From the micro-scale to the habitat: Assessment of soil bacterial community structure as shown by soil structure directed sampling

Natural structural units of a luvisol under maize crop were studied to assess if soil structure directed sampling could improve the understanding of arrangements of bacteria in spatially constraint location. Three habitats were defined: (i) soil around fine lateral roots (rhizo-aggregates), (ii) soil close to basal roots (core clods) and (iii) unplanted soil between rows (bare soil clods). These habitats were also investigated with maize plants resulting from Azospirillum lipoferum CRT1 inoculated seeds as a model of enhanced fine root system. Rhizo-aggregates were clearly separated from each other (disconnected habitat) in contrast to micro-samples (fragments) from clods, which belong to cohesive macro-structures. Genetic fingerprints on metagenomic extracts were used to characterize the structure of bacterial communities on 95 micro-samples from the three habitats. For eubacteria, automated RISA (Ribosomal Intergenic Spacer Analysis) of ITS (Internal Transcribed Spacer) profiles were performed. PCR-RFLP on nifH gene were used to describe the N-fixer guilds. Exploratory multivariate analyses (PCA and MDS) revealed bacterial community patterns in the sampled habitats. On the basis of ITS profiles, rhizo-aggregates harboured closely related communities, distant from those of the unplanted soil, and each sampled rhizo-aggregate could therefore be considered as a sub-unit of the whole macro-habitat, comprising all the fine roots. The observed low dissimilarity of disconnected rhizo-aggregates is likely to result from the direct influence of maize root tips on the recruitment of rhizosphere bacteria. Molecular fingerprints of nifH from basal root clods (core) were more similar to bare soil than to rhizo-aggregates, indicating similar ecological conditions without, or with, at least, poor maize exudating root influence. Although our study was performed on a limited number of situations, the distribution of bacteria was revealed to be patterned by soil structure units, which is a first step to improve the modelling of microbial ecology in soils.     

Beta-glucosidase from the grape native yeast Debaryomyces vanrijiae: purification,characterization, and its effect on monoterpene content of a Muscat grape juice

Six hundred ten yeast colonies isolated from various vineyards in Chile were screened for the presence of a beta-glucosidase activity as well as the resistance to glucose and ethanol inhibition. Among them, Debaryomyces vanrijiae was found to produce high levels of an extracelular beta-glucosidase which was tolerant to glucose (K(i) = 439 mM) and ethanol inhibitions. The enzyme (designated DV-BG) was purified to apparent homogeneity, respectively, by gel filtration, ion-exchange, and chromatofocusing techniques. Its molecular weight was 100 000, and its pI 3.0, optimum pH, and temperature activities were 5.0 and 40 degrees C, respectively, and had a V(max) of 47.6 micromol min(-)(1) mg(-)(1) and a K(m) of 1.07 mM. The enzyme was active against different beta-d-glucosides including glucosidic flavor precursors. The disaccharidic flavor precursors were not substrates for the enzyme. When added to a Muscat grape juice, the concentration of several monoterpenes increased as the consequence of its hydrolytic activity.     

Long-term submergence of non-methanogenic oxic upland field soils helps to develop the methanogenic archaeal community as revealed by pot and field experiments

