Do water regimes affect iron‐plaque formation and microbial communities in the rhizosphere of paddy rice?

Pot experiments were conducted to investigate the effect of soil water regimes on the formation of iron (Fe) plaque on the root surface of rice seedlings (Oryza sativa L.) and on the microbial functional diversity in a paddy soil. The rice seedlings were subjected to three moisture regimes (submergence, 100%, and 60% water‐holding capacity [WHC]), and were grown for 5 and 11 weeks. Aerobic lithotrophic Fe(II)‐oxidizing (FeOB) and acetate‐utilizing Fe(III)‐reducing bacteria (FeRB) in the rhizosphere and non‐rhizosphere soil were determined at 5 weeks using the most probable number (MPN) method. The carbon substrate use patterns of the microbial communities in the rhizosphere and non‐rhizosphere soil samples were determined at 11 weeks using Biolog‐GN2 plates. The amount of Fe plaque (per unit dry root weight) was much higher under submerged conditions than at lower soil moisture contents and decreased with plant age. There was a positive correlation between the amount of Fe plaque and phosphorus accumulated in the Fe plaque at both sampling times (r = 0.98 and 0.92, respectively, n = 12). Numbers of FeOB and FeRB in the submerged soil were lower than in aerobic soil, but by two orders of magnitude higher in the rhizosphere than in the bulk soil. On the other hand, the functional diversity of the rhizosphere microbial communities was much higher than that of the non‐rhizosphere soil, irrespective of soil water regimes. We conclude that soil flooding results in a decreased number and diversity of Fe‐oxidizing/reducing bacteria, while increasing the Fe‐plaque formation.     

Do nitrogen isotope patterns reflect microbial colonization of soil organic matter fractions?

Different theories have been brought forward to explain the commonly observed δ¹⁵N enrichment with depth in soil profiles, including the discrimination against ¹⁵N during N decomposition and the buildup of ¹⁵N-enriched microbial residues. A combination of soil organic matter (SOM) size and density fractionations, ¹⁵N determinations, and phospholipid fatty acid (PLFA) analyses was conducted on soils from a pristine N-limited Nothofagus forest in southern Chile. The purpose of this study was to investigate which SOM fractions mostly reflect the ¹⁵N-enrichment pattern and to link ¹⁵N SOM enrichment with microbial community composition. Nitrogen-15 enrichments were greater for the microaggregate (<150 μm) than for the macroaggregate (>150 μm) size fraction, with Rayleigh isotope enrichment factors averaging −8.5‰ and −3.7‰, respectively. The macro-organic matter density fractions (>150 μm) showed intermediate enrichment factors of −5.1‰ and −7.3‰ for the light (<1.37 g cm⁻³) and heavy (>1.37 g cm⁻³) fraction, respectively. The abundance of fungal and bacterial PLFAs was significantly higher in the microaggregate compared to the macroaggregate size fraction, but their relative abundance did not change between aggregate size fractions. Our data link differential ¹⁵N enrichment of SOM fractions to “total” microbial abundance and, as such, corroborates existing theories of microbial-induced ¹⁵N enrichment. Isotopic fractionation during microbial N decomposition processes alone could not explain the large ¹⁵N enrichment in the microaggregate size fraction (−8.5‰) and the heavy density fraction (−7.3‰). We therefore suggest that microbial turnover and accretion of ¹⁵N-enriched microbial (especially fungal) compounds was an additional driver for ¹⁵N enrichment of this soil profile.     

Do organic inputs alter resistance and resilience of soil microbial community to drying?

