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Subsoils are increasingly studied as they, first, store a great deal of terrestrial carbon (C) and possibly even more, and second, offer resources like water and nutrients to plants, potentially mitigating negative consequences of global change. As subsoil access is often hampered by compacted soil layers, the key to accessing subsoil resources and storing more C below ground might be in biopores. Appropriately nicknamed 'highways of root growth', biopores are macropores left behind by dying roots and earthworm activities, often enriched with organic matter (OM) and nutrients. They are thought to be the most abundant microbial hotspots in the subsoil, thus possibly accounting for a large part of C turnover, as well as offering pore wall nutrients to subsequent crops. Understanding the multifunctionality and complexities of biopores remains challenging. This contribution aims to showcase analytical ways to deepen our understanding of origin and functioning of biopores and hotspots. Regarding their biogeochemistry, biopore OM quality and its turnover can be better unravelled through compound‐specific analysis to deduct biopore‐specific OM turnover. Biopores can be reliably differentiated by their OM quality. A more profound understanding of subsoil C turnover in very contrasting hotspots is crucially important for managing subsoil functions. Biopores are often assumed to be beneficial in crop sequences. Roots making use of specific biopores can be, for the first time, quantified after radiotracer application, two‐step phosphor imaging, and image processing. Combining radioactive with stable isotopes as well as plant and microbial biomarkers allows to investigate the relevance of individual pore wall nutrients in plant growth in consideration of physical biopore properties. Biopore‐friendly management practices (e.g., reduced tillage, perennial cover cropping) could be part of smart subsoil management. Faster access to subsoil water and concentrated biopore nutrients may safeguard agricultural production—especially in times of rising fertiliser costs (both monetary and environmental) and more frequent droughts. [ABSTRACT FROM AUTHOR]

Rationale: Many bacteria synthesize carbon (C) and energy storage compounds, including water‐insoluble polyester lipids composed mainly or entirely of poly(3‐hydroxybutyrate) (PHB). Despite the potential significance of C and energy storage for microbial life and C cycling, few measurements of PHB in soil have been reported. Methods: A new protocol was implemented, based on an earlier sediment extraction and derivatization procedure, with quantification by gas chromatography/mass spectrometry (GC/MS) and 13C‐isotopic analysis by GC/combustion/isotope ratio mass spectrometry (GC/C/IRMS). Results: The PHB content was 4.3 μg C g−1 in an agricultural soil and 1.2 μg C g−1 in a forest topsoil. This was an order of magnitude more PHB than obtained by the existing extraction method, suggesting that native PHB in soil has been previously underestimated. Addition of glucose increased the PHB content by 135% and 1,215% over 5 days, with the largest increase in the relatively nutrient‐poor forest soil. In the agricultural soil, 68% of the increase was derived from added 13C‐labeled glucose, confirming synthesis of PHB from glucose for the first time in soil. Conclusions: The presence and responsiveness of PHB in both these contrasting soils show that PHB could provide a useful indicator of bacterial nutritional status and unbalanced growth. Microbial storage could be important to C and nutrient cycling and be a widespread strategy in the life of soil bacteria. The presented method offers new insight into the significance of this compound in soil. [ABSTRACT FROM AUTHOR]

Core Ideas: Our aim was to test whether mucilage promotes diffusion of nutrients in dry soil.Mucilage favors transport of nutrients in drying soil and their uptake by plant.Mucilage increases the soil moisture in the rhizosphere as soil dries.Mucilage maintains the connectivity of liquid phase in the rhizosphere as soil dries. Despite detailed investigations of its distinct biochemical properties and their effects on the availability of nutrients for plants, the biophysical aspects of the rhizosphere, particularly the effect of mucilage on the transport of water and nutrients, are poorly understood. The aim of this study was to investigate the effect of mucilage on the diffusion of nutrients and consequently their transport through the rhizosphere into the plant roots. Phosphor imaging technique determined the temporospatial distribution of 137Cs in a model rhizosphere (a sandy soil mixed with chia seed (Salvia hispanica L) mucilage. The observed profiles of activities were used to estimate the diffusion coefficient of K in soils. A diffusion–convection equation was numerically solved to predict the transport of K and its uptake by a single plant root in drying soil. The results suggest that mucilage (i) keeps the rhizosphere wet and (ii) maintains the connectivity of the liquid phase in drying soil. In these ways, mucilage moderates the drop in diffusive transport. The modeling results showed that the presence of mucilage in the rhizosphere (i) prevents depletion of nutrients in soils with a low nutrient concentration in the soil solution and (ii) delays the risk of nutrient and/or salt accumulation in the vicinity of the root in soils with a high concentration nutrient and/or salt the soil solution. In conclusion, mucilage appears to mitigate the risk of nutrient deficiency and salinity stress as it enhances the diffusive transport in drying soil. In this way, mucilage may favor the transport of nutrients within the rhizosphere and their uptake by plant roots in drying soil. [ABSTRACT FROM AUTHOR]

