Efficiency Of Substrate Use Research Articles

Fate of low molecular weight organics in paddy vs. upland soil: A microbial biomarker approach

Low-molecular-weight organic carbon (LMWOC) from root exudate influences soil organic carbon cycling via priming of microbial activity. However, the mechanisms underlying the uptake and utilization of specific exudates by microorganisms in soils remain unclear. To address this gap in knowledge, a one-month 13C (0.1 mg C﹒g soil) tracer incubation study was conducted to investigate the fate of the most abundant root exudate groups (using 13C-labeled glucose, acetic acid, and oxalic acid) in paddy vs. upland soil. After 2 days of incubation, the microbial substrate use efficiency (SUE) was >80% in paddy soil, which was approximately 1.9, 2.9, and 1.3 times that in uplands with glucose, acetic acid, and oxalic acid addition, respectively. The SUE in paddy soil with glucose or acetic acid addition was always higher than that in uplands over time (P < 0.05). In both soils, the SUE of glucose was 1–4 times that of carboxylic acids (P < 0.05). The recovery of 13C-labeled total phospholipid fatty acids (PLFAs) in paddy soils was 1.5–2 times that in uplands (P < 0.05). In both soils, bacteria preferred to utilize glucose and acetic acid to synthesize cellular components. Throughout the incubation period, bacteria dominated over fungi in terms of LMWOC consumption. Gram-positive and -negative bacteria were dominant in upland and paddy soils, respectively. From days 11–30, the contribution of fungi and actinomycetes to LMWOC utilization began to appear. Temperature positively regulated 13C distribution in microbial groups (P < 0.05), and increased dissolved organic carbon in upland soil accelerated microbial SUE. The results of this study clarify microbial effects on the high soil carbon sequestration capacity of paddy soil as compared with upland in subtropical areas.

Susceptibility of new soil organic carbon to mineralization during dry-wet cycling in soils from contrasting ends of a precipitation gradient

The persistence of soil organic carbon (SOC) is influenced by soil physicochemical properties, organic matter quality, and climatic conditions that govern its vulnerability to microbial activity. We compared the susceptibility of newly formed SOC to mineralization in two soils (Andosols) that developed under contrasting precipitation regimes. Soil from the high rainfall region (‘highrain’) had higher SOC and lower iron concentrations than soils exposed to less rainfall (‘lowrain’). We amended soils with 13C-labeled carbohydrates and measured the amount of substrate-derived SO13C mineralized when exposed to dry-wet cycling following months-long incubations. We hypothesized that susceptibility would differ due to iron content and mineralogy, initial SOC, substrate solubility (cellulose versus glucose amendment), and microbial substrate use efficiency (SUE). We found that SO13C was less susceptible to dry-wet cycling when more 13C was assimilated into microbial biomass and co-localized with mineral surfaces than when co-localized with existing organo-mineral surfaces, according to microscale NanoSIMS imaging. Considerably less SO13C was susceptible to mineralization in the ferrihydrite-rich (low SOC) lowrain soil than the leached (high SOC) highrain soil when C was added as either glucose (7.3-fold less C mineralized) or cellulose (15.2-fold less). The SUE of glucose was comparable to cellulose in lowrain soil where SO13C was less water soluble and coprecipitated with ferrihydrite, and used half as efficiently as cellulose in highrain soil. Our results show that the susceptibility of newly formed SOC to mineralization is modified by the effects of bioavailability on microbial metabolism and the availability of mineral surfaces for forming new organo-mineral complexes.

Towards a mechanistic understanding of microbial and nonmicrobial mediated topsoil organic carbon sequestration efficiency in a rice-wheat cropping system

