compare the output for soil organic C stocks (SOC) to estimates from a global data set. We also modify the assumptions about SOC turnover in two ways: (1) we assume distinct temperature sensitivities of SOC pools with different turnover time and (2) we assume a priming effect, such that the decomposition rate of native SOC increases in response to a supply of fresh organic matter. The standard model predicted the global distribution of SOC reasonably well in most areas, but it failed to predict the very high stocks of SOC at high latitudes. It also predicted too much SOC in areas with high plant productivity, such as tropical rainforests and some midlatitude areas. Total SOC at equilibrium was reduced by a small amount (

Temperate forest soils are important carbon (C) sinks, where the C-stock is largely determined by the balance of leaf inputs and losses through respiration. However, studies dealing with leaf inputs to coniferous forest soils are limited although coniferous forests are widespread through the Northern temperate zone. In this study, we focused on the effects of soluble, insoluble and whole-tissue coniferous needle fractions on soil organic matter (SOM) decomposition and C storage in soil fractions. In addition, the effect of future increased C input was tested by applying a doubled amount of the soluble fraction (whole-tissue + soluble fraction). 13C-labelled needles were produced from spruce seedlings in growth chambers and needle fractions were added to the coniferous forest soil in laboratory microcosms. CO2 respired during incubation from the microcosms was partitioned into needle- and SOM-derived components. After seven months, soils were destructively harvested and analysed for C content in soil fractions and microbial community composition. The soluble, insoluble and whole-tissue fractions resulted in cumulative priming (increased SOM-derived CO2 relative to unamended controls) of 25 ± 8%, 40 ± 1%, and 39 ± 7%, respectively. The doubled soluble-C addition caused a slightly lower priming (38 ± 2%) than the whole-tissue fraction alone. The addition of needle fractions did not significantly affect the C content of soil fractions. However, the soluble fraction retained in soil was mainly found adsorbed onto mineral particles, whereas the insoluble and whole-tissue fractions occurred mainly as free particulate organic matter or adsorbed onto mineral particles. The insoluble and whole-tissue fraction led to increased fungal abundance and decreased abundance of G+ bacteria and actinobacteria. All the fractions were primarily incorporated into fungal biomass after seven months suggesting that fungi were the main consumers of all needle fractions after the labile C had been depleted. When considering all the C gains and losses, the addition of all needle fractions resulted in net soil C increase. This suggests that, although the input of the coniferous needles leads to some C losses through the priming of SOM decomposition, these C losses are compensated by new C storage either in SOM fractions or microbial biomass.