Most subsoil carbon (C) turnover occurs in biopore hotspots such as root channels and earthworm burrows. Biopores allocate large C amounts into the subsoil, where a vast capacity for long-term C sequestration is predicted. We hypothesise that organic matter (OM) cycling in biopores depends on their origin. Earthworm and root biopores were induced under field conditions and were sampled from the subsoil (45–75 and 75–105 cm) after two years of biopore formation. The effects of biopore formation on OM decomposition were studied by biomarkers: neutral sugars, cutin and suberin-derived lipids, lignin-derived phenols and free lipids. The degradation stage of OM was biopore type-specific but was only governed by the soil depth in root biopores. Degradation of OM increased from earthworm biopores to root biopores and bulk soil. Hemicelluloses (GM/AX ratio) were more strongly degraded than lignin side-chains (relative change from initial values). Two years of microbial processing during biopore formation increased the GM/AX ratio in earthworm biopores from 0.65 to 1.05 and in root biopores from 0.15 to 1.35 (both relative to source biomasses). Root biopores and bulk soil had the highest GM/AX ratios (1.2–1.3), hinting to rapid processing of plant residues and accumulation of microbial residues. The regular, frequent OM inputs by earthworms stimulated microbial growth and processing of mostly bioavailable OM and, thus, relatively enriched more persistent OM (e.g. lignin). Syringyl subunits of lignin underwent low (ratio changed from 0.35 to 0.55 relative to initial input) and vanillyl subunits underwent almost no processing in earthworm biopores indicating the preferential microbial utilisation of the easily available compounds frequently replenished by earthworm activity. After two years of decomposition of the root detritus, mainly structural plant material was enriched in root biopores. Short periods (6 months) of earthworm activity effectively recharged the highly processed OM in root biopores with fresh OM. In total, deep-rooting catch crops and short-term earthworm activities promote C accumulation in the subsoil followed by biopore-specific microbial processing predominantly governed by the C input frequency. As root biopores are up to 40 times more common than earthworm biopores, they dominate the OM input into subsoils. Such C inputs create several years lasting hotspots for preferential root growth and nutrient mobilisation in the subsoil. We conclude that root- and earthworm-derived biopores are vertical pathways for plant C from the soil surface into the subsoil and for intensive processing of litter C and sequestration of microbial necromass. [ABSTRACT FROM AUTHOR]

In South-Central Chile, slopes degraded by former erosion have been afforested with exotic tree species since the 1950s for erosion protection. From 1975 on, primary and secondary forests have increasingly been replaced by tree plantations. This practice is often justified by claiming plantations would similarly protect the soil from erosion, even on areas which used to be natural forest. We assessed if plantations offer a comparable level of erosion protection as the natural forests. A six-year-old Eucalyptus globulus (Labill.) plantation was compared to an adjacent secondary forest using soil profiles and erosion proxies, i.e. topsoil parameters linked to erosion and 137 Cs inventories. These pointed to higher erosion in the plantation: the mean bulk density of the plantation was 22% higher compared to the forest site, the gravel content in the plantation was 61% higher, the organic matter content was 20% lower, the mean thickness of the litter layer was 2.2 cm lower and the total sand content was 20% higher. The soil loss of the plantation was estimated to be between 4.8 cm (mean profile truncation) and 6 cm ( 137 Cs approach). These results clearly hint to the conclusion, that the tree plantations in South-Central Chile might promote soil erosion instead of preventing it. Thus, current land use management practices seem to impose erosion risks on Chilean soils raising concern about the sustainable development within the study site. [ABSTRACT FROM AUTHOR]