Paddy soils constitute the largest anthropogenic wetlands on earth, where microbial and non-microbial pathways jointly determine the fate of carbon from organic amendments. However, the specific mechanisms underlying these processes remain poorly understood. Here, we examined the influence of microbial anabolism versus catabolism and iron (Fe)-mediated soil organic carbon (SOC) protection versus decomposition on the topsoil carbon sequestration efficiency (CSE) of exogenous organic amendments in a rice-wheat cropping system subjected to nine years of no fertilizer (CT), chemical fertilizer (CF), 50% CF plus pig manure compost (CFM), 100% CF plus straw (CFS), 50% CF plus pig manure compost and straw (CFMS), and 87.5% CF plus pig manure compost (OICF) amendments. The CSE under CT and CFM was approximately 1.5- to 2.4-fold higher than that under the other four treatments. A structural equation model indicated that Fe-mediated free radical reactions and exogenous carbon inputs were negatively correlated with CSE, whereas soil microorganisms were positively correlated with CSE. Microbial biomass carbon and Fe-bound organic carbon were higher while the metabolic quotient, the ratio of microbial carbon-use efficiency to nitrogen-use efficiency and the percentage of Fe-bound organic carbon to SOC were lower under CFM and CFMS than under CF, CFS and OICF. The concentrations of ferrous Fe, oxalate-extractable Fe oxides, hydrogen peroxide and hydroxyl radicals were lower, but the activity of catalase was higher under CFM and CFMS than under CF, CFS and OICF. Therefore, partial substitution of chemical fertilizer with compost enhances topsoil CSE in three ways: directly through the input of refractory organic carbon, indirectly through improving the microbial substrate-use efficiency, and to a lesser extent through promoting the formation of organo-Fe complexes and accelerating the decay of hydrogen peroxide, thereby possibly serving as a management tool for attenuating terrestrial carbon-climate feedbacks.

Assessing the sustainability of land use management of northern Ethiopian drylands by various indicators for soil health

Abstract Land use change and agricultural intensification in developing countries affect terrestrial carbon (C) stocks, CO2 efflux, microbial communities and overall soil health. This study assesses the effects of four land use types typical for northern Ethiopia (forests, exclosures, grazing lands and intensively cultivated croplands) on various soil health indicators. We quantified and compared microbial biomass carbon (MBC), water extractable organic carbon (WOC), metabolic quotient (qCO2), substrate use efficiency (SUE) and dynamics of 14C-labelled glucose added to soil. Irrespective of the land use, MBC but not SUE decreased 2- to 8-fold with increasing depth, demonstrating the C limitation of subsoil microbial communities under all land use forms. Sandy soils, however, which permit seepage and leaching of WOC into lower layers and promote subsoil microbial communities, adapted to frequent input of easily accessible C substrates. Significantly higher qCO2 were recorded in subsoils compared to topsoils, especially in croplands with low MBC. In croplands, high glucose-14C incorporation (≈20%) into their low microbial biomass indicates a high SUE and reflects a better nutrient supply of these microbial communities. Mineralization of up to 95% of 14C-labeled glucose in topsoils of forest and grazing lands was higher than in croplands, and exclosures never reached the level of natural ecosystems. This demonstrates that 6–10 years of exclosure establishment does not result in soil microbial communities and soil C dynamics resembling those of natural forests. Our study demonstrates that land use can negatively affect the ecological performance of microbial communities and that these impacts are more severe in sandy than in clayey soils. Mitigation strategies such as minimum tillage or residue retention in intensively cultivated croplands can increase microbial abundance and activity and help ensure environmental sustainability and mitigation of climate change. Nonetheless, such measures need to be carefully accompanied by monitoring indicators of soil health to confirm the sustainability of the chosen mitigation strategies.

Soil organic matter quality exerts a stronger control than stoichiometry on microbial substrate use efficiency along a latitudinal transect

A substantial portion of soil organic matter (SOM) is of microbial origin. The efficiency with which soil microorganisms can convert their substrate carbon (C) into biomass, compared to how much is lost as respiration, thus co-determines the carbon storage potential of soils. Despite increasing insight into soil microbial C cycling, empirical measurements of microbial C processing across biomes and across soil horizons remain sparse. The theory of ecological stoichiometry predicts that microbial carbon use efficiency (CUE), i.e. growth over uptake of organic C, strongly depends on the relative availability of C and nutrients, particularly N, as microorganisms will either respire excess C or conserve C while mineralising excess nutrients. Microbial CUE is thus expected to increase from high to low latitudes and from topsoil to subsoil as the soil C:N and the stoichiometric imbalance between SOM and the microbial biomass decrease. To test these hypotheses, we collected soil samples from the organic topsoil, mineral topsoil, and mineral subsoil of seven sites along a 1500-km latitudinal transect in Western Siberia. As a proxy for CUE, we measured the microbial substrate use efficiency (SUE) of added substrates by incubating soil samples with a mixture of 13C labelled sugars, amino sugars, amino acids, and organic acids and tracing 13C into microbial biomass and released CO2. In addition to soil and microbial C:N stoichiometry, we also determined the potential extracellular enzyme activities of cellobiohydrolase (CBH) and phenol oxidase (POX) and used the CBH:POX ratio as an indicator of SOM substrate quality. We found an overall decrease of SUE with latitude, corresponding to a decrease in mean annual temperature, in mineral soil horizons. SUE decreased with decreasing stoichiometric imbalance in the organic and mineral topsoil, while a relationship of SUE with soil C:N was only found in the mineral topsoil. However, contrary to our hypothesis, SUE did not increase with soil depth and mineral subsoils displayed lower average SUE than mineral topsoils. Both within individual horizons and across all horizons SUE was strongly correlated with CBH:POX ratio as well as with climate variables. Since enzyme activities likely reflect the chemical properties of SOM, our results indicate that SOM quality exerts a stronger control on SUE than SOM stoichiometry, particularly in subsoils were SOM has been turned over repeatedly and there is little variation in SOM elemental ratios.