Grassland ecosystems in south-eastern Australia are important for dairy and livestock farming. Their productivity relies heavily on water availability, as well as the ecosystem services provided by soil microbial communities including carbon and nutrient cycling. Management practices such as compost application are being encouraged as a means to improve both soil water holding capacity and fertility, thereby buffering against the impacts of increasing climate variability. Such buffering consists of two complementary processes: resistance, which measures the ability of an ecosystem to maintain community structure and function during a period of stress (such as drying); and resilience, which measures the ability of an ecosystem to recover community structure and function post-stress. We investigated the effects of compost on the resistance and resilience of the grassland soil ecosystem under drying and drying with rewetting events, in a terrestrial model ecosystem. Overall, compost addition led to an increase in soil moisture, greater plant available P and higher plant δ¹⁵N. Soil C:nutrient ratios, mineral N content (NH₄⁺ and NO₃⁻) and soil microbial PLFA composition were similar between amended and unamended soils. Rainfall treatment led to differences in soil moisture, plant above-ground and below-ground biomass, plant δ¹⁵N, soil mineral N content (NH₄⁺ and NO₃⁻) and microbial biomass C, N and P composition but had no effects on soil C:nutrient ratios, plant available P and soil microbial PLFA composition. There was little interaction between rainfall and compost. Generally, the soil microbial community was resistant and resilient to fluctuations in rainfall regardless of compost amendment. However, these properties of the soil microbial community were translated to resilience and not resistance in soil functions. Overall, the results below-ground showed much greater response to rainfall than compost amendment. Water was the key factor shaping the soil microbial community, and nutrients were not strong co-limiting factors. Future projections of increasing rainfall variability will have important below-ground functional consequences in the grassland, including altered nutrient cycling.     

Do general spatial relationships for microbial biomass and soil enzyme activities exist in temperate grassland soils?

In heterogeneous environments such as soil it is imperative to understand the spatial relationships between microbial communities, microbial functioning and microbial habitats in order to predict microbial services in managed grasslands. Grassland land-use intensity has been shown to affect the spatial distribution of soil microorganisms, but so far it is unknown whether this is transferable from one geographic region to another. This study evaluated the spatial distribution of soil microbial biomass and enzyme activities involved in C-, N- and P-cycling, together with physico-chemical soil properties in 18 grassland sites differing in their land-use intensity in two geographic regions: the Hainich National Park in the middle of Germany and the Swabian Alb in south-west Germany. Enzyme activities associated with the C- and N-cycles, namely β-glucosidase, xylosidase and chitinase, organic carbon (C_org), total nitrogen (N_t), extractable organic carbon, and mineral nitrogen (N_min) were higher in the Swabian Alb (Leptosols) than in the Hainich National Park (primarily Stagnosols). There was a negative relationship between bulk density and soil properties such as microbial biomass (C_mic, N_mic), urease, C_org, and N_t. The drivers (local abiotic soil properties, spatial separation) of the enzyme profiles (β-glucosidase, chitinase, xylosidase, phosphatase, and urease) were determined through a spatial analysis of the within site variation of enzyme profiles and abiotic properties, using the Procrustes rotation test. The test revealed that physical and chemical properties showed more spatial pattern than the enzyme profiles. β-glucosidase, chitinase, xylosidase, phosphatase, and urease activities were related to local abiotic soil properties, but showed little spatial correlation. Semivariogram modeling revealed that the ranges of spatial autocorrelation of all measured variables were site specific and not related to region or to land-use intensity. Nevertheless, land-use intensity changed the occurrence of spatial patterns measurable at the plot scale: increasing land-use intensity led to an increase in detectable spatial patterns for abiotic soil properties on Leptosols. The conclusion of this study is that microbial biomass and functions in grassland soils do not follow general spatial distribution patterns, but that the spatial distribution is site-specific and mainly related to the abiotic properties of the soils.     

Do elevated soil concentrations of metals affect the diversity and activity of soil invertebrates in the long‐term?

This study aimed to elucidate the response of diversity and activity of soil invertebrates to elevated soil metal concentrations that were a result of sewage sludge application. Field sampling of soil invertebrates was carried out from 2002 to 2004 at an experimental site established in 1982 to test the effects on crop production of metal contamination from sewage sludge applications with elevated concentrations of zinc (Zn), copper (Cu) and nickel (Ni) with certain treatments exceeding the current UK statutory limits for the safe use of sludge on land. At metal concentrations within the limits, none of the invertebrates sampled showed adverse effects on their abundance or overall community diversity (from Shannon–Weiner index). At concentrations above the limits, individual taxa showed sensitivity to different metals, but overall diversity was not affected. Earthworm abundance was significantly reduced at total Cu concentrations at and above 176 mg kg^?1, while nematode and enchytraeid abundances were sensitive to Cu and high Zn concentrations. Correspondingly, litter decomposition was lower in Zn and Cu treatments although there was no direct relationship between decomposition and soil invertebrate abundance or diversity. Such enduring changes in both soil biodiversity and biological activity around the current UK regulatory limits warrant further investigation to determine whether they indicate detrimental damage to soil functioning over the long‐term.     