Root mucilage modulates soil-plant-water dynamics, but its interactions with microbial community functioning remain poorly understood. The aims of this study were to estimate (I) the impacts of mucilage and soil water content on the microbial community composition and (II) the mucilage consumption by individual microbial groups. C4 root mucilage from maize (at 40 and 200 μg C per gram dry soil, corresponding to 10 and 50% of soil microbial biomass, respectively) was added in single pulses to a C3 soil at two moisture levels: optimum (80% of water-holding capacity (WHC)) and drought (30% of WHC). After 15 days of incubation, the microbial community composition was studied by phospholipid fatty acids (PLFA) analysis and incorporation of mucilage-derived C into individual microbial groups was determined by compound-specific isotope analysis. Microbial community composition remained largely unaffected by mucilage addition but was affected by moisture. Whereas an increase in water content reduced mucilage C recovery in PLFA for the low-dose mucilage amendment from 19 to 9%, it had no effect under the high-dose amendment (11-12%). This suggests that the role of mucilage for microbial functioning is especially pronounced under drought conditions. The fungal PLFA 18:2ω6,9 was present only under drought conditions, and fungi profited in their mucilage C utilisation from the lower competitiveness of many bacterial groups under drought. In this study, Gram-negatives (G−, characterised by PLFA 18:1ω9c, 18:1ω7c, 16:1ω7c and cy17:0) showed the highest mucilage-derived C in PLFA, especially at the high-dose amendment, suggesting them to be the major decomposers of mucilage, especially when the availability of this C source is high. Gram-positives (G+) included different sub-groups with distinct responses to moisture: G+ 1 (a15:0) were only competitive for mucilage C under drought, whereas G+ 3 (i17:0) were only able to utilise mucilage-derived C under optimal moisture conditions. During the 15-day incubation, they built up more than 40% of their membranes from mucilage-derived C, suggesting that in the case of high availability, mucilage can act as an important C source for this microbial group. However, under drought, G− 1 and fungi were incorporating the most mucilage C into their membranes (approx. 20% of PLFA-C). The observation that, for some groups, the high-dose mucilage amendments under drought led to higher C incorporation into PLFA than under optimum moisture suggests that mucilage can compensate drought effects for particular microbial groups. Thus, mucilage may not only act as a C source for microorganisms but may also mitigate drought effects for specific rhizosphere microbial groups. [ABSTRACT FROM AUTHOR]

Background and aims: Biopores as microbial hotspots provide additional nutrients to crops - but only if their roots grow within the biopores. Such reuse has never been quantified as pre-crop-specific biopores are hardly differentiated from the multitude of pre-existing biopores. Quantification requires e.g. radionuclide labelling of pre-crops (Cs, to label their biopores) and main crops (C, to detect new roots). Preliminary testing was performed on simulated biopore reuse: both nuclides given to the same plant were excreted into the same rhizosphere. Methods: Cichorium intybus (cv. Puna) and Medicago sativa (cv. Planet) were each sequentially labelled via the leaves with Cs and CO. β-signals were visualised by imaging of horizontal soil cuts - with and without shielding off the weaker C. Results: Both species allocated 7.1-9.4% of the Cs and 21-63% of the C below ground. The first image gave both activities; while the second gave only Cs. Subtracting the second from the first image gave the C distribution, resulting in successful separation of the signals. Thus, separate spatial representations of the roots were obtained. Main root locations by Cs and C showed a very high spatial overlap coefficient (> 0.95). Conclusions: Biopore reuse quantification likely becomes feasible with this sequential labelling and shielding approach. [ABSTRACT FROM AUTHOR]