An Endohyphal Bacterium (Chitinophaga, Bacteroidetes) Alters Carbon Source Use by Fusarium keratoplasticum (F. solani Species Complex, Nectriaceae).

Bacterial endosymbionts occur in diverse fungi, including members of many lineages of Ascomycota that inhabit living plants. These endosymbiotic bacteria (endohyphal bacteria, EHB) often can be removed from living fungi by antibiotic treatment, providing an opportunity to assess their effects on functional traits of their fungal hosts. We examined the effects of an endohyphal bacterium (Chitinophaga sp., Bacteroidetes) on substrate use by its host, a seed-associated strain of the fungus Fusarium keratoplasticum, by comparing growth between naturally infected and cured fungal strains across 95 carbon sources with a Biolog® phenotypic microarray. Across the majority of substrates (62%), the strain harboring the bacterium significantly outperformed the cured strain as measured by respiration and hyphal density. These substrates included many that are important for plant- and seed-fungus interactions, such as D-trehalose, myo-inositol, and sucrose, highlighting the potential influence of EHB on the breadth and efficiency of substrate use by an important Fusarium species. Cases in which the cured strain outperformed the strain harboring the bacterium were observed in only 5% of substrates. We propose that additive or synergistic substrate use by the fungus-bacterium pair enhances fungal growth in this association. More generally, alteration of the breadth or efficiency of substrate use by dispensable EHB may change fungal niches in short timeframes, potentially shaping fungal ecology and the outcomes of fungal-host interactions.

Temperature sensitivity of substrate-use efficiency can result from altered microbial physiology without change to community composition

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.

Impact of reduced tillage and crop residue management on soil properties and crop yields in a long-term trial in western Kenya

Sustainable farming practices are required to address the persistent problems of land degradation and declining crop productivity in Sub-Saharan Africa. Approaches such as reducing tillage and retaining crop residues as mulch are potential entry points for smallholder farmers to move towards sustainability. In this study, we assessed the impact of reduced tillage (RT) compared with conventional tillage (CT), each combined with crop residue reapplication, on soil quality indicators and crop yields under an 8-year trial in western Kenya. Our results indicate that RT combined with crop residue reapplication enhanced soil physical quality through increased macroaggregate (&gt;2000µm) proportions and mean weight diameter. Similarly, lower respiratory quotient values indicate that soil microbes under RT have better substrate-use efficiency than those under CT. Nevertheless, soil organic carbon (C), potentially mineralisable C, microbial biomass C and mineral nitrogen contents were all higher under CT with crop residue incorporated into the soil. Maize grain yield and aboveground biomass were also higher under CT. Thus, despite RT showing potential to improve soil physical properties, CT performed better. A stepwise approach is proposed towards the practice of conservation agriculture under resource-constrained smallholder farming conditions, starting with increased biomass production to provide crop residue for soil cover, followed by RT approaches.

Microbial physiology and soil CO2 efflux after 9 years of soil warming in a temperate forest - no indications for thermal adaptations.

