Impact of fumigation with metam sodium upon soil microbial community structure in two Japanese soils

The effects of fumigation with sodium methyl dithiocarbamate (metam sodium) on the microbial community structure and function in 2 soils were investigated using a variety of techniques. In both soils ca. 50% and 90% of the populations of total and culturable bacteria, respectively, were killed by fumigation, with recovery to levels prevailing in control soils 26 d after cessation of fumigation. The size of the ammonium and nitrite oxidiser populations was reduced by up to 4 orders of magnitude by fumigation, with the latter showing a slight recovery 105 d later. There were substantial changes in the C-utilisation (Biolog GN) profiles in the fumigated soils even 105 d later. The number and pattern of amplified 16S ribosomal DNA restriction analysis (ARDRA) fragments was changed by fumigation, and there was a shift in the %G+C profile toward a greater proportion of lower %G+C classes in treated soils. It appeared that DNA released from killed cells remained for some time after fumigation, and masked the apparent community DNA profiles. This study demonstrates that the effects of fumigation on the soil microbial community structure and function were pronounced and for some parameters very persistent. However, the effects on broad-scale properties such as total or culturable bacterial numbers were less enduring.     

Epibiotic microorganisms associated with microcrustaceans in overlying water of Philippine paddy fields

Epibiotic microorganisms associated with micro crustaceans in the overlying water of Philippine paddy fields were examined by scanning electron microscopy, and their associations were compared with those observed in Japanese paddy fields (Soil Sci. Plant Nutr., 43, 633-641, 651-664, 1997). Various types of microorganisms, including bacteria, protozoa, and algae, colonized microcrustaceans and their kinds and colonizing patterns varied depending on the kinds of microcrustaceans. Common associations between epibionts and respective micro crustaceans were observed in the Philippines and in Japan: e.g., rodshaped bacteria on Cyclopidae and Cypridopsidae; no microorganisms on Simocephalus spp.     

Microbial community indigenous to the earthworm Eisenia foetida

 Microbial populations of the earthworm Eisenia foetida, their casts and farmyard manure (FYM) in which E. foetida had lived were enumerated with the dilution plate method using several media. The microbial community of earthworms appeared to be similar to that of the FYM in which they had lived, while that of earthworms starved in distilled water for 24 h greatly differed from that of the FYM. The community of the starved earthworms consisted exclusively (more than 90%) of fast growers, which were defined as those that formed their colonies within 2 days, unlike that of the FYM (10–30%). About 30 isolates were randomly chosen and some physiological properties were examined. The community of starved earthworms consisted exclusively of Gram-negative, oxidase-positive, fermentative bacteria, whereas bacteria from the FYM were much more diverse and there were no fermentative bacteria in the FYM. The predominant bacteria species of the starved earthworms were identified as Aeromonas hydrophila and considered to be indigenous to the earthworm E. foetida. Received: 18 June 1999     

Involvement of microaerophilic iron-oxidizing bacteria in the iron-oxidizing process at the surface layer of flooded paddy field soil

Journal of Soils and Sediments - To reveal whether microaerophilic Fe(II)-oxidizing bacteria (FeOB) participate in the Fe(II) oxidation at the oxic-anoxic interface in flooded paddy field soil,...     

Retention of a European pear aroma model mixture using different types of saccharides

Eight types of microcapsules of European pear (La France) aroma model mixture were prepared, and their retained aroma components and sample microstructures (both surface and cross-section) were compared. The La France pear aroma model mixture was prepared by the mixing of hexanal and five kinds of esters. alpha-Cyclodextrin (alpha-CD), gum arabic (GA), soybean soluble polysaccharide (SSPS), and highly branched cyclic dextrin (HBCD) were used as carrier solids, and spray drying and freeze drying comprised the drying methods. The mean particle size of the microcapsules ranged from 8.34 microm for the microcapsules with alpha-CD to 9.67 microm for those with SSPS. The total aroma contents were different depending upon the microencapsulation systems (1.35 g/100 g of microcapsules for the spray-dried microcapsules with HBCD to 14.1 g/100 g of microcapsules for the freeze-dried microcapsules with GA). The microcapsules with alpha-CD and GA were stable against heat treatment (40, 80, or 120 degrees C for 60 min) under nitrogen gas flow.     

