PCR-DGGE analysis of bacterial communities in <Emphasis Type="Italic">funazushi</Emphasis>, fermented crucian carp with rice,during fermentation

Funazushi (fermented Crucian Carp with rice) is a fermented fish product found only around Lake Biwa in Shiga Prefecture, Japan. It is characterized by a unique cheese-like flavor and characteristic sour taste. We analyzed the changes in the microbial community during funazushi fermentation by denaturing gradient gel electrophoresis of PCR-amplified 16S rDNA fragments (PCR-DGGE) and by plate counts. The plate counts showed that lactic acid bacteria reached 8.0 log₁₀ CFU/g within 7 days of fermentation initiation before decreasing slowly to 4.0 log₁₀ CFU/g during the remainder of 1-year study period. PCR-DGGE revealed that the dominant bacteria in the initial (days 14 and 30) and latter (days 90, 180, and 360) periods of fermentation were Lactobacillus plantarum and L. acetotolerans. This is the first identification of L. acetotolerans in funazushi as traditional cultivation techniques have not been sufficiently sensitive. This is the first report of PCR-DGGE being used to assess the microbial community in funazushi. This technique was also found to be effective in profiling microbial diversity.     

Spatial variation in respiration from coarse woody debris in a temperate secondary broad-leaved forest in Japan

We measured the rates of respiration from snags and logs (“coarse woody debris”, CWD) of Japanese red pine (Pinus densiflora Sieb. et Zucc.) to examine the rate of decomposition and CO₂ efflux from these materials in a temperate secondary broad-leaved forest in Japan. At this site, a high quantity of CWD of P. densiflora had accumulated as a result of pine wilt disease during the 1970s. Respiration rates were measured using a dynamic closed chamber method combined with an infrared gas analyzer. We measured the respiration rate of 7 samples of snags and 10 samples of logs from August 2003 to January 2004. The responses of the respiration rates of snags (R_snag) and logs (R_log) to changing temperature were both exponential and the responses to water content were quadratic, and the same function could be used to estimate annual values of both R_snag and R_log. Intensive measurements of water contents of snags and logs showed a marked difference in water content. The mean water content of snags was 20% of log water content. This difference was likely responsible for the observed difference in annual R_snag and R_log. The decay rate constants estimated from the respiration rates measurement of snags and logs were 0.019 and 0.081 year⁻¹, respectively. Despite being lower than R_log, R_snag was a significant compartment of the CWD carbon budget at this site.     

Patterns of root respiration rates and morphological traits in 13 tree species in a tropical forest

The root systems of forest trees are composed of different diameters and heterogeneous physiological traits. However, the pattern of root respiration rates from finer and coarser roots across various tropical species remains unknown. To clarify how respiration is related to the morphological traits of roots, we evaluated specific root respiration and its relationships to mean root diameter (D) of various diameter and root tissue density (RTD; root mass per unit root volume; gcm(-3)) and specific root length (SRL; root length per unit root mass; mg(-1)) of the fine roots among and within 14 trees of 13 species from a primary tropical rainforest in the Pasoh Forest Reserve in Peninsular Malaysia. Coarse root (2-269mm) respiration rates increased with decreasing D, resulting in significant relationships between root respiration and diameter across species. A model based on a radial gradient of respiration rates of coarse roots simulated the exponential decrease in respiration with diameter. The respiration rate of fine roots (<2mm) was much higher and more variable than those of larger diameter roots. For fine roots, the mean respiration rates for each species increased with decreasing D. The respiration rates of fine roots declined markedly with increasing RTD and increased with increasing SRL, which explained a significant portion of the variation in the respiration among the 14 trees from 13 species examined. Our results indicate that coarse root respiration in tree species follows a basic relationship with D across species and that most of the variation in fine root respiration among species is explained by D, RTD and SRL. We found that the relationship between root respiration and morphological traits provides a quantitative basis for separating fine roots from coarse roots and that the pattern holds across different species.     

Automated analysis of fine‐root dynamics using a series of digital images

Information related to the growth of fine roots is important for understanding C allocation in trees and the mechanisms of C cycling in ecosystems. Observations using a camera or scanner embedded in the soil enabled us to obtain continuous images of fine‐root‐growth dynamics. However, these methods are still labor‐intensive because the image analysis has to be conducted manually. We developed an automated method for tracking movement or elongation of fine roots using a sequence of scanner images. We also show how data obtained with these methods can be used for calculating fine‐root behavior. Two A4‐size scanners were buried in a mixed forest in Japan and images were taken continuously from within the soil. We preprocessed these images by extracting the fine‐root area from the images and developed an automated calculation plug‐in we named A‐root for tracking growth movement of the tips of fine roots. A‐root and manual‐tracking results were compared using the same images. The results show the A‐root and manual‐tracking methods yielded similar levels of accuracy. The average growth rate of 17 fine roots tracked using the program was 0.16 mm h^–1. The observation of the direction of growth in fine roots showed the direction may be influenced by the original root's growth where the fine roots branched, distribution of soil particles, other roots, and the force of gravity. The A‐root analysis also suggested there may be an interaction between speed of growth and changes in direction of growing fine roots.