Genetic relationships among improved varieties of rice (<Emphasis Type="Italic">Oryza sativa</Emphasis> L.) in Indonesia over the last 60 years as revealed by morphological traits and DNA markers

Morphological traits and two kinds of molecular markers were employed to study the genetic relationships among improved rice (Oryza sativa ) varieties of Indonesia since 1943. Dendrograms based on morphological traits and both molecular markers (simple sequence repeats, SSR and single nucleotide polymorphism, SNP) agreed in separating the varieties into two primary groups. Based on the morphological traits, a larger group (>60 %) contains varieties with smaller sizes compared with those in the smaller group (<40 %). SSR and SNP markers revealed that most of the varieties belonged to indica (88; 89 %) and japonica (9; 8 %) subspecies, and 3 % of varieties were not involved in two subspecies. The molecular markers revealed that the genetic diversity (H) stagnated between stage II (1967–1985) and stage III (1986–2003). However, during stage I (1943–1966), H was higher than in the other stages as revealed by SNP markers, while H in stage I was lower than in the other stages as revealed by SSR markers. In this study, the two molecular data sets were positively correlated and positive correlations between the phenotypic and molecular data depended on the kind of molecular marker: SNP had higher Mantel r values than SSRs. Besides, SSR markers seem to be appropriate for pedigree studies, while SNP markers could be used to reveal genomic relationships. These findings were attributable to the different properties of these two different markers. These results suggested that the diversity and differentiation of both the phenotypic and molecular marker variations were probably resulted from the crossing and selection in rice breeding in Indonesia. We suggest that Indonesia needs another strategy to improve new varieties to avoid a reduction in genetic diversity and similarity.     

Experimental Study of Tidal Effects on Coastal Groundwater and Pollutant Migration

The problem of current urban groundwater pollution is very serious, which has influenced social development and people’s daily life. Around the land-sea interface, tide obviously changes nearshore the groundwater flow regime and makes the pollutant migration process become more complex. In the present study, the effect of tide-induced groundwater table fluctuations and on the pollutants migration in beach aquifers is investigated by constructing a two-dimensional sand trough physical experimental model. The model considered brackish-water density differences and the tide by controlling experimental medium properties and boundary conditions. The results showed that the groundwater table fluctuation cycle is the same as the tidal cycle and the fluctuation lag time increases linearly with the increase of the offshore distance. Tidal fluctuation flattens brackish-freshwater interface, widens the dispersion zone, and generates the upper saline and the freshwater belt. Time lag corresponding relationships between saline water and tidal fluctuation was observed. With the pollutant approaching the saline water area, the profile of the pollutant migration is gradually developed into a spindle shape until the strip shape, and the pollutant enters the saline water body along the curved edge of the upper part of the saline water. The transverse dispersion of pollutants is larger than the longitudinal dispersion in a tidal cycle and its outline presents a strip shape development. No mixing or exchange between the pollutants and the saline water body happened during the whole process. This study can provide scientific references for nearshore groundwater pollution prevention and control in the future.     

Trials of Treating Decentralized Domestic Sewage from a Residential Area by Potassium Ferrate(VI)

The present study aims to investigate the performance of potassium ferrate(VI) in treating decentralized domestic sewage from a rural scattered residential area. Major results were that around 90% of total phosphorus (TP) and 40% of chemical oxygen demand (COD) could be reduced when 25 mg L^?1 of ferrate(VI) was applied. The removal of ammonia and total nitrogen (NH₃–N and TN) was also monitored. However, the nitrogen removal during the chemical dosing was rather low. Big fluctuations of removal rates were observed against shock pollutants concentrations. Considering its strong ability in removing emerging organic pollutants and P, ferrate(VI) is competitive in the treatment of decentralized domestic sewage as an advanced treatment unit following some traditional treatment units.     

Performance of Anaerobic Biotrickling Filter and Its Microbial Diversity for the Removal of Stripped Disinfection By-products

The objective of this research was to evaluate the biodegradation of chloroform by using biotrickling filter (BTF) and determining the dominant bacteria responsible for the degradation. The research was conducted in three phases under anaerobic condition, namely, in the presence of co-metabolite (phase I), in the presence of co-metabolite and surfactant (phase II), and in the presence of surfactant but no co-metabolite (phase III). The results showed that the presence of ethanol as a co-metabolite provided 49% removal efficiency. The equivalent elimination capacity (EC) was 0.13 g/(m³ h). The addition of Tomadol 25-7 as a surfactant in the nutrient solution increased the removal efficiency of chloroform to 64% with corresponding EC of 0.17 g/(m³ h). This research also investigated the overall microbial ecology of the BTF utilizing culture-independent gene sequencing alignment of the 16S rRNA allowing identification of isolated species. Taxonomical composition revealed the abundance of betaproteobacteria and deltaproteobacteria with species level of 97%. Azospira oryzae (formally dechlorosoma suillum), Azospira restrica, and Geobacter spp. together with other similar groups were the most valuable bacteria for the degradation of chloroform.     

