Bacterial community incorporating carbon derived from plant residue in an anoxic non-rhizosphere soil estimated by DNA-SIP analysis

Purpose

Plant residues are one of the main sources of soil organic matter in paddy fields, and elucidation of the bacterial communities decomposing plant residues was important to understand their function and roles, as the microbial decomposition of plant residues is linked to soil fertility. We conducted a DNA stable isotope probing (SIP) experiment to elucidate the bacterial community assimilating 13-carbon (¹³C) derived from plant residue under an anoxic soil condition. In addition, we compared the bacterial community with that under the oxic soil condition, which was elucidated in our previous study (Lee et al. in Soil Biol Biochem 43:814–822, 2011).

Materials and methods

We used the ¹³C-labeled dried rice callus cells as a model of rice plant residue. A paddy field soil was incubated with unlabeled and ¹³C-labeled callus cells. DNA extracted from the soils was subjected to buoyant density gradient centrifugation to fractionate ¹³C-enriched DNA. Then, polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) analysis of bacterial 16S rDNA band patterns and band sequencing method were used to evaluate bacterial community.

Results and discussion

DGGE analysis showed that the band patterns in the ¹³C-enriched fractions were distinctly changed over time, while the changes in the community structure before fractionation were minor. Sequencing of the ¹³C-labeled DGGE bands revealed that Clostridia were a major group in the bacterial communities incorporating the callus-derived carbon although Gram-negative bacteria, and Actinobacteria also participated in the carbon flow from the callus under the anoxic condition. The proportion of Gram-negative bacteria and Actinobacteria increased on 14 days after the onset of incubation, suggesting that the callus was decomposed by diverse bacterial members on this phase. When the bacterial groups incorporating the ¹³C were compared between under anoxic and oxic soil conditions, the composition was largely different under the two opposite conditions. However, some members of Gram-negative bacteria were commonly found under the anoxic and oxic soil conditions.

Conclusions

The majority of bacterial members assimilating the callus carbon was Clostridia in the soil under anoxic conditions. However, several Gram-negative bacterial members, such as Acidobacteria, Bacteroidetes, and Proteobacteria, also participated in the decomposition of callus under anoxic soil conditions. Our study showed that carbon flow into the diverse bacterial members during the callus decomposition and the distinctiveness of the bacterial communities was formed under the anoxic and oxic soil conditions.

     

Suppressive effect of saturated acyl L-ascorbate on the oxidation of linoleic acid encapsulated with maltodextrin or gum arabic by spray-drying

6-O-Palmitoyl L-ascorbate was added to linoleic acid at various molar ratios of the ascorbate to the acid, the mixtures were emulsified with a maltodextrin or gum arabic solution, and the emulsions were spray-dried to produce microcapsules. At higher molar ratios, the oil droplets in the emulsions were smaller, and the oxidative stabilities of the encapsulated linoleic acid were higher for both the maltodextrin- and gum arabic-based microcapsules. 6-O-Capryloyl, caproyl, and lauroyl L-ascorbates, which were synthesized through lipase-catalyzed condensation in acetone, were also used for the microencapsulation of linoleic acid. Except for capryloyl L-ascorbate, the addition of a saturated acyl ascorbate, especially caproyl ascorbate, to linoleic acid was effective for preparing oil droplets of small particle diameter and for suppressing the oxidation of the encapsulated linoleic acid.     

Herbivore-induced volatiles from tea (Camellia sinensis) plants and their involvement in intraplant communication and changes in endogenous nonvolatile metabolites

As a defense response to attacks by herbivores such as the smaller tea tortrix ( Adoxophyes honmai Yasuda), tea ( Camellia sinensis ) leaves emit numerous volatiles such as (Z)-3-hexen-1-ol, linalool, α-farnesene, benzyl nitrile, indole, nerolidol, and ocimenes in higher concentration. Attack of Kanzawa spider mites ( Tetranychus kanzawai Kishida), another major pest insect of tea crops, induced the emission of α-farnesene and ocimenes from tea leaves. The exogenous application of jasmonic acid to tea leaves induced a volatile blend that was similar, although not identical, to that induced by the smaller tea tortrix. Most of these herbivore-induced plant volatiles (HIPV) were not stored in the tea leaves but emitted after the herbivore attack. Both the adaxial and abaxial epidermal layers of tea leaves emitted blends of similar composition. Furthermore, HIPV such as α-farnesene were emitted mostly from damaged but not from undamaged leaf regions. A principal component analysis of metabolites (m/z 70-1000) in undamaged tea leaves exposed or not to HIPV suggests that external signaling via HIPV may lead to more drastic changes in the metabolite spectrum of tea leaves than internal signaling via vascular connections, although total catechin contents were slightly but not significantly increased in the external signaling via HIPV.     

