Long-term changes in microbial community structure in soils subjected to different fertilizing practices revealed by quinone profile analysis

Quinone profile analysis of stored air-dried soils gave an approximation of the long-term changes in the microbial community structure in four soils subjected to different types of fertilizer application from 1987 to 1997: unfertilized soil (NF-soil), soil amended with chemical fertilizers (CF-soil), soil amended with chemical fertilizers and 40 t ha^-1 y^-1 of farmyard manure (CF+ FYM-soil), and soil amended with 400 t ha^-1 y^-1 of farmyard manure (FYM-soil). The carbon content increased, and the soil pH remained higher in the soils receiving farmyard manure. Principal component analysis of the quinone profiles of the soils indicated that the microbial community structure showed a high similarity among the four soils before the onset of cultivation and changed to a different community structure specific to the respective fertilizing practices except for the NF-soil. The specific quinone profile became stable after two cropping seasons in the FYM-soil, after 10 cropping seasons in the CF+ FYM-soil and after 15 cropping seasons in the CF-soil, respectively. The quinone profile of the NF-soil did not become stable, and no specific profile was developed. The specific quinone profiles in the FYM- and CF+ FYM-soils were both characterized by large mole fractions of menaquinone with seven isoprenoid units (MK-7). Farmyard manure itself contained a large mole fraction of MK-7. It was suggested that the amount of MK-7 increased due to the application of farmyard manure. MK-7 indicates the presence of Gram-positive bacteria with low guanine plus cytosine contents such as Bacillus and Gram-negative bacteria of the Cytophaga-Flavobacterium complex. The specific quinone profile in the CF-soil was characterized by the presence of menaquinone with seven isoprenoid units dihydrated (MK-7(H₂)and MK-7(H₄). Although Brevibacterium and Kocuria contain MK-7(H₂), no microorganisms are known to have MK- 7(H.) as major quinone. The common major quinones were MK-8, MK-10(H₄) and a mixture of MK-8(H₄) and MK-9, suggesting the predominance of Grampositive bacteria in all the soils. Mole fractions of Ubiquinone with 8 isoprenoid units (Q-8) and Q-10 increased at various times in all the soils, indicating the sporadic growth of Gram-negative bacteria.     

A practical formula for quantifying the thermal conductivity of Tottori dune sand

Abstract

Sustainable agriculture needs appropriate management of water, chemicals and heat in soil. In this study, we focused on thermal conductivity, which is among the various soil physical properties that are crucial for the sustainable management of agricultural fields. To expand the Mochizuki model, which describes thermal conductivity as a function of water content and solution concentration, we considered the water content, solution concentration and temperature as independent variables. The thermal conductivity of Tottori dune sand was measured under conditions of various combinations of these three independent variables. We observed that the thermal conductivity increased linearly with increasing water content, 0.054–0.276 m³ m^?3, for fixed temperature and solution concentration, and varied linearly with solution concentration for fixed temperature and water content. These results are consistent with the Mochizuki model. Using the Mochizuki model, the experimental parameters, which are dependent variables of water content and solution concentration, are shown as functions of water content. From regression analyses of the relationships between the experimental parameters and temperature, we expanded the Mochizuki model into a new practical formula that quantifies the soil thermal conductivity as a function of water content, solution concentration and temperature.     

High Performance Size Exclusion Chromatography of Water Extract from Sewage Sludge-Soil Mixture

In order to investigate the degradation or synthetic process of organic matter in soil, some instrumental analyses on the water extract from soil have been recently performed. SCHAUMBERG et al. (1) who observed the changes in the chemical nature of water-soluble components of sewage sludge-soil mixtures by using infrared spectroscopy, supplied valuable information on the fate of sludge organic components in soil. The authors reported (2, 3) that the stabilization process of sewage sludge in soil can be monitored by the conventional gel chromatography method with Sephadex G-15 in water extracts from sewage sludge-soil mixtures.

The previous works (2, 3) showed that macromolecular compounds which cannot be separated by Sephadex G-15 gel were present in the water extracts from sewage sludge-soil mixtures. High performance size exclusion chromatography (HPSEC) offers the possibility to estimate the molecular size distribution of such macromolecules, because HPSEC allows rapid size separation and high resolution. In the size separation of water-soluble compounds by HPSEC, however, the charge exclusion and the hydrophobic interaction between solutes and the stationary phase of the column caused accelerated or retarded transportation of water-soluble compounds through the column, leading to the erroneous estimation of the molecular size (4).

In this study, the authors applied HPSEC to water extracts from sewage sludgesoil mixtures during their process of decomposition in soil to observe the change of the molecular size distribution of the components.     

Sequences and polymorphisms of the canine monoamine transporter genes SLC6A2, SLC6A3, and SLC6A4 among five dog breeds

Monoamine transporters have roles to regulate the monoamine concentrations in synaptic clefts in the central nervous system and are the targets of antidepressants and psychostimulants. They include transporters for norepinephrine, dopamine and serotonin, which are encoded by the SLC6A2, SLC6A3, and SLC6A4 genes, respectivily. We sequenced the full lengths of the coding regions of these genes for dogs and identified four single nucleotide polymorphisms (SNPs) in SLC6A2 and four in SLC6A3. One SLC6A3 SNP was non-synonymous and caused an amino acid substitution from threonine to serine. The genotype frequencies of these polymorphisms differed significantly among five breeds with different behavioral traits, suggesting that novel SLC6A2 and SLC6A3 SNPs would provide additional useful information for behavioral genetic studies in dogs.     