Soil microbial communities and enzyme activities in a reclaimed coastal soil chronosequence under rice–barley cropping

Purpose

A field experiment with a reclamation chronosequence under rice?Cbarley cropping was conducted to investigate soil enzyme activities and microbiology in a coastal saline soil. The aim of this study was to test whether changes in enzyme activity and microbial community structure are directly impacted by changes in soil pH, electrical conductivity (EC), and organic carbon (SOC) due to reclamation.

Materials and methods

The research area is located in south-eastern China. Four experimental sites were reclaimed in 1976, 1984, 1996, and 2006, respectively, and each site was divided into three plots, each of which was 22?m?×?10?m. Each year, the plots were planted with rice (cv Xiushui) in summer and barley (cv Yanmai) in winter. Soil pH and EC were determined in an aqueous suspension with a 1:5 ratio of soil and water. Soil organic carbon content was measured by dichromate oxidation with heating. Measured soil enzyme activities included catalase, urease, and protease. Soil microbial community structures were assessed using denaturing gradient gel electrophoresis.

Results and discussion

Reclamation under rice?Cbarley cropping reduced EC and pH, but increased SOC, the activities of catalase, urease and protease, and the cell numbers of bacteria, actinomycetes, and fungi, resulting in an increase in the bacterial community diversity. The enzyme activities and bacterial community diversity were significantly positively correlated with SOC, and negatively correlated with pH and EC. Five bacterial groups related to Gaetbulibacter, Sporosarcina, Flavobacterium, Aequorivita, and Gillisia, which have been associated with saline waters, did not appear in the soils that had been reclaimed prior to 1996.

Conclusions

Results of this field study suggest that soil properties which affect microbial activity such as EC, pH, and SOC significantly influence the activities of catalase, urease, and protease, and microbial community composition. More than 10?years after reclamation under rice?Cbarley cropping, EC had decreased and bacteria typically found in marine and saline environments had disappeared from the soil.     

Do boundaries of soil animal and plant communities coincide? A case study of a Mediterranean forest in Russia

We studied the relationship between plant and soil animal communities by geostatistical analysis in a piedmont forest close to Novorossiysk (Southern Russia). Vegetation on the slope of a hill was an oak-ash-hornbeam forest, while the vegetation on the foot of the hill was a maple-ash-hornbeam forest. Two plots were studied each including both slope and foot habitats. On every plot samples collected formed a grid of 10 × 5 units with a 5 m distance between them. Soil macroinvertebrates were hand-sorted from the samples, and several soil parameters (soil, pebble, and litter mass, soil moisture) were measured.The analysis did not reveal coincidence between the boundaries of plant and soil animal communities on the bend of the hill. Soil animal communities of the plots were dominated by woodlice, diplopods, and insect larvae, reaching an abundance of 680–990 individuals m⁻² throughout the plots. Number of taxonomic groups per sample and overall animal abundance in the bend were the highest in both plots, whilst these parameters on the slope were the lowest. Variograms and maps of spatial distribution indicated that the boundary between soil animal communities was situated further up on the slope than the vegetation boundary. The size of the animal community was smaller than the size of plots sampled, what probably explained the lack of coincidence between the boundaries. There was a significant correlation between distribution of litter mass and parameters of soil animal communities, which was modulated by depth of soil layer and soil moisture. Soil parameters were more important for explaining boundaries between soil animal communities than plant communities in the forest considered.     

