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The concept of biomass growth is central to microbial carbon (C) cycling and ecosystem nutrient turnover. Microbial biomass is usually assumed to grow by cellular replication, despite microorganisms' capacity to increase biomass by synthesizing storage compounds. Resource investment in storage allows microbes to decouple their metabolic activity from immediate resource supply, supporting more diverse microbial responses to environmental changes. Here we show that microbial C storage in the form of triacylglycerides (TAGs) and polyhydroxybutyrate (PHB) contributes significantly to the formation of new biomass, i.e. growth, under contrasting conditions of C availability and complementary nutrient supply in soil. Together these compounds can comprise a C pool 0.19 ± 0.03 to 0.46 ± 0.08 times as large as extractable soil microbial biomass and reveal up to 279 ± 72% more biomass growth than observed by a DNA-based method alone. Even under C limitation, storage represented an additional 16–96% incorporation of added C into microbial biomass. These findings encourage greater recognition of storage synthesis as a key pathway of biomass growth and an underlying mechanism for resistance and resilience of microbial communities facing environmental change. Microbes are often assumed to reproduce as much as possible, but it has now been shown that soil microbes actually store a large part of their carbon intake. This could help microbial communities withstand environmental changes. [ABSTRACT FROM AUTHOR]

Aims: This study investigated the influence of climate and soil on the exudation rate and polysaccharide composition of aerial nodal root mucilage from drought-resistant and drought-susceptible maize varieties. Methods: Two maize varieties were grown in two different soils (sandy-clay loam Acrisol and loam Luvisol) under simulated climatic conditions of their agroecological zones of origin in Kenya and Germany. The exudation rate of mucilage from the aerial nodal roots was quantified as dry weight per root tip per day and the mucilage was characterized for its polysaccharide composition. Results: On average, the mucilage exudation rate was 35.8% higher under the Kenyan semi-arid tropical than under the German humid temperate climatic conditions. However, cultivation in the loam Luvisol soil from Germany led to 73.7% higher mucilage exudation rate than cultivation in the sandy-clay loam Acrisol soil from Kenya, plausibly due to its higher microbial biomass and nutrient availability. The drought-resistant Kenyan maize variety exuded 58.2% more mucilage than the drought-susceptible German variety. On average, mucilage polysaccharides were composed of 40.6% galactose, 26.2% fucose, 13.1% mannose, 11% arabinose, 3.5% glucose, 3.2% xylose, 1.3% glucuronic acid, and 1% an unknown uronic acid. Overall, significantly higher proportions of the uronic acids were found in the mucilage of the plants grown in the Kenyan sandy-clay loam soil and under the Kenyan semi-arid tropical climatic conditions. Conclusions: Maize is able to enhance its mucilage exudation rate under warm climatic conditions and in soils of high microbial activity to mitigate water stress and support the rhizosphere microbiome, respectively. [ABSTRACT FROM AUTHOR]

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]

Aims: Visualization of enzymatic activity links microbial functioning to localization in heterogeneous soil habitats. To assess enzymatic reactions in soil thin layer at the microscopic level, we developed a micro-zymography approach and tested it by visualization of the potential activity of phosphomonoesterase for aggregates collected from the rhizosphere of Zea mays L. Methods: We evaluated micro-zymography by applying fluorogenically-labeled substrate i) on individual soil aggregates freshly sampled from the rhizosphere, ii) on thin layers of aggregates (≈ 500 µm) saturated with substrate to assess the dynamics of phosphomonoesterase activity, and iii) on maize roots under laser scanning microscope upon the identified hotspots by membrane-based zymography. Results: We found super transparent silicon as the most appropriate fixative to prevent sample drying. We optimized microscope settings to eliminate the soil auto-fluorescence. The fluorescent signal shifted from the free liquid phase towards the aggregate boundaries within 30 min after substrate addition and was finally detectable at the surface of a few aggregates. This was probably due to higher microbial abundance and enzymatic activity on the soil aggregates compared to the liquid phase. The enzymatic activity appeared patchy at the aggregate and root surfaces indicating heterogeneous distribution of hotspots. Conclusions: The methodology including calibration, sample preparation, fixation, and monitoring was developed. The novel membrane-free micro-zymography approach is a promising tool to identify functional specificity and niche differentiation on roots and soil aggregates. This approach revealed unexplained complexity of competing processes (biochemical, hydrolytic, and physical) due to differently charged reaction products and enzyme-clay complexes. [ABSTRACT FROM AUTHOR]

