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.

     

Promotive and inhibitory effects of rice straw and cellulose application on rice plant growth in pot and field experiments

Abstract

Quantitative characterization of crusts is necessary to evaluate the crusting susceptibility of soils, to reveal the soil properties affecting soil crust development and, thus, to predict the occurrence of crusting. For the quantification of the morphological characteristics of soil surface crusts, the authors applied an image analyzing method to quantify the state of pores, in terms of apparent porosity, using vertical thin sections of the surface crust formed under simulated rainfall.     

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.     

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.     

Humus composition of soils under forest, coffee and arable cultivation in hilly areas of south Sumatra, Indonesia

To understand the effect of land use changes on the composition of humus in tropical soils, samples from land under primary forest, secondary forest, coffee plantation, and arable crops were investigated at three sites in south Sumatra, Indonesia. Total carbon and total nitrogen contents were 1.7 to 4.3 times and 1.1 to 2.8 times greater in the topsoil under primary forest than under the other types of land use. Following change from primary forest to other uses, the proportion of humic acids in the organic matter of the topsoils decreased while that of the fulvic acid fraction increased. Within the range of land uses, differences in the yields of humic acids and fulvic acid fractions were, respectively, larger and smaller than those in total carbon content. The humic acids were classified into the low and middle classes in the degree of humification. Absorption due to the green fraction of humic acids, Pg, was detected in the UV‐visible spectra of almost all the humic acids. No relation was observed between the degree of humification of humic acids or the strength of Pg absorption in their spectra and land use change. The fulvic acid fractions were fractionated on insoluble polyvinylpyrrolidone (PVP) into the adsorbed fractions consisting of humic substances and the non‐adsorbed fractions consisting of non‐humic substances. A positive correlation between the amount of the fulvic acid fraction and the percentage of the PVP‐adsorbed fraction within it indicated that the variation in the amount of the fulvic acid fraction was attributable to acid‐soluble humic substances. The ionization difference spectra of solutions between pH 12 and pH 7 suggested that the chemical structures of the PVP‐adsorbed fulvic acids have been altered by land use change.     

New sources of compact spike morphology determined by the genes on chromosome 5A in hexaploid wheat

Little is known about the relationship between compact spike loci in hexaploid wheat species. We studied two new compact spike mutants of common wheat Triticum aestivum L. (2n?=?6x?=?42, genome formula BBAADD). The new compact spike genes, C ⁷³⁹ of MCK 739 and Cp of near-isogenic line Mironovskaya 808 (Vrn1), were mapped using aneuploid stocks and microsatellite markers. The C ⁷³⁹ and Cp loci were distally linked with the microsatellite marker Xbarc319 in the F₂ populations of MCK 739?×?‘Novosibirskaya 67’ and Cp-Mironovskaya 808 (Vrn1)?×?‘Saratovskaya 29’. It was evident that the loci affecting compact spikes in T. aestivum mutants were located on chromosome 5AL distal from Q locus. These loci also affected to semi-dwarfism. We named this locus Cp1 (C ompact p lant 1) for all accessions. Cp1 was allelic to C ¹⁷⁶⁴⁸ gene located on the chromosome 5AL of tetraploid wheat [Triticum durum Desf. (2n?=?4x?=?28, genome formula BBAA)]. These dominant genes on chromosome 5AL will be utilized as new gene resources of compact spike morphology in hexaploid wheat. Relationship between loci Q and Cp1 was also discussed.     

Source of soil protease based on the splitting sites of a polypeptide

Abstract

Soil protease is an important enzyme in the nitrogen cycle which plays an essential role in the growth of various crops. We have attempted to identify a microbial source of soil protease. Selective soil incubation using antibiotics was suitable for a rough estimation of the groups of microorganisms responsible for the production of soil protease (Hayano and Watanabe 1990; Hayano 1993). Enumeration of proteolytic microorganisms in the field and analysis of their protease-producing ability enabled to evaluate the potential of various soil microorganisms for soil protease production (Watanabe and Hayano 1993a; Watanabe et al. 1994). For the accurate estimation of the soil protease source, the characteristics of the soil protease and microbial protease must be compared directly based on enzymatic properties as indices.     