Thermal adaptations of soil microorganisms could mitigate or facilitate global warming effects on soil organic matter (SOM) decomposition and soil CO2 efflux. We incubated soil from warmed and control subplots of a forest soil warming experiment to assess whether 9 years of soil warming affected the rates and the temperature sensitivity of the soil CO2 efflux, extracellular enzyme activities, microbial efficiency, and gross N mineralization. Mineral soil (0–10 cm depth) was incubated at temperatures ranging from 3 to 23 °C. No adaptations to long‐term warming were observed regarding the heterotrophic soil CO2 efflux (R 10 warmed: 2.31 ± 0.15 μmol m−2 s−1, control: 2.34 ± 0.29 μmol m−2 s−1; Q 10 warmed: 2.45 ± 0.06, control: 2.45 ± 0.04). Potential enzyme activities increased with incubation temperature, but the temperature sensitivity of the enzymes did not differ between the warmed and the control soils. The ratio of C : N acquiring enzyme activities was significantly higher in the warmed soil. Microbial biomass‐specific respiration rates increased with incubation temperature, but the rates and the temperature sensitivity (Q 10 warmed: 2.54 ± 0.23, control 2.75 ± 0.17) did not differ between warmed and control soils. Microbial substrate use efficiency (SUE) declined with increasing incubation temperature in both, warmed and control, soils. SUE and its temperature sensitivity (Q 10 warmed: 0.84 ± 0.03, control: 0.88 ± 0.01) did not differ between warmed and control soils either. Gross N mineralization was invariant to incubation temperature and was not affected by long‐term soil warming. Our results indicate that thermal adaptations of the microbial decomposer community are unlikely to occur in C‐rich calcareous temperate forest soils.

Effects of silver nanoparticles on the microbiota and enzyme activity in soil

AbstractTo assess the impact of silver nanoparticles (SNP) on soil microbial biomass, microbial activity, and enzyme activities, a medium‐term experiment over four months was performed in which soil was applied with increasing SNP‐application rates compared to a control. The treatments included a single SNP‐application dose analogous to 3.2 (SNP‐1), 32 (SNP‐10), and 320 (SNP‐100) μg Ag (kg dry soil)–1 and a control without SNP application, respectively. At the end of the experiment, clear evidence was found that microbial biomass was significantly decreased with increasing SNP‐application rate, while basal respiration was increased in this direction. In addition, metabolic quotients were increased in the SNP treatments compared to the control. This is at least circumstantial evidence that the efficiency of substrate use was lowered in SNP‐treated soils. Another suggestion might be that after four months microbial‐community composition was changed due to SNP. No treatment effects were found for microbial biomass N, fluorimetric enzymes, and the abiotic soil parameters pH and soil organic C.

Defoliation effects on carbon and nitrogen substrate import and tissue‐bound efflux in leaf growth zones of grasses

ABSTRACTGrassland plants suffer regular defoliation, causing loss of photosynthetic activity and internal resources. Consequently, re‐foliation may be substrate‐limited. The present study was undertaken to test the hypothesis that decreased C import in leaf growth zones is (partially) compensated by: (i) mobilization of substrate within growth zones; and (ii) increased efficiency of substrate use in leaf area expansion; but (iii) that these processes depend on the C status of growth zones at defoliation. Mixtures of a C3 (Lolium perenne L.) and a C4 grass (Paspalum dilatatum Poir.) were grown at 15 °C (C3 dominance) and 23 °C (C4 dominance). Individual plants thus grew in contrasting (light and temperature) environments before being defoliated. Defoliation caused a drastic and immediate decrease in C import, but effects on leaf area expansion were buffered by biomass mobilization in the growth zone and increases in specific leaf area of produced tissue. Thus, over the first 2 d post‐defoliation, the amount of leaf area produced per unit imported C increased by 39 to 102% depending on treatment. The magnitude of these buffering responses was correlated with the concentration of water soluble carbohydrates in the growth zone at defoliation. Similar responses were observed for N, although defoliation effects were smaller and delayed relative to those on C import. This study demonstrates refoliation is sustained by short‐term mobilization of reserves within the growth zone and reduced costs of produced leaf area, but that these mechanisms depend on growth zone C status at defoliation.

