Polymorphism analysis of Fagaceae and DNA-based identification ofFagus species grown in Japan based on therbcL gene

Fagaceae species in Japan were identified by restriction fragment length polymorphism (RFLP) and sequence comparison of a region ofrbcL. Of nine restriction endonucleases used for digestion, three (MspI,RsaI,HaeIII) produced different restriction patterns in Fagaceae. Digestion byMspI yielded four patterns: Fagus species,Castanea crenata, Pasania glabra, and others. Digestion byRsaI andHaeIII afforded two patterns:Fagus species and others. These facts indicate thatCastanea crenata andPasania glabra can be identified byMspI restriction patterns ofrbcL. Sequence comparison of a region of therbcL gene among 20 species of Fagaceae showed that: (1) they could be divided into seven groups; (2) there is a site mutation betweenFagus crenata andF. japonica. The latter indicates that the wood of both Fagus species are identifiable at the species level, which is not the case using conventional methods. This result indicates the possibility of wood identification based on DNA polymorphism in Fagaceae at the intrageneric level.Part of this paper was presented at the 46th annual meeting of the Japan Wood Research Society, Kumamoto, April 3–5, 1996 and the 47th annual meeting of the Japan Wood Research Society, Kochi, April 3–5, 1997     

Molecular Structure and Some Physicochemical Properties of High‐Amylose Barley Starches

The molecular structure and some physicochemical properties of starches from two high‐amylose cultivars of barley, high‐amylose Glacier A (HAG‐A) and N (HAG‐N), were examined and compared with those of a normal cultivar, Normal Glacier (NG). The true amylose contents of HAG‐A, HAG‐N, and NG were 41.0, 33.4, and 23.0%, respectively. Iodine affinities before and after defatting of starch, and thermograms of differential scanning calorimetry, indicated that HAG‐A and HAG‐N starches had a higher proportion of amylose‐lipid complex than did NG starch. The amylopectins from HAG‐A and HAG‐N were similar to NG amylopectin in average chain length (18–19), β‐amylolysis limit (β‐AL 56–57%), number‐average degrees of polymerization (DP_n 6,000–7,500) and chain length distribution. Very long chains (1–2%) were found in amylopectins from all cultivars. HAG‐A amylopectin had a larger amount of phosphorus (214 ppm) than the others. The amyloses from HAG‐A and HAG‐N resembled NG amylose in DP_n (950–1,080) and β‐AL (70–74%). However, HAG‐A and HAG‐N had a larger number of chains per molecule (NC 2.4–2.7) than NG amylose (1.8) and contained the branched amylose with a higher NC (9.5–10.6) than that of NG amylose (5.8), although molar fractions of the branched amylose (15–20%) were similar.     

Carbon and nitrogen stocks and their mineralization potentials are higher under organic than conventional farming practices in Japanese Andosols

ABSTRACT

This study aimed at understanding whether and how long-term organic rice farming affects soil carbon (C) and nitrogen (N) stocks and their mineralization potentials in submerged rice paddies in Tochigi, Japan. An incubation experiment was carried out to assess the impacts of internal nutrient cycling after organic farming (OF) for 4–5 years (4OF), 8–9 years (8OF), and 12 years (12OF), compared with a conventional rice field (CF). Soil samples were collected at 0–15 cm and 15–20 cm in flooded rice fields after harvest in October 2013. pH and bulk density at 0–15 cm were significantly lower in 12OF fields than in CF fields (by 0.22 unit pH and 17.5%, respectively). Compared with CF, 12OF fields showed significant differences in soil organic carbon (SOC) and total nitrogen (TN), but 4OF and 8OF fields did not. In 8OF fields, the C decomposition (Co) and N mineralization (No) potentials were significantly higher (by 34.0% and 35.6%, respectively, at 0–15 cm, and by 67.1% and 24.5% at 15–20 cm) than in CF fields. Similarly, in 8OF fields at 0–15 cm, the Co:SOC and No:TN ratios were 19.8% and 23.2% higher, respectively, than in CF fields. Co, No, Co:SOC, and No:TN in 12OF fields were higher than those in CF fields, demonstrating the effects of prolonged organic rice farming. Additionally, in 12OF fields, C and N stocks were significantly higher (by 15.5% and 17.2%, respectively, at 0–15 cm, and by 4.8% and 12.1% at 15–20 cm) than in CF fields. Our findings suggest that long-term organic rice farming increases soil C and N stocks as well as C and N mineralization in Japanese Andosols.     