• Legumes interacted with abiotic site-characteristics affecting soil microbial activity. • Abiotic environmental factors indirectly controlled the basal respiration of microorganisms. • Soybean cultivation helped to overcome C limitation in savannah soils with low C stocks. Unsustainable farming systems for a growing population in Sub-Saharan Africa stress natural resources and lead to soil degradation. Legume cultivation, however, promotes soil microbial communities and may help reverse soil degradation. The soil properties (pH, texture, C and nutrient contents) of a set of contrasting sites from two agro-ecological zones of Cameroon were determined. This study characterises the microbial activities and functioning in rhizosphere soils of the four legumes Phaseolus vulgaris L., Glycine max L., Arachis hypogea L. and Vigna subterranea L. in a laboratory incubation experiment. Ecological indicators (total respiration, microbial biomass determined as total phospholipid fatty acids, metabolic quotient) of soil health were quantified after microbial activation by 14C-glucose and related to site-specific parameters as well as to the effects of legume cultivation. Microbial activation after glucose addition was frequently site-specific. Cumulative glucose respiration increased over time, and glucose pulses repeatedly boosted glucose respiration and total respiration at all sites. The microbial biomass was lowest after the experiment in the soil from the High Guinean Savannah except for soils under soybean cultivation. Among the four legumes cultivated, only soybeans strongly increased microbial biomass in the High Guinean savannah reaching even the level of microbial biomass in Western Highland soils. The lowest metabolic quotient in soybean rhizosphere soil and lowest glucose respiration compared to the soils of other legumes suggests a high carbon use efficiency, presumably due to C limitation in the High Guinean Savannah. Abiotic soil properties (pH, clay content) strongly influenced microbial habitat properties and thus had a positive effect on the CO 2 efflux, irrespective of glucose addition. Within the set of tested legumes, soybean cultivation can, therefore, be strongly recommended as a long-term sustainable crop to boost soil microbial functioning and probably also nutrient cycling, especially under low total organic carbon stocks. [ABSTRACT FROM AUTHOR]

In arable fields, biopores are primarily formed by taproots, but may also be bored by earthworms. Irrespective of the pore origin, repeated use by anecic earthworms yields a wall coating that is rich in carbon, nutrients and microorganisms. However, this effect is halted by routine tillage, and it remains unclear how quickly earthworms are able to alter biopore properties in subsoil. We conducted an earthworm incubation field experiment in arable soil to test the capacity of Lumbricus terrestri s to i. increase total nutrient contents including plant available P, ii. alter the microbial community and iii. increase enzyme activities in biopore walls over one vegetation period. Firstly, biopores that contained chicory roots were identified on a plot scale (4.2 × 1.5 m). After two years under fallow, roots were decomposed. We then inserted individual earthworms at 45 cm depth into a subset of these pores, afterwards refilling with topsoil. After six months, earthworms were removed and soil was opened at 45–75 cm and 75–105 cm soil depth layers. The inner pore wall (1 mm) of individual root biopores (‘RBP’) or root biopores modified by earthworms (‘EBP’) as well as the bulk soil were sampled in 6 depth intervals of 10 cm each and analyzed for total C, N, S content, plant available P, microbial biomass, phospholipid fatty acids (PLFA) and enzyme activity. Biochemical properties of bulk soil, RBP and EBP clearly differed after one vegetation period as indicated by principal component analysis. PLFA markers of fungi and protozoa were detected only in biopores. Compared with the bulk soil, total C, N, S were enriched in RBP by a factor of 2.0–3.1, plant available P by a factor of 8–10, and microbial biomass by a factor of 12–36. In EBP, all of these parameters were as in RBP or elevated even further (C, N, S: factor 1.0–1.4, plant available P: factor 1.3–1.5, microbial biomass: factor 1.5–2.0, PLFA markers of fungi: factor 2.6–4.4, PLFA markers of protozoa: factor 9.2–14.2). PLFA markers indicative of the ratio of Gram-positive to Gram-negative bacteria (G+: G−) were 5–10 fold lower in RBP than in bulk soil, the microbial metabolic quotient ( q CO 2 ) was 0.4–0.6 times as high. In EBP, these parameters were further reduced (ratio G+: G−: factor 0.7, q CO 2 : factor 0.7–0.8). RBP were particularly characterized by high contents of 10-methyl branched fatty acid indicators of actinobacteria. Activities of enzymes involved in the C-cycle (xylanase, cellobiohydrolase, ß-glucosidase) and N-cycle (chitinase, chitotriosidase, leucine aminopeptidase) were also elevated in RBP as compared to the bulk soil (factor 1.1–3.6) and further increased in EBP (factor 1.2–3.7). All these effects were more pronounced in the 45–75 cm soil layer. We conclude that, in only six months, L. terrestris in arable fields modified ordinarily nutrient-rich biopores into ‘super-hotspots’ of microbial biomass, enzyme activity and nutrient availabilities. Hence, even short-term promotion of earthworm populations by agricultural management practices can increase microbial biomass and enzyme activity in biopores and its coupling to nutrient mobilization in the subsoil. [ABSTRACT FROM AUTHOR]