Purpose: Mucilage plays crucial roles in root-soil interactions. Collection systems for maize (Zea mays L.) use primary and seminal roots of aeroponically-grown seedlings (CSA), or brace roots of soil-grown plants (CSB). While each method represents specific plant developmental stages, and root types growing in specific (micro-)environments, these factors are rarely considered. It is unclear whether mucilage exhibits distinct physico-chemical properties related to collection system-inherent factors. Methods: Mucilage of maize genotype B73 was collected from systems CSA and CSB. Chemical composition was assessed by pH, nutrient contents, neutral sugar composition, and polysaccharide polymer length. Viscosity, surface tension and contact angle represented physical properties. Results: The share of hexoses among total polysaccharides was 11% higher in CSB than in CSA, whereas pentoses were predominant in CSA, together with higher nutrient concentrations and pH values. Mannose was detected only in CSB, which also exhibited higher surface tension, viscosity and contact angle compared to CSA. Conclusions: Physico-chemical differences between the two mucilages are related to root type functions, environmental root growth conditions, and plant developmental state. Higher fractions of pentoses in CSA mucilage seem related to semi-sterile system conditions. Higher viscosity of CSB mucilage might reflect the need for enhanced water holding capacity of brace roots growing in drier conditions. A strong influence of environmental factors on mucilage properties even for a single genotype might play additional roles e.g. in the attraction of microbiomes. These aspects are relevant when assessing the role of mucilage in the rhizosphere, or when developing models of rhizosphere processes. [ABSTRACT FROM AUTHOR]

Comprehensive climate change mitigation necessitates soil carbon (C) storage in cultivated terrestrial ecosystems. Deep-rooted perennial crops may help to turn agricultural soils into efficient C sinks, especially in deeper soil layers. Here, we compared C allocation and potential stabilization to 150 cm depth from two functionally distinct deep-rooted perennials, i.e., lucerne (Medicago sativa L.) and intermediate wheatgrass (kernza; Thinopyrum intermedium), representing legume and non-legume crops, respectively. Belowground C input and stabilization was decoupled from nitrogen (N) fertilizer rate in kernza (100 and 200 kg mineral N ha−1), with no direct link between increasing mineral N fertilization, rhizodeposited C, and microbial C stabilization. Further, both crops displayed a high ability to bring C to deeper soil layers and remarkably, the N2-fixing lucerne showed greater potential to induce microbial C stabilization than the non-legume kernza. Lucerne stimulated greater microbial biomass and abundance of N cycling genes in rhizosphere soil, likely linked to greater amino acid rhizodeposition, hence underlining the importance of coupled C and N for microbial C stabilization efficiency. Inclusion of legumes in perennial cropping systems is not only key for improved productivity at low fertilizer N inputs, but also appears critical for enhancing soil C stabilization, in particular in N limited deep subsoils. [ABSTRACT FROM AUTHOR]

Optimization of land-use practices of rice cultivation for the mitigation of the most significant greenhouse gas (GHG) emissions from agriculture methane (CH4) and nitrous oxide (N2O) is challenging and requires confirmation from field studies. In northern Vietnam, we investigated the effects of water and rice residue management on GHG emissions and yields of rice. We used a 2 × 4 factorial design, comparing alternate wetting and drying (AWD) and conventional continuous flooding (Flood) water management, each with four different rice residue treatments: composted residues (compost), on-site burning (ash), plowing residues under (plow), and a control with removal of residues (CT). All plots received equal amounts of NPK fertilizer application. Water management was a major factor in reducing CH4 emissions. AWD management led to a reduction of CH4 emissions by 15−42% under the compost treatment, by 27−47% under ash, and by 36−45% under the plow treatment. Similarly, AWD management resulted in a reduction of the global warming potential (GWP) by 16−36% (CT), 15−39% (compost), 27−40% (ash), and 35−40% (plow), respectively. The latter led to the highest CH4 emissions, while the control (CT) showed the lowest CH4 emissions under both water management systems. Significantly higher N2O emissions were observed for all treatments under AWD water management compared to the respective treatments under flood management. This was especially pronounced after fertilization events. In conclusion, we recommend a combination of plowing under rice residues and AWD water management, as this combination resulted in reduced GHG emissions and lower GWP while ensuring high rice yields. [ABSTRACT FROM AUTHOR]