The community structure of methanogenic archaea is relatively stable,i.e.,it is sustained at a high abundance with minimal changes in composition,in paddy field soils irrespective of submergence and drainage.In contrast,the abundance in non-methanogenic oxic soils is much lower than that in paddy field soils.This study aimed to describe methanogenic archaeal community development following the long-term submergence of non-methanogenic oxic upland field soils in pot and field experiments.In the pot experiment,a soil sample obtained from an upland field was incubated under submerged conditions for 275 d.Soil samples periodically collected were subjected to culture-dependent most probable number(MPN)enumeration,polymerase chain reaction-denaturing gradient gel electrophoresis(PCR-DGGE)analysis of archaeal 16 S r RNA gene,and quantitative PCR analysis of the methyl-coenzyme M reductase alpha subunit gene(mcr A)of methanogenic archaea.The abundance of methanogenic archaea increased from 102 to 103 cells g-1 dry soil and 104 to 107 copies of mcr A gene g-1 dry soil after submergence.Although no methanogenic archaeon was detected prior to incubation by the DGGE analysis,members from Methanocellales,Methanosarcinaceae,and Methanosaetaceae proliferated in the soils,and the community structure was relatively stable once established.In the field experiment,the number of viable methanogenic archaea in a rice paddy field converted from meadow(reclaimed paddy field)was monitored by MPN enumeration over five annual cycles of field operations.Viability was also determined simultaneously in a paddy field where the plow layer soil from a farmer’s paddy field was dressed onto the meadow(dressed paddy field)and an upland crop field converted from the meadow(reclaimed upland field).The number of viable methanogenic archaea in the reclaimed paddy field was below the detection limit before the first cultivation of rice and in the reclaimed upland field.Then,the number gradually increased over five years and finally reached 103–104 cells g-1 dry soil,which was comparable to that in the dressed paddy field.These findings showed that the low abundance of autochthonous methanogenic archaea in the non-methanogenic oxic upland field soils steadily proliferated,and the community structure was developed following repeated and long-term submergence.These results suggest that habitats suitable for methanogenic archaea were established in soil following repeated and long-term submergence.     

Using a mixture of microalgae,biochar, and organic manure to increase the capacity of soil to act as carbon sink

Purpose

Microalgae, biochar, or organic manure (OM) can be used as soil amendments to enhance soil organic carbon (OC) content. In the present study, a mixture of all three was used to test whether they could further improve soil OC content and the soil’s ability to retain and fix carbon.

Materials and methods

A laboratory incubation study was carried out to evaluate the efficacy of using microalgae, biochar, OM, or their mixture, as a soil amendment to improve OC in soil extract. Metabolic processes and soil microbial community structuring were analyzed to explore the mechanism by which the mixture increased the capacity of soil to act as a carbon sink.

Results and discussion

OC increased markedly (2.9 times its initial level) following the amendment of the soil with a treatment comprising microalgae, biochar, and the highest dose of OM. Microalgal metabolites were utilized by soil microorganisms as a carbon source. Biochar reduced the concentration of extracellular polysaccharides, whereas OM increased extracellular protein concentration. These metabolites affected the relative proportions of different groups of soil microorganisms, thereby increasing the proportion of Rhodobacter and Runella, which exerted a positive synergistic effect on soil OC and increased the soil’s capacity to fix carbon.

Conclusions

A mixture including microalga, biochar, and OM as a soil amendment improved the OC of soil extract, and its effect was greater than that of any of its components alone. The findings of this study can help in devising ways to increase the OC content and the CO₂-fixing capacity of the soil.

     

Organic matter decomposition and carbon content in soil fractions as affected by a gradient of labile carbon input to a temperate forest soil

Labile carbon (C) input to soils is expected to affect soil organic matter (SOM) decomposition and soil organic C (SOC) stocks in temperate coniferous forests. We hypothesized that the SOM...     

Soil organic matter turnover as a function of the soil clay content: consequences for model applications

Based on a literature review including 201 surface soils from wet, mild, mid-latitude climates and 290 soils from the Lower Saxony soil monitoring programme (Germany), we investigated the relationship between soil clay content and soil organic matter turnover. The relationship was then used to evaluate the clay modifier for microbial decomposition in the organic matter module of the soil-plant-atmosphere model DAISY. A positive relationship was found between soil clay content and soil microbial biomass (SMB) C. Furthermore, a negative relationship was found between soil clay content and metabolic quotient (qCO₂) as an indicator of specific microbial activity. Both findings support the hypothesis of a clay dependent capacity of soils to protect microbial biomass. Under the differing conditions of practical agriculture and forestry, no or only very weak relationships were found between soil clay content and non-living soil organic matter C (humus C). It is concluded that the stabilising effect of clay is much stronger for SMB than for humus. This is in contrast to the DAISY clay modifier assuming the same negative relationship between soil clay content, on the one hand, and turnover of SMB and turnover of soil humus on the other. There is a positive relationship between SMB and microbial decomposition activity under steady-state conditions (microbial growth≈microbial death). The original concept of a biomass-independent simulation of organic matter turnover in the DAISY model must therefore be rejected. In addition to the original modifiers of organic matter turnover, a modifier based on the pool size of decomposing organisms is suggested. Priming effects can be simulated by applying this modifier. When using this approach, the original modifiers are related to specific microbial activity. The DAISY clay modifier is a useful approximation of the relationship between the metabolic quotient (qCO₂) as an indicator of specific microbial activity and soil clay content.     

