Appendix B. Analyses by MANOVA of the effects of distance, density, and light on seedling survival of S. controversa at age 0.5 yr and 1 yr.

Analyses by MANOVA of the effects of distance, density, and light on seedling survival of S. controversa at age 0.5 yr and 1 yr

Appendix C. A table showing the annual relation between seedling height of S. controversa and each environmental variable at age 0 – 5 yr, analyzed by Spearman's coefficient of correlation.

A table showing the annual relation between seedling height of S. controversa and each environmental variable at age 0 – 5 yr, analyzed by Spearman's coefficient of correlation

Appendix D. Analyses by two-way ANOVA of effects of light, herbs, and their interaction on seedling height of S. controversa each year for ages 0 – 5 yr.

Analyses by two-way ANOVA of effects of light, herbs, and their interaction on seedling height of S. controversa each year for ages 0 – 5 yr

Appendix A. Analyses by the proportional-hazard model of the effects of distance, density, and light on seedling survival.

Analyses by the proportional-hazard model of the effects of distance, density, and light on seedling survival

How long do tree seeds survive in soil seedbanks? A multi-species comparison in an old-growth deciduous temperate forest

We evaluated the performance of tree seeds in the soil seedbank of a temperate deciduous old-growth forest with respect to the total proportion of seeds that emerged as seedlings (PTOTAL) and the average time seeds were in the soil prior to emergence as seedlings (TAVERAGE). We analyzed 12 years of data on the seed dispersal and seedling emergence of 16 important tree species collected from more than 100 seed traps and quadrats. Using these estimates, we assessed whether seed banking is an effective regeneration strategy in forests compared to other life-history strategies. Persistence in the soil did not necessarily increase overall seed mortality. Phylogenetic constraints played a limited role in variations in PTOTAL and TAVERAGE among species, likely due to pronounced differences between closely related species. Estimated values of TAVERAGE were mostly less than 1.5 years. Some species had a PTOTAL greater than 0.20, despite having seeds with no known physical or chemical protection mechanisms. Seed size was not associated with seed performance. By contrast, greater per capita fecundity appeared to compensate for lower performance of banked seeds. Contrary to our expectations, species with longer TAVERAGE values exhibited higher seedling survivorship, implying an absence of trade-offs between seed banking and seedling banking, and even implying a synergy between these strategies. In old-growth forests, seeds stored in soil seedbanks likely provide a buffer during years with little or no seed production; however, seedbanks may not promote adequate regeneration following natural or artificial large-scale disturbances that remove parent trees.</p

Species richness of the understory woody vegetation in Japanese cedar plantations declines with increasing number of rotations

<p>The possibility of restoring natural broadleaf forests may be decreased by the effects of plantation management, particularly in sites that undergo repeated rotation. We investigated the following two working hypotheses about the effects of repeated plantation of conifers on the natural regeneration of woody saplings in cool-temperate Japanese cedar plantations: (1) that repeated plantation of conifers decreases sapling species richness, and (2) that repeated plantation of conifers changes sapling species compositions. Our result supported the first hypothesis, because species richness was significantly lower in second-rotation plantations than in first-rotation plantations. The second hypothesis was not supported, because no significant or substantial differences in species composition were observed between plantations with different numbers of rotations. However, the abundance of tree (nonshrub) and gravity-dispersed species decreased after the second rotation of large saplings, albeit not those of small saplings, suggesting that response to repeated rotation depended on sapling size. Our results suggest that it is important to consider factors affecting the maintenance of a species in the plantations, such as distance from natural forests and seed sources, to minimize the effects of repeated plantation.</p

Relationship between the Decomposition Process of Coarse Woody Debris and Fungal Community Structure as Detected by High-Throughput Sequencing in a Deciduous Broad-Leaved Forest in Japan

<div><p>We examined the relationship between the community structure of wood-decaying fungi, detected by high-throughput sequencing, and the decomposition rate using 13 years of data from a forest dynamics plot. For molecular analysis and wood density measurements, drill dust samples were collected from logs and stumps of <i>Fagus</i> and <i>Quercus</i> in the plot. Regression using a negative exponential model between wood density and time since death revealed that the decomposition rate of <i>Fagus</i> was greater than that of <i>Quercus</i>. The residual between the expected value obtained from the regression curve and the observed wood density was used as a decomposition rate index. Principal component analysis showed that the fungal community compositions of both <i>Fagus</i> and <i>Quercus</i> changed with time since death. Principal component analysis axis scores were used as an index of fungal community composition. A structural equation model for each wood genus was used to assess the effect of fungal community structure traits on the decomposition rate and how the fungal community structure was determined by the traits of coarse woody debris. Results of the structural equation model suggested that the decomposition rate of <i>Fagus</i> was affected by two fungal community composition components: one that was affected by time since death and another that was not affected by the traits of coarse woody debris. In contrast, the decomposition rate of <i>Quercus</i> was not affected by coarse woody debris traits or fungal community structure. These findings suggest that, in the case of <i>Fagus</i> coarse woody debris, the fungal community structure is related to the decomposition process of its host substrate. Because fungal community structure is affected partly by the decay stage and wood density of its substrate, these factors influence each other. Further research on interactive effects is needed to improve our understanding of the relationship between fungal community structure and the woody debris decomposition process.</p></div

Results of the PCA ordination of individual pieces of <i>Fagus</i> CWD and fungal OTUs.

<p>Fungal OTUs are presented by subdivision or class to avoid redundancy.</p

Results of the SEM analysis of the decomposition rate index of <i>Quercus</i> CWD.

<p>See the legend of <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131510#pone.0131510.g005" target="_blank">Fig 5</a> for an explanation of the values and arrows.</p

SEM analysis results of the decomposition rate index of <i>Fagus</i> CWD.

<p>Numbers beside the arrows represent path coefficients. All paths included in the analysis are presented. Straight single-headed arrows represent causal pathways. Curved, double-headed arrows indicate covarying variables. Thick, straight, black arrows indicate significant causal pathways at the level of <i>p</i> < 0.05. Thick, gray, curved arrows indicate significant covarying relationships at the level of <i>p</i> < 0.05. Dashed, straight, curved arrows indicate non-significance (<i>p</i> > 0.05).</p