Breaking the crossability barriers between disomic tetraploid Solanum acaule and tetrasomic tetraploid S. tuberosum

Summary A combination of compatible second pollinations and embryo rescue was applied for systematic production of true tetraploid hybrids from crosses between disomic tetraploid Solanum acaule and tetrasomic tetraploid potato, S. tuberosum. Several genotypes of tetraploid potatoes were pollinated with S. acaule, and the compatible second pollinations were made on the following day, with a genotype of S. phureja, IvP 35 to promote fruit development. Embryo rescue was carried out in 21 families, 14 to 27 days after the first pollination. A total of eight plants were obtained from the embryo rescue and their chromosome numbers were counted in the root tips. Three of the eight plants were identified as tetraploid, and five others as diploid. Morphology, isozyme banding patterns, and pollen stainability, as well as potato spindle tuber viroid (PSTVd) resistance, indicated the hybrid nature of the three plants. This is the first report of successful tetraploid hybrid production between disomic tetraploid S. acaule (4x) and tetrasomic tetraploid potatoes. Seed set from the crosses between one of hybrids and diploid potatoes indicated workable levels of both male and female fertility for introgression of valuable genes from S. acaule into the cultivated potato gene pool. The methodology used may be applied to other disomic tetraploid tuber-bearing Solanum species and with some modifications also to distantly related solanaceous species and genera.     

Identification and quantification of short oligomeric proanthocyanidins and other polyphenols in boysenberry seeds and juice

Proanthocyanidins and other polyphenols in the seeds and juice of boysenberry were quantitatively analyzed. Polyphenolic extracts were prepared from the waste seeds and commercial juice by chromatographic fractionation. Compositional analysis revealed that both extracts contained six polyphenolic classes: flavanol monomers, proanthocyanidins, anthocyanins, ellagic acid, ellagitannins, and flavonol glycosides. Ellagitannins were the most abundant polyphenols in both extracts. Proanthocyanidins were present as short oligomers consisting of dimeric and trimeric procyanidins and propelargonidins, with the most abundant component being procyanidin B4 in both extracts. Quantification by high-performance liquid chromatography-mass spectrometry (HPLC-MS) revealed that the seeds contained a 72-fold higher amount of proanthocyanidins than the juice. These results indicate that boysenberry fruits contain short oligomeric proanthocyanidins along with flavanol monomers and the seeds represent a good source of short oligomeric proanthocyanidins.     

Near-isogenic lines of durum wheat: their development and plant characteristics

Summary The effect of specific plant characteristics on the grain and biomass yield of durum wheat can be accurately determined by using isogenic lines, which, however, were not usually available. This study reported the effects of long glume, glaucousness, glume pubescence, black glume and purple culm on the yield and its associated characteristics in near-isogenic lines of durum wheat cv. LD222, which were developed by continuous backcrossing. The long glume trait which resulted in a large photosynthetic area did not enhance yield. Increased glume size associated with the P gene tended to increase the main culm dominance, characterized such as vigorous main culm and weak tillers, and plant height, but to reduce tillering and spike number. Consequently, grain yield and harvest index declined. Under the adequate water supplying condition of the present study, the glaucous trait was beneficial for grain yield. The trait of glume pubescence did not excert any significant effect on the yield related characteristics in the LD222 background. The traits of black glume and purple culm reduced the number of spikes per unit area and the number of kernels per unit area.     

Classification of Azolla spp., section Azolla

Summary Azolla accessions (section Azolla) from the germplasm collections of the International Rice Research Institute and Washington State University were fingerprinted and classified by enzyme electrophoresis and leaf trichome morphology. A. filiculoides was enzymatically distinctive and also reliably identified by its prominent one-celled trichomes. Neotropical accessions labelled as A. filiculoides proved to be members of other species. Two groups of isolates were designated A. rubra, but those from Japan were identified as A. filiculoides. The A. rubra of Australia-New Zealand was biochemically unique and possessed less protuberant trichomes than A. filiculoides. A. microphylla, A. mexicana, and A. caroliniana were phenetically similar, but a. microphylla was identifiable from the others in the banding patterns of certain enzymes. A. mexicana and A. caroliniana were closely related enzymatically. The two-celled leaf trichomes of these three species were similar in size and shape.     