Impact of mineral and organic fertilization on yield,C content in the soil,as well as on C,N and energy balances in a long-term field experiment

Data from a 49-year-long organic–mineral fertilization field experiment with a potato–maize–maize–wheat–wheat crop rotation were used to analyse the impact of different fertilizer variations on yield ability, soil organic carbon content (SOC), N and C balances, as well as on some characteristic energy balance parameters. Among the treatments, the fertilization variant with 87 kg ha^?1 year^?1 N proved to be economically optimal (94% of the maximum). Approximately 40 years after initiation of the experiment, supposed steady-state SOC content has been reached, with a value of 0.81% in the upper soil layer of the unfertilized control plot. Farmyard manure (FYM) treatments resulted in 10% higher SOC content compared with equivalent NPK fertilizer doses. The best C balances were obtained with exclusive mineral fertilization variants (?3.8 and ?3.7 t ha^?1 year^?1, respectively). N uptake in the unfertilized control plot suggested an airborne N input of 48 kg ha^?1 year^?1. The optimum fertilizer variant (70 t ha^?1 FYM-equivalent NPK) proved favourable with a view to energy. The energy gain by exclusive FYM treatments was lower than with sole NPK fertilization. Best energy intensity values were obtained with lower mineral fertilization and FYM variants. The order of energy conversion according to the different crops was maize, wheat and potato.     

Evaluating the transferability of measurements from simple constructed non weighable gravitation lysimeters to predict the water regime on field scale—a case study

The transfer of lysimeter‐based water balances to field scale is still a challenge, whereby the reliability of measured data from non‐weighable gravitation lysimeters (NWGL) is more questioned than the transferability of data from more modern lysimeter devices. The hypothesis of this study was to predict the water regime of a drained arable field (81 ha) based on measurement results of three neighboring (distance of 20 km northern Altmark region Saxony‐Anhalt, Germany) NWGL (surface area of 1 m², depth of 1.25 m) for three hydrological years (HY) from 11/1/2012 to 10/31/2015. For the first two HY, manually collected monthly outflow rates from the NWGL were comparable to registered (data logger) drain rates of the field. But NWGL outflow was underestimated as compared to field drainage in the third HY. This deficit in the lysimeter water balance was caused by heavy rain events in summer 2014 in combination with wind and interception by the crop canopy (Zea maize). Precipitation did not match the NWGL surface whereas this canopy effect did not play a role at the field site. Thus, further numerical simulations of the soil water flow with the HYDRUS 1D/2D‐software package, which were based only on input data determined at the NWGL (stand precipitation, potential evaporation/ transpiration) without taking into account the canopy effect, described registered outflow of the field adequately for the whole observation period. But determining precipitation matching the NWGL surface, which was not registered due to the missing weighing mechanism, is absolutely required to interpret deviating measured outflow rates.     

Investigation on the contamination of field crops by artificial radioactivities as a result of the H-bomb tests at Bikini Atoll

Introduction

As a result of the H-bomb explosion tests of the U.S.A. in the Southern Pacific Ocean, rain-out in Japan is contaminated considerably by fission products, and field crops also show apparently artificial radioactivities. Many workers are now investigating to clarify degree and regional extent of contamination or sorts of radioactive elements.     

The effects of compost in a rice–wheat cropping system on aggregate size,carbon and nitrogen content of the size–density fraction and chemical composition of soil organic matter,as shown by 13C CP NMR spectroscopy