Possible influence of termites (Macrotermes bellicosus) on forms and composition of free sesquioxides in tropical soils

There has been less concern about soil mineralogical alteration than about soil physical, chemical and biological changes induced by termite nest-building activity. Furthermore, much less attention has been paid to free sesquioxides than to phyllosilicate minerals. In the present study, we conducted field morphological observations and selective dissolution analysis to characterize free sesquioxides in termite (Macrotermes bellicosus) mounds as compared with surrounding pedons in different toposequence positions, i.e., seasonally flooded valley bottom, hydromorphic fringe and well-drained upland sites. Distinctive redoximorphic features, such as surface yellowish layers on mound structures from the fringe site, indicate possible alteration of iron sesquioxide forms in the mounds due to the transportation of soil from reductive (aquic subsoil) to oxidative (epigeal mound) environments by the nest-building activity of M. bellicosus. On the other hand, the iron-soluble content in the dithionite-citrate-bicarbonate (DCB) system (Fe_d) was generally higher in the mound structures than at the adjacent sub-surface (Ap2) horizon at each toposequence position, while there was less difference in the content of acid ammonium oxalate (AAO) extractable iron (Fe_o) as compared to Fe_d. As a consequence, the iron activity index (Fe_d/Fe_o ratio) was found for the most part to be lower in the mound structures than in the neighboring Ap2 horizon. In addition, the content of Fe_d, AAO-soluble Al (Al_o) and DCB-extractable Al (Al_d) was significantly correlated with clay content in these soils. These findings suggest that M. bellicosus preferentially collects clay particles, probably from the clay-rich subsoils, such as the argillic horizon, which has been formed by the co-migration of phyllosilicate minerals and relatively crystalline sesquioxides. The species then likely incorporates them into the mounds, which induces an increase in the Fe_d content relative to that of Fe_o, resulting in a decreased iron activity index in the mound structures.     

Antihyaluronidase action of ellagic acid effectively prevents polyspermy as a result of suppression of the acrosome reaction induced by sperm-zona interaction during in vitro fertilization of porcine oocytes

The present study was conducted to examine the effects of three tannin relatives (tannic acid, TA; gallic acid, GA; and ellagic acid, EA) on antihyaluronidase and reactive oxygen species (ROS) scavenging activity, in vitro fertilization (IVF) parameters, and the acrosome reaction (AR) induced by sperm-zona interaction. Among the three tannin relatives, TA and EA showed the strongest potency for blocking the hyaluronidase activity of boar sperm, with concentration-dependent inhibition over the range of 2-10 microg/ml. In contrast, ROSs were effectively scavenged by TA and GA, but not EA. When cumulus-free oocytes were inseminated in IVF medium containing 5 microg/ml of the tannin relatives, polyspermy was significantly reduced by TA and EA (32 and 29%, respectively) compared with oocytes treated with or without GA (51 and 69%, respectively) under conditions that maintained a high sperm penetration rate (P<0.05). Interestingly, induction of the AR by treatment of preincubated sperm with progesterone was blocked by TA and GA as a result of their higher levels of ROS scavenging activity, while EA, which possessed weak ROS scavenging activity, did not disturb induction of the AR with progesterone. However, the incidence of AR induced by sperm-zona interaction was significantly decreased by the strong antihyaluronidase actions of TA and EA compared with that in the absence of these compounds. Treatment with the compounds caused neither a protective proteolytic modification of the zona pellucida matrix before fertilization nor a reduction in acrosomal proteolytic activity or the number of zona-bound sperm. These findings suggest that the antihyaluronidase action of EA effectively prevents polyspermy by suppression of AR functionality induced by sperm-zona interaction and that hyaluronidase intervention is therefore required during porcine IVF.     