Impact of soil fumigation practices on soil nematodes and microbial biomass

This study was designed to understand the impact of methyl bromide (MB) (CHaBr) and its alternatives on both free-living and root-knot nematodes in the soil. A randomized complete block experiment with six treatments and 4 replicates (each replicate in a separate greenhouse) was established in Qingzhou, Shandong Province, China. In addition to MB and untreated control (CK) treatments there were four alternative soil fumigation practices including MB virtually impermeable films (VIF), metam sodium (MS), MS VIF and soil solarization combined with selected biological control agents (SS BCA). Two tomato (Lycopersicum esculentum Mill.) cultivars, cv. Maofen-802 from the Xian Institute of Vegetable Science, China, and cv. AF179 Brillante from the Israeli Hazera Quality Seeds, were selected as test crops. The results indicated that Rhabditidae was the most dominant population with percentage abundance as high as 85% of the total number of identified free-living nematodes, followed by that of Cephalobidae. Methyl bromide and its alternatives except for the non-chemical SS BCA treatment controlled the target pest, root-knot nematodes. Also, the impact of the three chemical alternatives on free-living nematode number and functional group abundance was similar to the impact associated with a typical methyl bromide application. Chemical fumigation practices, especially that with MB, significantly reduced the number of nematodes in the soil and simultaneously significantly reduced the number of nematode genera thereby reducing nematode diversity. All the four soil chemical fumigation activities decreased soil microbial biomass and had an obvious initial impact on microorganism biomass. Furthermore, both plant-parasitic and fungivore nematodes were positively correlated with soil microbial biomass.     

Does antimony affect microbial respiration in Mediterranean soils? A microcosm experiment

The aim of this study was to determine the effects of antimony on soil microbial respiration. Two Mediterranean calcareous soils were sampled: a contaminated soil close to an abandoned lead and silver smelter and a soil far from the pollution source and considered not to be contaminated. Two forms of antimony, antimony trioxide (Sb₂O₃) and potassium antimonyl tartrate trihydrate (C₈H₄K₂O₁₂Sb₁₂·3H₂O), were tested at three concentrations (50, 500 and 5000 ppm) in controlled conditions under short- (3 days) and medium- (3 months) term incubation. Modifications in the substrate-induced respiration (SIR) were assessed by gas chromatography respirometric measurements. Results clearly showed that SIR was immediately and significantly more affected by Sb input in a non-contaminated soil than in a long-term contaminated soil, especially since the concentration was high and Sb was added to a more soluble and available form (tartrate instead of mineral oxide).     

Biochar amendment changes temperature sensitivity of soil respiration and composition of microbial communities 3 years after incorporation in an organic carbon-poor dry cropland soil

Topsoil samples were collected from plots in a dry cropland in the North China Plain 3 years after a single incorporation of biochar at 20 and 40 t ha^?1 and analyzed for abundances and composition of microbial community and for respiration under controlled laboratory conditions at 15, 20, and 25 °C. The addition of biochar generally reduced soil respirations at the three temperatures and the temperature sensitivity (Q₁₀) at 15–20 °C. Biochar amendment significantly increased bacterial 16S rRNA gene abundances and fungal ITS gene diversity and induced clear changes in their community compositions due to improvements in soil chemical properties such as soil organic C (SOC) and available N contents and pH. Illumina Miseq sequencing showed that the relative abundances of Actinobacteria, Gammaproteobacteria, Firmicutes, and Alternaria within Ascomycota, capable of decomposing SOC, were significantly decreased under biochar at 40 t ha^?1. The Q₁₀ values at 15–20 °C were significantly correlated with fungal diversity and dehydrogenase activity. Our results suggest that after 3 years a single biochar amendment could induce a shift in microbial community composition and functioning towards a slower organic C turnover and stability to warming, which may potentially reduce soil C loss in dryland under climate warming in the future.     

Can sieving size affect the determination of soil available micronutrients?

<正>Dear Editor,Globally, approximately two billion people suffer from micronutrient deficiencies(Tulchinsky, 2010; Myers et al.,2014).Soil micronutrient availability is of great importance for the evaluation of soil fertility and the determination of appropriate measures for improving crop quality and human health.The diethylenetriamine-penta-acetic(DTPA)     

Does altered rainfall regime change pesticide effects in soil? A terrestrial model ecosystem study from Mediterranean Portugal on the effects of pyrimethanil to soil microbial communities under extremes in rainfall