Plastics accumulating in the environment, especially microplastics (defined as particles <5 mm), can lead to a range of problems and potential loss of ecosystem services. Polyhydroxyalkanoates (PHAs) are biodegradable plastics used in mulch films, and in packaging material to minimize plastic waste and to reduce soil pollution. Little is known, however, about the effect of microbioplastics on soil-plant interactions, especially soil microbial community structure and functioning in agroecosystems. For the first time, we combined zymography (to localize enzyme activity hotspots) with substrate-induced growth respiration to investigate the effect of PHAs addition on soil microbial community structure, growth, and exoenzyme kinetics in the microplastisphere (i.e. interface between soil and microplastic particles) compared to the rhizosphere and bulk soil. We used a common PHAs biopolymer, poly (3-hydroxybutyrate- co -3-hydroxyvalerate) (PHBV) and showed that PHBV was readily used by the microbial community as a source of carbon (C) resulting in an increased specific microbial growth rate and a more active microbial biomass in the microplastisphere in comparison to the bulk soil. Higher β-glucosidase and leucine aminopeptidase activities (0.6–5.0 times higher V max) and lower enzyme affinities (1.5–2.0 times higher K m) were also detected in the microplastisphere relative to the rhizosphere. Furthermore, the PHBV addition changed the soil bacterial community at different taxonomical levels and increased the alpha diversity, as well as the relative abundance of Acidobacteria and Verrucomicrobia phyla, compared to the untreated soils. Overall, PHBV addition created soil hotspots where C and nutrient turnover is greatly enhanced, mainly driven by the accelerated microbial biomass and activity. In conclusion, microbioplastics have the potential to alter soil ecological functioning and biogeochemical cycling (e.g., SOM decomposition). [Display omitted] • Microplastisphere (soil-MPs interface) is localized and visualized by zymography. • MPs stimulates microbial turnover and nutrient efficiency in microplastisphere. • MPs increases soil enzyme activity and shifts bacterial community to K -strategy. • MPs have the potential to alter soil functioning and biogeochemical cycling. [ABSTRACT FROM AUTHOR]

Biogeochemical cycles of phosphorus (P) and iron (Fe) are tightly interlinked, especially in highly weathered acidic subtropical and tropical soils rich in iron (oxyhydr)oxides (Fe(III)). The quantitative contribution of the reductive dissolution of Fe(III)-bound inorganic P (P i) (Fe–P) in low-redox paddy soils may cover the demands of rice plants (Oryza sativa L.) and microorganisms. We hypothesized that microbially-driven Fe(III) reduction and dissolution can cover the P demand of microorganisms but not of the young rice plants when the plants' P demand is high but their root systems are not sufficiently developed. We grew pre-germinated rice plants for 33 days in flooded rhizoboxes filled with a paddy soil of low P availability. 32P-labeled ferrihydrite (30.8 mg kg−1) was supplied either (1) in polyamide mesh bags (30 μm mesh size) to prevent roots from directly mobilizing Fe–P (pellets-in-mesh bag treatment), or (2) in the same pellet form but without a mesh bag to enable roots accessing the Fe–P (pellets-no-mesh bag treatment). Without mesh bags, P i was more available leading to increases in microbial biomass carbon (MBC) by 18–55% and nitrogen (MBN) by 4–108% in rooted soil as compared to P i pellets not directly available to roots. The maximum enzyme activities (V max) of phosphomonoesterase and β-glucosidase followed this pattern. During rice root growth, day 10 to day 33, MBC and microbial biomass phosphorus (MBP) contents in both rooted and bottom bulk (15–18 cm) soil gradually decreased by 28–56% and 47–49%, respectively. In contrast to our hypothesis, the contribution of Fe–P to MBP remarkably decreased from 4.5% to almost zero from 10 to 33 days after rice transplantation, while Fe–P compensated up to 16% of the plant P uptake at 33 days after rice transplantation, thus outcompeting microorganisms. Although both plants and microorganisms obtained P i released by Fe(III) reductive dissolution, this mechanism was not sufficient for the demand of either organism groups. [Display omitted] • 32P application can assess plant-microbial competitive dynamics for P absorbed by Fe. • Contribution of Fe–P to MBP decreased from 4.5% to almost zero with rice growth. • Fe–P compensated up to 16% of rice P uptake during 33 days after rice transplantation. • Rice plants outcompeted microorganisms for P at the tillering stage. [ABSTRACT FROM AUTHOR]