Soil structure and characteristics of organic matter in two orchards differing in earthworm activity

By consuming plant remains and soil, earthworms incorporate organic matter (OM) into the soil and form biogenic soil structures, which can affect OM dynamics. We carried out a (micro)morphological study of soil structure development and OM distribution in two orchards (45 year) in a Dutch calcareous marine loam: RI − without, and KR + with high earthworm activity, the result of different levels of heavy metal contamination from fungicides. In both soils, sedimentary–stratification was absent to 60 cm depth and equal amounts of biogenic calcite spheroids were counted, suggesting similar earthworm activity in the past. In RI − the current vol.% of worm-worked groundmass in thin sections was 6% in the Ah and 7% in the Bw horizon compared with 51% in the Ah and 16% in the Bw horizon of KR +. Disappearance of earthworms with time in RI − gave rise to a compacted physicogenic soil structure with angular and prismatic aggregates and the absence of earthworm biopores. Due to restricted fragmentation and incorporation of OM fragments in casts, a litter layer formed at the soil surface. OM coatings were present in fissures and root pores of the Ah horizon, indicating the absence of mixing of organic and mineral soil materials. OM fragments were relatively coarse (>50 μm) and heterogeneously distributed through the Ah groundmass. Stronger decalcification in RI − than in KR + could be ascribed to higher production of organic acids in the litter layer of RI − and the absence of soil homogenisation by earthworms. In KR + earthworm activity was high, which has resulted in a biogenic structure with granular and subangular blocky aggregates and many worm casts and biopores. Particulate OM was relatively fine (<50 μm) and encapsulated with clayey material in casts and micro-aggregates. The organic C content was not significantly ( P<0.05) higher in the Ah horizon of KR +, than in the Ah horizon of RI − (15.7 and 13.7 g kg −1, respectively). The lower C mineralization rates in KR + below 6 cm depth, however, might be an indication of higher microbial substrate-use efficiency or physical protection of OM against decomposition. The latter explanation would accord with the observed encapsulation of OM in micro-aggregates, and with studies on other management systems that favour biogenic aggregate formation. The quality of the soil macro- and microstructures, degree of soil compaction and decalcification and soil OM dynamics were strongly determined by the occurrence of earthworms in soils.

Assessing changes in physical and biological properties in a soil contaminated by oil sludges under semiarid Mediterranean conditions

We have studied the changes in biological and physical properties of a soil, in a semiarid area, contaminated by hydrocarbons in order to predict the potential for bioremediation of this soil. The microbial biomass C, the basal respiration and the metabolic quotient ( qCO 2) of contaminated soil were significantly higher than that of the control soil, which points to a markedly reduced efficiency of substrate use and to a possible toxic effect of hydrocarbons in the soil. The low global rate of mineralisation in the contaminated soil also indicates the presence of hydrocarbons resistant to biodegradation. The dehydrogenase activity and the activities of hydrolases involved in the N and P cycles (urease, protease and phosphatase) were stimulated by the contamination with hydrocarbons. Soil total porosity was increased by the contamination, about 15-fold in comparison with the control soil. The contamination by hydrocarbons led to an increase in cracks in the 100–200 μm size classes, which can be regarded as a reservoir to hold water for plants and microorganisms. The biodegradation of hydrocarbons in this soil would require long periods of time, and it would be advisable to apply methods of bioremediation to this contaminated soil.

NICCE: a model for cycling of nitrogen and carbon isotopes in coniferous forest ecosystems

A process-oriented dynamic simulation model for turnover of N and C isotopes in coniferous forest ecosystems has been developed. The model is used to interpret results of experiments on nitrogen saturation and reversibility of nitrogen saturation conducted within a gradient of N-deposition in Europe. Observed and simulated nitrate concentrations in the soil solution both responded quickly to reduced input in an experiment, with N-input in throughfall excluded. Foliar N-concentrations decreased more slowly, and were observed to be unchanged over a 2-year period. Due to isotope fractionation processes δ 15N values of ecosystem compartments are predicted to increase for systems approaching N-saturation, due to output of nitrate and denitrification products being relatively depleted in 15N. Sensitivity analysis of the model revealed a strong influence of the microbial substrate-use efficiency for organic carbon on input/output budgets of N. Factors causing an increase of primary production such as increasing CO 2 concentration are predicted to result in decreased nitrate concentrations. The model has hitherto been calibrated with conventional 14N data. Labeling with 15N on the scale of forest stands, and small head-water catchments, is currently being carried out to follow the fate of atmospheric nitrogen input, and to compare model behavior with turnover of 15N in coniferous forest ecosystems.