Spectrophotometric assay of a wood preservative, <Emphasis Type="Italic">N,N</Emphasis>-didecyl-<Emphasis Type="Italic">N</Emphasis>-methylpoly(oxyethyl) ammonium propionate (DMPAP), in aqueous solution

A spectrophotometric assay based on the color reaction between N,N-didecyl-N-methyl-poly(oxyethyl) ammonium propionate (DMPAP) and 4-[4-(dipropylamino) phenylazo]-benzenesulfonic acid (propyl orange) was used to determine DMPAP concentrations as a wood preservative. The assay was carried out using a propyl orange solution at pH 2.9. The visible absorption spectrum of propyl orange showed an absorption maximum at 510 nm, which decreased linearly with increasing DMPAP concentration from 0 to 10 ppm. To apply this assay method to determine DMPAP retention in treated wood, the influence of wood extractives on the assay was investigated. Extractives from Japanese cedar, hinoki cypress, and Japanese larch were found to increase apparent DMPAP concentration. However, it was also found that measuring visible absorption at 477 nm prevented overestimation and gave precise values. This assay can be a viable alternative to the current methods for the determination of DMPAP concentrations.     

Analysis of respiratory quinones in soil for characterization of microbiota

Method for the analysis of respiratory quinones in soil was developed to characterize soil microbiota. The respiratory quinones were extracted with a mixture of chloroform and methanol using a Wahling blender or a sonicator and cleaned-up by a silicagel column cartridge. The quinone species were determined by reverse-phase high performance liquid chromatography. Spectra of peaks were measured with a photodiode array detector to examine the purity. More than 90% of extractable quinones in soil were recovered by three extractions. The recovery of quinones, added to soil as freeze-dried powder of microorganisms, was higher than 96%. This procedure led to higher representative results as follows. Fluctuations within 95% of cumulative frequency were 13% for the extracted amount of quinones and 20% for the dissimilarity, respectively. The quinone profiles of four soils were determined as follows: a soil from the aerobic layer of a paddy field, an ando soil and two yellow upland soils which had received chemical fertilizers with and without farmyard manure. The quinone profiles displayed clear differences in the microbial composition and in the microbial diversity among the soils. It was demonstrated that the analysis of the respiratory quinone profile was useful to characterize the microbial community structure in soil.     

Analysis of deflection and dynamic plant characteristics of Cyperus malaccensis Lam

ABSTRACT

In this study, flexural rigidity, natural frequency, and damping coefficient of Cyperus malaccensis Lam. with long stems were measured for application for fluid–structure interaction simulation in a field. Numerical solutions of deflection and natural frequency were calculated by ANSYS with finite element method (FEM). The triangular cross-section shape of C. malaccensis stem has a big neighbourhood of the root and the cross-section has taper structure to become small towards tip direction. Two numerical simulation models for FEM have Model A with a triangular prism shape and Model B with a truncated trigonal pyramidal shape to evaluate the effects of stem tapering. Because of large C. malaccensis stem deflection, an equation for nonlinear deflection was introduced to solve a problem regarding flexural rigidity. Natural frequencies of the stem were estimated using amplitude ratio during stem swinging by forced vibration, captured using a high-speed camera. The Model B corresponded with the measurement, and the results suggested that the stem characteristics were affected by cross-section shape. Damping coefficient was calculated using free vibration response, which was consistent with the analytical solution and numerical data calculated using measured characteristics.     

Lignification in poplar tension wood lignified cell wall layers

The lignification process in poplar tension wood lignified cell wall layers, specifically the S(1) and S(2) layers and the compound middle lamella (CML), was analysed using ultraviolet (UV) and transmission electron microscopy (TEM). Variations in the thickness of the gelatinous layer (G-layer) were also measured to clarify whether the lignified cell wall layers had completed their lignification before the deposition of G-layers, or, on the contrary, if lignification of these layers was still active during G-layer formation. Observations using UV microscopy and TEM indicated that both UV absorbance and the degree of potassium permanganate staining increased in the CML and S(1) and S(2) layers during G-layer formation, suggesting that the lignification of these lignified layers is still in progress during G-layer formation. In the context of the cell-autonomous monolignol synthesis hypothesis, our observations suggest that monolignols must go through the developing G-layer during the lignification of CML and the S(1) and S(2) layers. The alternative hypothesis of external synthesis (in the rays) does not require that monolignols go through the G-layer before being deposited in the CML, or the S(1) and S(2) layers. Interestingly, the previous observation of lignin in the poplar G-layer was not confirmed with the microscopy techniques used in the present study.     

Genome‐wide association studies reveal additional related loci for fatty acid composition in a Duroc pig multigenerational population

The aim of the present study was to detect quantitative trait loci affecting fatty acid composition in back fat and intramuscular fat in a Duroc pig population comprising seventh‐generation pedigrees using genome‐wide association studies (GWAS). In total, 305 animals were genotyped using single nucleotide polymorphisms (SNPs) array and five selected SNPs from regions containing known candidate genes related to fatty acid synthesis or metabolism. In total, 24 genome‐wide significant SNP regions were detected in 12 traits, and 76 genome‐wide suggestive SNP regions were detected in 33 traits. The Sus scrofa chromosome (SSC) 7 at 10.3 Mb was significantly associated with C17:0 in intramuscular fat, while the SSC9 at 13.6 Mb was significantly associated with C14:0 in intramuscular fat. The SSC12 at 1.0 Mb was significantly associated with C14:0 in back fat and the SSC14 at 121.0 Mb was significantly associated with C18:0 in intramuscular fat. These regions not only replicated previously reported loci containing some candidate genes involved in fatty acid composition (fatty acid synthase and stearoyl‐CoA desaturase) but also included several additional related loci.