In this century, agroecosystems are subjected to multiple global change stressors acting in concert such as alterations in rainfall regimes and pesticide use. Alterations in rainfall regimes, characterised by more extreme intra-annual rainfall regimes, have been forecasted for the Mediterranean region. At the same time, the use of pesticides continues to rise. Here, we report the responses of soil microbial community to a model pesticide, i.e., fungicide pyrimethanil (PYR) under altered rainfall regimes (i.e., drought and heavy rainfall) two and eight weeks after PYR application. We measured the functional responses as enzyme activities, potential nitrification and BIOLOG carbon substrate utilisation. We also characterised the soil bacterial communities using polymerase chain reaction–denaturing gradient gel electrophoresis (PCR–DGGE) method. After two weeks, enzyme activities were mainly responsive to PYR and kinetic parameters, calculated from BIOLOG carbon substrate utilisation, indicated interaction effects from PYR and rain treatments. Bacterial band richness increased with PYR treatment under normal rain and drought regimes, but bacterial band richness was higher at 1X than 5X PYR under heavy rainfall. Bacterial community structure was also different with the PYR and rainfall treatments. By week eight, PYR treated soils remained functionally different from untreated soils. Bacterial band richness was consistent across PYR treatment regardless of rain regime. However, the bacterial community structure remained significantly different among the PYR treatments under different rain regimes. We conclude that rainfall extremes can alter the effect of PYR on the soil microbial community structure without altering PYR effects on soil functions (measured as enzyme activities, potential nitrification and BIOLOG carbon substrate utilisation).     

Do different agronomic soil tests identify similar nutrient deficiencies?

Traditionally, locally calibrated soil tests were used for fertilizer and lime recommendations. Farmers and advisors are increasingly using new ‘universal’ soil tests without local calibration. The objective of this study was to compare five commercially available soil tests and to determine whether they would provide similar recommendations. In total, 24 fields in Western Finland were sampled for 4 years while being treated with fertilizers, lime and manure. The soil samples were analysed with Mehlich-3, ammonium acetate, H3A, hydrochloric acid and mild acetic acid (Spurway) extractants. In addition, Soil Health Tool (CO₂ burst, water-soluble C and N) and tissue testing were conducted. The different tests extracted different orders of magnitude of nutrients (especially P and Mg), but the results from the different extractions were correlated. Mehlich-3 degree of phosphorus saturation (DPS) presented a threshold, below which soluble phosphorus was not detected. Similar thresholds were found for P, S and Mg. Mehlich-3 and ammonium acetate provided similar results for Ca, Mg and K and can be used interchangeably for liming recommendations. Mehlich-3 identified more fields with Zn, Cu, B and S deficiencies and less fields with Mn deficiencies compared with ammonium acetate + EDTA and tissue testing. The tests had strong correlation, but the determination of nutrient deficiencies needs local calibration of deficiency limits.     

Do water molecules bridge soil organic matter molecule segments?

One of the most valuable ecological potentials of soil organic matter (SOM) is based on its highly dynamic nature, which enables flexible reactions to a variety of environmental conditions. SOM controls a large part of the processes occurring at biogeochemical interfaces in soil and may contribute to sequestration of organic chemicals. This contribution focuses on dynamics in SOM from a viewpoint that regards SOM as an amorphous matrix, in which weak intermolecular interactions rather than covalent binding are considered. This view is based on the conception of SOM as a supramolecular assembly, which was first suggested in studies by A. Piccolo and R. L. Wershaw. Based on our recent results on thermal analysis of SOM, our central hypothesis is that regardless of the individual molecular mass, SOM undergoes physicochemical matrix aging, driven by dynamics in intermolecular cross‐linking via bridges of water molecules. In this study, we have made the first efforts to evaluate the water‐bridge hypothesis with proton NMR relaxation and proton wideline NMR. The results clearly indicate changes in relaxation time and proton line shape induced by manipulations of thermal history, which suggests an increase in side‐chain mobility upon heating that remains after cooling. Side‐chain mobility slowly decreases again within at least 1–2 weeks. Our current results strongly suggest even longer aging periods. This observation supports the hypothesis that water molecules bridge molecular segments of SOM. The bridges may be easily disrupted, while re‐formation is slow due to diffusion limitation in the SOM matrix.     

Does variability in litter quality determine soil microbial respiration in an Amazonian rainforest?