We investigated whether the long‐term application of compost from agricultural waste improved soil physical structure, fertility and soil organic matter (SOM) storage. In 2006, we began a long‐term field experiment based on a rice–wheat rotation cropping system, having a control without fertilizer (NF) and three treatments: chemical fertilizers (CF), pig manure compost (PMC) and a prilled mixture of PMC and inorganic fertilizers (OICF). Following the harvest of wheat in 2010, the mean‐weight diameter (MWD) of water‐stable aggregates and the concentration of C and N in bulk soil (0–20 cm; <2 mm fraction) were significantly greater (P < 0.05) in PMC and NF plots than in CF or OICF plots. Pig manure compost significantly increased the proportion of >5‐mm aggregates, whereas CF significantly increased the proportion of 0.45‐ to 1‐mm aggregates. The C and N contents of all density fractions were greater in PMC than in other treatments with levels decreasing in the following order: free particulate organic matter (fPOM) >occluded particulate organic matter (oPOM) > mineral‐combined SOM (mineral–SOM). Solid‐state ¹³C CPMAS NMR spectra showed that alkyl C/O‐alkyl C ratios and aromatic component levels of SOM were smaller in PMC and OICF plots than in CF plots, suggesting that SOM in PMC and OICF plots was less degraded than that in CF plots. Nevertheless, yields of wheat in PMC and NF plots were smaller than those in CF and OICF plots, indicating that conditions for producing large grain yields did not maintain soil fertility.     

From marl to rock powder: On the history of soil fertility management by rock materials

The ancient practice of marling and the recent application of rock powder to soils are interventions into the orogenic energy budget of soils. Both are slow‐release, long‐term fertilizers or better, soil conditioners. Marls and their uses are reviewed by a study of knowledge and practices from the 1st century AD to the 1800s, for rock powders, a review of the recent theoretical and experimental literature is presented. Under pre‐industrial conditions, paucity of energy prevented the wide‐spread use of such materials, today they are marketed as by‐product of industrial operations. For marls and rock powders alike, their positive effect depends to a large extent on the soil matrix to which the minerals are applied, on the cultivar, and the specific type of applied material. Drawing parallels between the two materials, we suggest that the long‐term experience with marls could be used to study the effects of rock powders, as duration of experiments with these is most often too limited to allow conclusions.     

A method for predicting soil susceptibility to the compaction of surface layers as a function of water content and bulk density

Identifying the vulnerability of soils to compaction damage is becoming an increasingly important issue when planning and performing farming operations. Soil compaction models are efficient tools for predicting soil compaction due to agricultural field traffic. Most of these models require knowledge of the stress/strain relationship and of mechanical parameters and their variations as a function of different physical properties. Since soil compaction depends on the soil's water content, bulk density and texture, good understanding of the relations between them is essential to define suitable farming strategies according to climatic changes. In this work we propose a new pedotransfer function for 10 representative French soils collected from cultivated fields, a vineyard and forests. We investigate the relationship between soil mechanical properties, easily measurable soil properties, water content and bulk density. Confined compression tests were performed on remoulded soils of a large range of textures at different initial bulk densities and water contents. The use of remolded samples allowed us to examine a wide range of initial conditions with low measurement variability. Good linear regression was obtained between soil precompression stress, the compression index, initial water content, initial bulk density and soil texture. The higher the clay content, the higher the soil's capacity to bear greater stresses at higher initial water contents without severe compaction. Initial water content plays an important role in clayey and loamy soils. In contrast, for sandy soils, mechanical parameters were less dependent on initial water content but more related to initial bulk density. These pedotransfer functions are expected to hold for the soils of tilled surface layers, but further measurements on intact samples are needed to test their validity.     

Cotton growth and the fate of N fertilizer as affected by saline water irrigation and N fertigation in a drip-irrigated field

The objective of this two-year field experiment was to study the effects of irrigation amount, N rate, and irrigation water salinity on cotton growth and the fate of N fertilizer. The movement of N through the plant-soil system was traced using ¹⁵N-labeled urea. The study consisted of twelve treatments, including two irrigation amounts (405 and 540?mm, I405 and I540, respectively); two N application rates (240 and 360?kg?N/ha, N240 and N360, respectively); and three irrigation water salinity levels [0.35, 4.61 and 8.04?dS/m, representing fresh water (FW), brackish water (BW), and saline water (SW), respectively]. A randomized complete block design was used with three replications. The results showed that cotton biomass, N uptake, and yield increased as irrigation amount and N amount increased; however, all three variables were significantly less in SW than in FW and BW. Plant ¹⁵N recovery rates were greater (i) in the I540 treatments than in the I405 treatments and (ii) in the N360 treatments than in the N240 treatments. Plant ¹⁵N recovery rates in BW were 7.98% and 30.01% greater than those in FW and SW, respectively. Residual soil ¹⁵N increased as N fertilizer amount increased but declined as irrigation amount increased. Residual soil ¹⁵N in BW and SW was 6.02% and 21.44% greater, respectively, than in FW. Total ¹⁵N recovery was significant greater in BW than in FW and SW. The ¹⁵N leaching losses increased significantly with increases in irrigation amount, irrigation water salinity, and N rate. Our study suggests that if appropriate amounts of irrigation water and N fertilizer are used, then brackish irrigation water (4.61?dS/m) will not affect cotton growth, yield and N recovery. In contrast, saline irrigation water (EC?>?8?dS/m) reduces cotton growth, yield, and N use efficiency.     