Mucilage, a gelatinous substance comprising mostly polysaccharides, is exuded by maize nodal and underground root tips. Although mucilage provides several benefits for rhizosphere functions, studies on the variation in mucilage amounts and its polysaccharide composition between genotypes are still lacking. In this study, eight maize (Zea mays L.) genotypes from different globally distributed agroecological zones were grown under identical abiotic conditions in a randomized field experiment. Mucilage exudation amount, neutral sugars and uronic acids were quantified. Galactose (∼39–42%), fucose (∼22–30%), mannose (∼11–14%), and arabinose (∼8–11%) were the major neutral sugars in nodal root mucilage. Xylose (∼1–4%), and glucose (∼1– 4%) occurred only in minor proportions. Glucuronic acid (∼3–5%) was the only uronic acid detected. The polysaccharide composition differed significantly between maize genotypes. Mucilage exudation was 135 and 125% higher in the Indian (900 M Gold) and Kenyan (DH 02) genotypes than in the central European genotypes, respectively. Mucilage exudation was positively associated with the vapor pressure deficit of the genotypes’ agroecological zone. The results indicate that selection for environments with high vapor pressure deficit may favor higher mucilage exudation, possibly because mucilage can delay the onset of hydraulic failure during periods of high vapor pressure deficit. Genotypes from semi-arid climates might offer sources of genetic material for beneficial mucilage traits. [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]

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]

Biopores are hotspots of nutrient mobilisation and shortcuts for carbon (C) into subsoils. C processing relies on microbial community composition, which remains unexplored in subsoil biopores. Phospholipid fatty acids (PLFAs; markers for living microbial groups) and amino sugars (microbial necromass markers) were extracted from two subsoil depths (45-75 cm ; 75-105 cm) and three biopore types: (I) drilosphere of Lumbricus terrestris L., (II) 2-year-old root biopores and (III) 1.5-year-old root biopores plus six 6 months of L. terrestris activities. Biopore C contents were at least 2.5 times higher than in bulk soil, causing 26-35 times higher Σ PLFAs g soil. The highest Σ PLFAs were found in both earthworm biopore types; thus, the highest soil organic matter and nutrient turnover were assumed. Σ PLFAs was 33% lower in root pores than in earthworm pores. The treatment affected the microbial community composition more strongly than soil depth, hinting to similar C quality in biopores: Gram-positives including actinobacteria were more abundant in root pores than in earthworm pores, probably due to lower C bioavailability in the former. Both earthworm pore types featured fresh litter input, promoting growth of Gram-negatives and fungi. Earthworms in root pores shifted the composition of the microbial community heavily and turned root pores into earthworm pores within 6 months. Only recent communities were affected and they reflect a strong heterogeneity of microbial activity and functions in subsoil hotspots, whereas biopore-specific necromass accumulation from different microbial groups was absent. [ABSTRACT FROM AUTHOR]

Biopores are pores or voids in soil produced by roots, by earthworms, or by the occupation of earthworms in root pores, which are considered important microbial hotspots, especially in subsoil. We hypothesized that earthworms ( Lumbricus terrestris L.) exert stronger effects on microbial activities than decaying plant roots (of Cichorium intybus L.) in the subsoil because of the addition of pre-digested organic material. We tested this hypothesis by analyzing microbial biomass (C), total organic C (C), and activities of eight enzymes (cellobiohydrolase, β-glucosidase, xylanase, acid phosphomonoesterase, leucine aminopeptidase, tyrosine aminopeptidase, chitotriosidase, and n-acetylglucosaminidase) down to 105-cm depth. The C increase was associated with a two- to threefold increase of C content in biopores as compared to bulk soil. The highest percentage of C-to-C (3.7 to 7.3 %) in the drilosphere demonstrated the enhancement of microbial efficiency for organic matter decomposition by earthworms. The availability of organic matter in biopores increased the activities of C- and N-targeting enzymes by 1.2-11.3 times, but reduced acid phosphomonoesterase activity by 10-40 % in biopores versus bulk soil. Introducing earthworms in root biopores caused 1.5-1.8 times higher microbial biomass and 1.2-1.9 times increased enzyme activities compared to the sole effect of earthworms. Soil depth showed a strong effect on the drilosphere, but only slight effects on the biochemical properties of root biopores and bulk soil. In conclusion, biopores are important microbial hotspots of C, N, and P transformations in subsoil. Earthworms exerted stronger effects on biochemical properties of biopores than decaying roots. [ABSTRACT FROM AUTHOR]