Tree species-rich tropical rainforests are characterized by a highly variable quality of leaf litter input to the soil at small spatial scales. This diverse plant litter is a major source of energy and nutrients for soil microorganisms, particularly in rainforests developed on old and nutrient-impoverished soils. Here we tested the hypothesis that the variability in leaf litter quality produced by a highly diverse tree community determines the spatial variability of the microbial respiration process in the underlying soil. We analyzed a total of 225 litter-soil pairs from an undisturbed Amazonian rainforest in French Guiana using a hierarchical sampling design. The microbial respiration process was assessed using substrate-induced respiration (SIR) and compared to a wide range of quality parameters of the associated litter layer (litter nutrients, carbon forms, stoichiometry, litter mass and pH). The results show that the variability of both litter quality and SIR rates was more important at large than at small scales. SIR rates varied between 1.1 and 4.0 μg g⁻¹ h⁻¹ and were significantly correlated with litter layer quality (up to 50% of the variability explained by the best mixed linear model). Total litter P content was the individual most important factor explaining the observed spatial variation in soil SIR, with higher rates associated to high litter P. SIR rates also correlated positively with total litter N content and with increasing proportions of labile C compounds. However, contrary to our expectation, SIR rates were not related to litter stoichiometry. These data suggest that in the studied Amazonian rainforest, tree canopy composition is an important driver of the microbial respiration process via leaf litter fall, resulting in potentially strong plant-soil feedbacks.     

Do interactions with soil organisms mediate grass responses to defoliation?

Defoliation-induced changes in grass growth and C allocation are known to affect soil organisms, but how much these effects in turn mediate grass responses to defoliation is not fully understood. Here, we present results from a microcosm study that assessed the role of arbuscular mycorrhizal (AM) fungi and soil decomposers in the response of a common forage grass, Phleum pratense L., to defoliation at two nutrient availabilities (added inorganic nutrients or no added nutrients). We measured the growth and C and N allocations of P. pratense plants as well as the abundance of soil organisms in the plant rhizosphere 5 and 19 d after defoliation. To examine whether defoliation affected the availability of organic N to plants, we added ¹⁵N-labelled root litter to the soil and tracked the movement of mineralized ¹⁵N from the litter to the plant shoots.When inorganic nutrients were not added, defoliation reduced P. pratense growth and root C allocation, but increased the shoot N concentration, shoot N yield (amount of N in clipped plus harvested shoot mass) and relative shoot N allocation. Defoliation also reduced N uptake from the litter but did not affect total plant N uptake. Among soil organisms, defoliation reduced the root colonization rates of AM fungi but did not affect soil microbial respiration or the abundance of microbe-grazing nematodes. These results indicate that interactions with soil organisms were not responsible for the increased shoot N concentration and shoot N yield of defoliated P. pratense plants. Instead, these effects apparently reflect a higher efficiency in N uptake per unit plant mass and increased relative allocation of N to shoots in defoliated plants. The role of soil organisms did not change when additional nutrients were available at the moment of defoliation, but the effects of defoliation on shoot N concentration and yield became negative, apparently due to the reduced ability of defoliated plants to compete for the pulse of inorganic nutrients added at the moment of defoliation.Our results show that the typical grass responses to defoliation—increased shoot N concentration and shoot N yield—are not necessarily mediated by soil organisms. We also found that these responses followed defoliation even when the ability of plants to utilize N from organic sources, such as plant litter, was diminished, because defoliated plants showed higher N-uptake efficiency per unit plant mass and allocated relatively more N to shoots than non-defoliated plants.     

Do sulfhydryl groups affect aggregation and gelation properties of ovalbumin?

The aim of this work is to evaluate the impact of sulfhydryl groups on ovalbumin aggregation and gelation. Ovalbumin was chemically modified to add sulfhydryl groups in various degrees. The rate of aggregation was not affected by the introduction of sulfhydryl groups, and disulfide bond formation was preceded by physical interactions. Hence, disulfide interactions may not be the driving force for the aggregation of ovalbumin. Investigation of the aggregates and gels by electron microscopy and rheology suggested that a critical number of sulfhydryl groups can be introduced beyond which the microstructure of the aggregates transforms from fibrillar into amorphous. Rheological studies further suggested that covalent networks, once formed, do not have the possibility to rearrange, reducing the possibility to attain a stronger network. These results show that, even though aggregation of ovalbumin may be primarily driven by physical interactions, formed disulfide bonds are important to determine the resulting aggregate morphology and rheological properties.