Spatial–temporal variations in the composition of two <Emphasis Type="Italic">Zostera</Emphasis> species in a seagrass bed: implications for population management of a commercially exploited grass shrimp

We examined spatial and temporal variations in the species composition of two seagrass species, Zostera marina and Z. caespitosa, in a lagoon facing the Sea of Okhotsk. We also considered how those variations affected habitat quality for motile epifauna, especially for a commercial shrimp. A long-interval comparison between 1996 and 2013 showed that seagrass species composition in the lagoon did not vary, while their relative abundances did. A survey in 2012 revealed that the abundance of Z. caespitosa was affected by the abundance of Z. marina, water depth, and location in the lagoon. Although these seagrass species have similar aboveground morphology, differences in their fine structures were detected. Diversities of motile animals inhabiting the seagrass species were the same. Differences in seagrass utilization were observed when we focused on a commercial shrimp, Pandalus latirostris. This shrimp always preferred higher densities of shoots irrespective of the species and seasonally changed their preference for the number of leaves per shoot. They were therefore more abundant in Z. caespitosa, which had those structural characteristics. The results suggest that the management of shrimp resources could be improved by flexibly changing protected areas in accordance with the dynamics of seagrass distribution in the lagoon.     

T4-type bacteriophage communities estimated from the major capsid genes (g23) in manganese nodules in Japanese paddy fields

The present study compared the capsid gene ( g23 ) of T4-type bacteriophages (phages) in Mn nodules with those in the plow layer soil and subsoils of two Japanese paddy fields by applying the primers MZIA1bis and MZIA6 to DNA extracts from the nodules and soils. The deduced amino acid sequences of the g23 genes in the Mn nodules were similar to those in the plow layer soil and in the subsoils. This result indicated that similar T4-type phage communities developed at these sites and that the diversity of T4-type phage communities was wide enough to cover those in the plow layer soil and in the subsoils. The majority of g23 clones formed several clusters with the clones and phages obtained from far-apart paddy fields, and the sequences of two clones were completely identical to a phage and a clone from other paddy fields at the nucleotide or amino acid level, indicating horizontal transfer of g23 genes between those paddy fields. A clone with a long nucleotide residue (686 bp) and a distribution remote from the other clones in the phylogenetic tree indicated that there were many uncharacterized, novel g23 genes in the paddy fields.     

Effects of sika deer (Cervus nippon) and dwarf bamboo (Sasamorpha borealis) on seedling emergence and survival in cool-temperate mixed forests in the Kyushu Mountains

Effects of sika deer (Cervus nippon) and dwarf bamboo (“sasa;” Sasamorpha borealis) on seedling emergence and survival were investigated in cool-temperate mixed forests in the Kyushu mountain range, Japan. We compared the effects of sika deer between two sites with different sika deer densities. One site (no-sasa forest) has sparse cover of S. borealis and a high density of sika deer, and the other site (sasa forest) has dense cover of S. borealis with a low density of sika deer. In the no-sasa forest, more seedlings emerged and the survival rate of the seedlings was higher compared with the sasa forest. Compared with the sasa forest, the canopy in the no-sasa forest was more open, the organic layer was shallower and drier, the mean daily soil temperature was higher, and soil temperature fluctuated more widely. Those environmental parameters did not differ between unfenced and fenced plots. The comparison between the sasa and no-sasa forests suggested that removal of S. borealis by sika deer had an indirect positive effect on seedling emergence and survival. However, the fenced-plot experiments indicated that sika deer inhibited seedling emergence and survival. These contradictory conclusions could result from the much larger negative effects of S. borealis on seedling emergence and survival compared with the effects of sika deer browsing.