Use of NaCN to increase the growth of N2-fixing bacteria in a model spermosphere mimicked by sucrose and amino acids leached by seeds

In order to study the establishment of a spermosphere, the C₂H₂ reduction activity of N₂-fixing bacteria isolated from river sand was examined in a simulated spermosphere in the river sand which contained sucrose, an amino acid mixture, and CN^- released from plant seeds. The sand incubated with 10^-10 to 10^-9 mol CN^- 30 g sand^-1 exhibited higher C₂H₂ reduction activity than that without CN^-. The change in the most probable number of N₂ fixers with increasing quantities of CN^- roughly corresponded to that in C₂H₂ reduction activity. However, the most probable number of non-N₂-fixing bacteria decreased except for CN^--tolerant ones. Both C₂H₂ reduction activity and proliferation of the N₂ fixers isolated on a modified Burk's medium were almost similar to those in the bacteria in the sand. In contrast, the proliferation of some nonfixers decreased with an increasing CN^- concentration. C₂H₂ reduction activity of N₂ fixers cultured in combination with non-fixers exhibited a clear peak at 10^-7 M CN^- as for C₂H₂ reduction activity in the sand. We therefore speculate that cyanide evolved from seeds during a pregermination period may suppress the growth of general bacteria, but may promote the proliferation of N₂ fixers, thus contributing to the establishment of a spermosphere.     

Ingestion of sand and soil by phytophagous earthworm Eudrilus eugeniae: a finding of relevance to earthworm ecology as well as vermitechnology

Epigeic earthworms are phytophagous in habit and are believed to prefer organic matter, principally phytomass, in various degrees of decay. To check whether epigeics will ingest soil/sand even when there is luxury availability of phytomass, the present work was carried out. It was seen that not only soil but even sand particles were ingested by epigeic (Eudrilus eugeniae) tested by us, even as there was availability of phytomass and cow manure in abundance. But the consumption of sand and soil decreased as the days progressed. Moreover, the ingestion of sand and soil with phytomass and cow dung did not show any significant influence on growth and survival of earthworms. It did increase the vermicast mass due to the presence of soil/sand as was confirmed by microphotography using polarizing microscope. The findings have important implications in the design of vermireactors for maximizing their efficiency.     

Transfer of carbon incubation parameters to model the SOC and SON dynamics of a field trial with energy crops applying digestates as organic fertilizers

The fertilization with organic amendments and digestates from biogas plants is increasingly used to increase carbon stock and to improve the soil quality, but little is still known about their long-term effects. A common method to analyse organic amendments and their mineralization is incubation experiments, where amendments get incubated with soil while CO₂ release is measured over time. In a previous study, carbon models have been applied to model the carbon dynamics of incubation experiments. The derived parameters describing the carbon turnover of the CCB model (CANDY Carbon Balance) are used to simulate the SOC and SON dynamics of a long-term field trial. The trial was conducted in Berge (Germany) where organic amendments like slurry, farmyard manure or digestates were systematically applied. To grant a higher model flexibility, the amounts of crop residues were calculated for roots and stubble separately. Furthermore, the mineralization dynamics of roots and stubble are considered by the model parameters for each crop. The model performance is compared when using the dry matter and carbon content received from the field trial and the incubation experiments, to evaluate the transferability. The results show that the incubation parameters are transferable to the field site, with rRMSE < 10% for the modelled SOC and rRMSE between 10% and 15% for the SON dynamics. This approach can help to analyse long-term effects of unexplored and unusual organic fertilizers under field conditions, whereat the model is used to upscale the C dynamics from incubation experiments, considering environmental conditions.