Kinetic and Thermodynamic Studies of Chlorinated Organic Compound Degradation by Siderite-Activated Peroxide and Persulfate

The efficacy of two oxidant systems, iron-activated hydrogen peroxide (H₂O₂) and iron-activated hydrogen peroxide coupled with persulfate (S₂O₈ ^2?), was investigated for treatment of two chlorinated organic compounds, trichloroethene (TCE) and 1,2-dichloroethane (DCA). Batch tests were conducted at multiple temperatures (10–50 °C) to investigate degradation kinetics and reaction thermodynamics. The influence of an inorganic salt, dihydrogen phosphate ion (H₂PO₄ ^?), on oxidative degradation was also examined. The degradation of TCE was promoted in both systems, with greater degradation observed for higher temperatures. The inhibition effect of H₂PO₄ ^? on the degradation of TCE increased with increasing temperature for the iron-activated H₂O₂ system but decreased for the iron-activated hydrogen peroxide-persulfate system. DCA degradation was limited in the iron-activated hydrogen peroxide system. Conversely, significant DCA degradation (87% in 48 h at 20 °C) occurred in the iron-activated hydrogen peroxide-persulfate system, indicating the crucial role of sulfate radical (SO₄ ^??) from persulfate on the oxidative degradation of DCA. The activation energy values varied from 37.7 to 72.9 kJ/mol, depending on the different reactants. Overall, the binary hydrogen peroxide-persulfate oxidant system exhibited better performance than hydrogen peroxide alone for TCE and DCA degradation.     

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.

     

Impact of Desalination on Physical and Mechanical Properties of Lanzhou Loess

Soluble salt in soil has a significant influence on the physical and mechanical properties of the soil. We performed desalination experiments on Lanzhou loess, a typical sulfate saline soil, to study the effects of salt on the physical and mechanical properties of the loess and compare variations in the soil properties after desalination. The Atterberg limits of the soil increased after desalination as a result of changes in the soil particle composition and grain refinement. The shear and uniaxial compressive strength of the soil increased as a result of decreased calcitic cementation and other changes to the soil structure. Scanning electron microstructure (SEM) and mercury intrusion porosimetry (MIP) procedures revealed changes to the microstructure and pore-size distribution of the Lanzhou loess after desalination.     

Functional Mapping of Multiple Dynamic Traits

Many biological phenomena undergo developmental changes in time and space. Functional mapping, which is aimed at mapping genes that affect developmental patterns, is instrumental for studying the genetic architecture of biological changes. Often biological processes are mediated by a network of developmental and physiological components and, therefore, are better described by multiple phenotypes. In this article, we develop a multivariate model for functional mapping that can detect and characterize quantitative trait loci (QTLs) that simultaneously control multiple dynamic traits. Because the true genotypes of QTLs are unknown, the measurements for the multiple dynamic traits are modeled using a mixture distribution. The functional means of the multiple dynamic traits are estimated using the nonparametric regression method, which avoids any parametric assumption on the functional means. We propose the profile likelihood method to estimate the mixture model. A likelihood ratio test is exploited to test for the existence of pleiotropic effects on distinct but developmentally correlated traits. A simulation study is implemented to illustrate the finite sample performance of our proposed method. We also demonstrate our method by identifying QTLs that simultaneously control three dynamic traits of soybeans. The three dynamic traits are the time-course biomass of the leaf, the stem, and the root of the whole soybean. The genetic linkage map is constructed with 950 microsatellite markers. The new model can aid in our comprehension of the genetic control mechanisms of complex dynamic traits over time.     

Seasonal Variability in Stormwater Quality Treatment of Permeable Pavements Situated Over Heavy Clay and in a Cold Climate

Permeable pavements mitigate the impacts of urbanization on surface waters through pollutant load reduction, both by sequestration of pollutants and stormwater volume reduction through exfiltration. This study examined the non-winter water quality performance of two side-by-side permeable pavements in the Ohio snowbelt. The permeable interlocking concrete pavements were designed to drain impervious catchments 2.2 (large) and 7.2 (small) times larger than their surface area, were located over clay soils, and incorporated the internal water storage design feature. Nutrient reduction was similar to past studies—organic nitrogen and particulate phosphorus were removed through filtration and settling, while dissolved constituents received little treatment. Because of 16 and 32 % volume reductions in the small and large installations, respectively, nutrient loads were often significantly reduced but generally by less than 50 %. Aluminum, calcium, iron, magnesium, lead, chloride, and total suspended solids (TSS) concentrations and loads often increased after passing through the permeable pavements; effluent TSS loads were three- to five-fold higher than influent TSS loads. This was apparently due to seasonal release of clay- and silt-sized particles from the soils underlying the permeable pavement and inversely related to elapsed time since winter. The application of de-icing salt is thought to have caused deflocculation of the underlying soils, allowing particulates to exit with stormwater as it discharged from the underdrain of the permeable pavements. By autumn, both permeable pavements discharged metals and TSS concentrations similar to others in the literature, suggesting the de-icing effects lasted 3–6 months post-winter. Sodium may substantially affect the performance of permeable pavements following winter de-icing salt application, particularly when 2:1 clay minerals, such as vermiculites and smectites, predominate.