Artificial neural network modeling for predicting final moisture content of individual Sugi (Cryptomeria japonica) samples during air-drying

Sugi (Cryptomeria japonica D. Don) lumber is known to have a large variability in final moisture content (MC_f) and is difficult to dry. This study assessed the capability of artificial neural networks (ANNs) to predict the MC_f of individual wood samples. An ANN model was developed based on initial moisture content, basic density, annual ring orientation, annual ring width, heartwood ratio and lightness (L ^* in the CIE L ^* a ^* b ^* system). The performance of the ANN model was compared with a principal component regression (PCR) model. The ANN model showed good agreement with the experimentally measured MC_f with a higher correlation coefficient (r) and a lower root mean square error (RMSE) than the PCR model, demonstrating the importance of nonlinearity of the variables and the higher capability of the ANN model than the PCR model. By adding redness (a ^* ) and yellowness (b ^* ) and drying time to the input variables of ANNs, r and RMSE values were improved to 0.98 and 1.2 % for the training data set, and 0.85 and 2.2 % for the testing data set, respectively. Although the developed ANNs are available under the limited conditions of this study, our results suggest that the ANNs proposed offer reliable models and powerful prediction capability for the MC_f, even though wood properties vary considerably and their complex interrelations are not fully elucidated.     

Factors affecting forest growth and possible effects of climate change in the Taihang Mountains, northern China

To estimate the possible effects of site factors and climatechange on forest growth in the Taihang Mountains, northern China,we assessed the factors influencing forest growth by using forestinventory data from 712 forest sample plots. Meteorologicaldata from 77 meteorological stations in the region were usedto estimate temperature and precipitation at each site fromelevation and longitude. Analyses showed that temperature, aspect,precipitation and soil thickness all significantly influencedforest growing stock (FGS), i.e. stem volume. When temperaturerose, FGS was reduced, possibly because increasing temperatureincreased evapotranspiration. Precipitation had a positive effecton FGS. The effect of aspect on FGS was perfectly expressedas a cosine function, with south-west- and south-facing slopeshaving the lowest FGS and north-facing slopes having the highest.We developed multifactorial regression models to predict changesin FGS in the Taihang Mountains. Temperature, forest age, forestcover, soil thickness, precipitation and aspect were well relatedto FGS. The effects of a temperature decrease and a precipitationincrease on FGS would be 2.5–8 per cent per degree centigradeand 10 per cent per 100 mm, respectively. The combination oftemperature increase and precipitation changes under futureclimate change is likely to result in a decrease of FGS, thoughthis does not take account the effect of increasing CO₂. Wealso used multifactorial regression models to analyse the effectsof site factors on FGS of Pinus tabulaeformis Carr. and Robiniapseudoacacia L., two major species used in afforestation inthe Taihang Mountains. Although site factors had similar effectson FGS, diameter at breast height and tree height of both species,prediction accuracy (regression coefficient) was improved greatlywhen we treated the species separately.     

Distribution of boron in wood treated with aqueous and methanolic boric acid solutions

The distributions of boron in Japanese cedar (Cryptomeria japonica D. Don) sapwood blocks treated with aqueous or methanolic boric acid [B(OH)₃] solutions were explored through Raman spectroscopy and prompt gamma-ray analysis (PGA). B(OH)₃ was the sole boron species observed in Raman spectra of the wood blocks treated with either solution. Plots of weight gain of the treated wood blocks versus boron concentration in treatment solutions were found to be linear. The results indicated that the methanolic solution makes it possible to impregnate wood with much larger amounts of boron than the aqueous solution. PGA confirmed that B(OH)₃ was highly enriched near the end grains of the treated wood blocks. Raman measurements suggested that boron content in the bulk of the wood block is not as large as expected from the weight gain of the treated wood blocks when an ordinary air-drying method is used. It was concluded that the aqueous solution impregnates the cell walls of wood with boron more easily than the methanolic solution. Part of this report was presented at the 55th (Kyoto, March 2005) and 56th (Akita, August 2006) Annual Meetings of the Japan Wood Research Society. This article follows the previous rapid communication “Analysis of boron in wood treated with boric acid solutions using Doppler broadening method of prompt gamma-rays.” J Wood Sci (2006) 52:279–281