Hyperproduction and application of alpha-agarase to enzymatic enhancement of antioxidant activity of porphyran

The nucleotide sequence of the gene for the alpha-agarase, AgaA33, from Thalassomonas sp. strain JAMB-A33 was determined. The open reading frame for AgaA33 was revealed to encode 1463 amino acid residues. We succeeded in extracellular production of recombinant -agarase (AgaA33) efficiently using Bacillus subtilis as a host. This is the first report of recombinant production of -agarase. Furthermore, we demonstrated that hydrolysis of alpha-1,3 linkages in porphyran, a sulfated polysaccharide from marine red algae, by alpha-agarase is an important step for improvement of its antioxidant activity with regard to free-radical-scavenging capacity and superoxide radical anion scavenging activity, whereas the hydrolysis of beta-1,4 linkages in porphyran by beta-agarase did not increase on the antioxidant activity markedly.     

An in vitro screening assay to discover novel inhibitors of 4-coumarate:CoA ligase

4-Coumarate:CoA ligase (4CL, EC 6.2.1.12) exists only in plants and plays an important role in the phenylpropanoid pathway. Identification of inhibitors targeting 4CL provides a novel approach for developing effective plant growth inhibitors (PGIs). The full-length gene of tobacco 4CL (Nt4CL1) was cloned and expressed in Escherichia coli Cast & Chalm. The recombinant 4CL protein was extracted and purified by several purification steps including gel-filtration and anion-exchange chromatography. 4CL activity assay was miniaturized and optimized using a 96-well microplate and a reader. Among 28 existing herbicides, propanil and swep strongly inhibited in vitro 4CL enzyme activity, and they were selected for further studies. The process of this assay can be developed into a high-throughput screening system of PGI targeting 4CL in the phenylpropanoid pathway.     

Introduction of a point mutation in the KRAS gene of in vitro fertilized porcine zygotes via electroporation of the CRISPR/Cas9 system with single-stranded oligodeoxynucleotides

This study aimed to investigate the efficiency of KRAS gene editing via CRISPR/Cas9 delivery by electroporation and analyzed the effects of the non-homologous end-joining pathway inhibitor Scr7 and single-stranded oligodeoxynucleotide (ssODN) homology arm length on introducing a point mutation in KRAS. Various concentrations (0–2 µM) of Scr7 were evaluated; all concentrations of Scr7 including 0 µM resulted in the generation of blastocysts with a point mutation and the wild-type sequence or indels. No significant differences in the blastocyst formation rates of electroporated zygotes were observed among ssODN homology arm lengths, irrespective of the gRNA (gRNA1 and gRNA2). The proportion of blastocysts carrying a point mutation with or without the wild-type sequence and indels was significantly higher in the ssODN20 group (i.e., the group with a ssODN homology arm of 20 bp) than in the ssODN60 group (gRNA1: 25.7% vs. 5.4% and gRNA2: 45.5% vs. 5.9%, p < .05). In conclusion, the CRISPR/Cas9 delivery with ssODN via electroporation is feasible for the generation of point mutations in porcine embryos. Further studies are required to improve the efficiency and accuracy of the homology-directed repair.     

Soil ecosystem engineering by the train millipede Parafontaria laminata in a Japanese larch forest

Periodic swarming by adult train millipedes Parafontaria laminata (Attems, 1909) occurs in central Japan on an 8-year cycle, and the emergence of new adults is highly predictable. Millipede biomass reaches a maximum and feeding habits change upon the emergence of adults. Larvae are geophagous while adults feed on both litter and soil. We hypothesized that the shift in the developmental stages of P. laminata influenced the carbon dynamics in the soil and conducted a field mesocosm experiment in a larch plantation forest over 2 years (1999 and 2000) using three developmental stages: sixth- and seventh-instar larvae and adults. By experimentally manipulating millipede density at four levels, we obtained the following results: larvae were geophagous, while adults consumed both litter and soil (mixed-feeding) and consequently showed stronger density effects on litter decomposition rates than larvae; adult activities in the high-density treatment increased soil microbial biomass but not at low adult densities or at the larval stages; and adults increased the carbon accumulation in soil layers especially at high densities due to their mixed-feeding on litter and soil. We determined that due to synchronized postembryonic development with high densities and changes in feeding habits, the train millipede periodically sequestered carbon in this forest.