Prediction of grain protein content in winter wheat through leaf color measurements using a chlorophyll meter

A field trial was conducted over a 3-year period at the Hokkaido Kitami Agricultural Experiment Station to examine whether the grain protein content (GPC) of a winter wheat cultivar (Triticum aestivum L. cv. Chihokukomugi) suitable for Japanese noodle-making could be predicted before harvest. The prediction of the GPC was accurate based on the color of the second leaf (just below the flag leaf) at the end of the emergence of the inflorescence, when nitrogen application was graded. In order to evaluate the reliability of this test, a survey of 95 wheat fields in the eastern part of Hokkaido was also carried out during a 3-year period. The prediction of the GPC for this cultivar based on the color of the second leaf was less accurate across many sites. The results of this survey, however, suggested that the leaf color could be used as an index for ranking the GPC as low or high in relation to processing requirements. When the leaf color value of the second leaf measured with a chlorophyll meter at the end of the emergence of the inflorescence was less than 40, it was predicted that the GPC would be lower than the processing requirement. This index could be applied to the cultivars grown in the eastern part of Hokkaido, except for those grown on peat soils.     

Combining pre-transplanting phosphorus application and green manure incorporation: a trial for reducing fertilizer input

Pre-transplanting phosphorus application is a fertilization method that can reduce phosphorus (P) fertilization of the field and increase P use efficiency. We investigated whether P use efficiency can be increased further by combining pre-transplanting phosphorus application and the green manure practice, using cabbage as a test plant in a field experiment performed from 2006 to 2008. The pre-transplanting phosphorus application successfully reduced P fertilization of the field to half without any yield losses in 2006 and 2008. However, growth and yield could not be maintained with the pre-transplanting phosphorus application when P fertilization was halved in 2007. Differences among seasons and discrepancies in the results compared to previous studies may have arisen from the differences in the field management and the nursery soil used. No benefits of green manure in terms of the subsequent cabbage yield were detected. Consequently, there was no positive effect of the combination of pre-transplanting phosphorus application and incorporation of green manure. Studies with mycorrhizal plants as test plants may be necessary to verify the mechanism of enhanced P supply by the incorporation of green manure, and to examine any potential benefit of combining green manure and pre-transplanting phosphorus application practices.     

Genotype by environment interactions (GEIs) for barley grain yield under salt stress condition

Changes in the relative genetic performance of genotypes across environments are referred to as genotype × environment interactions (GEIs). GEIs can affect barley breeding improvement for salt tolerance because it often complicates the evaluation and selection of superior genotypes. The present study evaluated the GEIs over 60 barley genotypes for yield components and grain yield in six salinity environments in North Delta, Egypt. Data were analyzed using the additive main effects and multiplicative interaction (AMMI) and Tai’s stability parameters. GEIs effects on yield explained 20.3, 20.1, 14.6, and 33.0% of the total variation besides, the first two principal components account for 67.3, 56.3, 64.3, and 83.7% of the explained variance in the four sets, respectively. Six genotypes namely G-4, G-7, G-20, G-34, G-36, and G-39 were found to be most stable and high yielding across environments (GY >2.00 t ha^-1), and located close to zero projection onto the AEC ordinate. Tai’s stability parameters demonstrated that these genotypes were more responsive to the environmental changes. The genotypes G-50 and G-53 showed perfect/static stability (α = -0.95, -0.91, respectively). In contrast, the genotype; G-36 had α = 0 and λ = 1.10, indicating parallel with the environmental effects followed by G-44. Overall, we found that GEIs for grain yield are highly significant in all sets, suggesting that responded differently across environments. This interaction may be a result of changes in genotypes’ relative performance across environments, due to their differential responses to various abiotic factors.