Plants stimulate microbial enzyme production in the rhizosphere, regulating soil organic matter decomposition and nutrient cycling. The availability of labile organic compounds (i.e. exudates) and water is the main prerequisite for such microbial activity and enzyme production, thus shaping the rhizosphere. Root morphology (i.e., root hairs) and exudate composition define the spatial distribution of properties and functions in the rhizosphere. However, the role of root architecture and exudate composition in this spatial self-organization of the rhizosphere remains unknown. We coupled three in situ imaging approaches: 14C imaging to localize exudates, soil zymography to analyze enzyme activity distribution, and neutron radiography for water fluxes to trace the spatial structure of the rhizosphere of three maize genotypes (wild-type, mutant with defective root-hair prolongation rth3 , and mutant with reduced benzoxazinoid content in root exudates bx1). The co-localization of these three soil images revealed the pivotal role of both optimal water content (neutron radiography) and root exudation (14C imaging) for β-glucosidase production by the rhizosphere microbiome and its hydrolytic activity (zymography). Root hairs increased the exudate release and enlarged the spatial extent of increased β - glucosidase activity around the root axis by 35%, leading to a two-fold faster decomposition of 14C exudates compared to the mutant with defective root hairs. In contrast, benzoxazinoids suppressed β - glucosidase activity by 30%, reflecting decreased microbial activity, whereas their absence broadened the rhizosphere. Overall, root hairs in wild-type maize increased microbial activity (i.e. β - glucosidase production), whereas the benzoxazinoids in root exudates suppressed microorganisms. [Display omitted] • Zymography, 14C imaging, and neutron radiography were coupled to localize rhizosphere processes. • Exudates are released at root tip in wild-type maize, but along the whole root in rth3 and bx1 mutants. • Root hairs enlarged the spatial extent of increased β - glucosidase activity around the root by 35%. • Benzoxazinoids (secondary metabolites) suppressed β - glucosidase activity in the rhizosphere by 30%. • Hotspot co-localization revealed that exudates and water increased β - glucosidase activity. [ABSTRACT FROM AUTHOR]

Despite the importance of subsoil carbon (C) deposition by deep-rooted crops in mitigating climate change and maintaining soil health, the quantification of root C input and its microbial utilization and stabilization below 1 m depth remains unexplored. We studied C input by three perennial deep-rooted plants (lucerne, kernza, and rosinweed) grown in a unique 4-m deep RootTower facility. 13C multiple pulse labeling was applied to trace C flows in roots, rhizodeposition, and soil as well as 13C incorporation into microbial groups by phospholipid fatty acids and the long-term stabilization of microbial residues by amino sugars. The ratio of rhizodeposited 13C in the PLFA and amino sugar pools was used to compare the relative microbial stability of rhizodeposited C across depths and plant species. Belowground C allocation between roots, rhizodeposits, and living and dead microorganisms indicated depth dependent plant investment. Rhizodeposition as a fraction of the total belowground C input declined from the topsoil (0–25 cm) to the deepest layer (360 cm), i.e., from 35%, 45%, and 36%–8.0%, 2.5%, and 2.7% for lucerne, kernza, and rosinweed, respectively, where lucerne had greater C input than the other species between 340 and 360 cm. The relative microbial stabilization of rhizodeposits in the subsoil across all species showed a dominance of recently assimilated C in microbial necromass, thus indicating a higher microbial stabilization of rhizodeposited C with depth. In conclusion, we traced photosynthates down to 3.6 m soil depth and showed that even relatively small C amounts allocated to deep soil layers will become microbially stabilized. Thus, deep-rooted crops, in particular lucerne are important for stabilization and storage of C over long time scales in deep soil. Image 1 • Rhizodeposition strongly declined with depth across all plant species. • Microbial stabilization of rhizodeposits increases with depth. • Deep-rooted crops are important for storage and stabilization of rhizodeposition. [ABSTRACT FROM AUTHOR]