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[en] Lake Inba is one of the most eutrophic lakes in Japan. This data paper reports the abundance of phytoplankton species sampled biweekly from April 1986 to March 2016 at four stations in Lake Inba. Monitoring has been carried out by Chiba Prefectural Government, and phytoplankton count data have been collected since 1986. A total of 340 phytoplankton species were identified and enumerated by microscopy, as numbers of cells or colonies. The abundance of each species was expressed as cells per milliliter lake water. Total cell density ranged from 102 to 108 cells ml−1. The dominant cell class density was Cyanobacteria throughout the year. Cyanobacteria, such as Phormidium spp., Microcystis aeruginosa, and Anabaena spp. (Dolicospermum spp.), were the most dense in all months. The dominant cyanobacteria species reached concentrations of 107 cells ml−1. Diatoms, such as Aulacoseira granulata and A. ambigua, were also abundant, reaching 106 cells ml−1. These data can be used to appreciate how anthropogenic disturbances, such as eutrophication and global warming, affect density and community composition of phytoplankton.
[en] Regeneration niches for tree seedlings are defined as possessing the biotic and abiotic requirements to successfully replace adults. However, two critical discrepancies obscure our understanding of the role of regeneration niches in forest community assembly: a weak association between seedling assemblages and environmental factors, and an uncoupling between seedling and adult-tree assemblages. However, understory plants, which may interact with microenvironments and seedlings, may be a better spatial descriptor of regeneration habitats. To test this, the spatial variations of seedling assemblages in a montane cloud forest of Taiwan were analyzed in terms of their association with neighborhood assemblages of understory plants, the shrub layer, and overstory trees, as well as environmental variables. We found that the understory plant spatial structure contributed most in explaining spatial variations of the seedling assemblages (especially for widespread Lauraceae and patchy Fagaceae) and facilitated the identification of patches of different regeneration habitats for specific seedling assemblages. Moreover, among these regeneration patches, tall herbs affected seedling density and diversity differently. We found segregation between tall herbs and Lauraceae seedlings, indicating that tall herbs shape seedling assemblages and uncouple the association between seedling and adult stages. However, positive covariations between seedlings/tall herbs and between seedlings/adults were found for Fagaceae and Pentaphylacaceae in different regeneration patches, suggesting that positive, neighboring effects and dispersal limitation may cause the patchy distribution of seedling assemblages and affect their coupling with adults. Thus, the understory plant spatial structure shapes seedling assemblages and provides a better link to spatial associations with regeneration habitats.
[en] EcoPlate quantifies the ability of a microbial community to utilize 31 distinct carbon substrates, by monitoring color development of microplate wells during incubation. Well color patterns represent metabolic profiles. Previous studies typically used color patterns representing average values of three technical replicates on the final day of the incubation and did not consider substrate chemical diversity. However, color fluctuates during incubation and color varies between replicates, undermining statistical power to distinguish differences among samples in microbial functional composition and diversity. Therefore, we developed a protocol to improve statistical power with two approaches. First, we optimized data treatment for color development during incubation and technical replicates. Second, we incorporated chemical structural information for the 31 carbon substrates into the computation. Our framework implemented as the protocol in the R environment is able to compare the statistical power among different calculation methods. When we applied it to data from aquatic microcosm and forest soil systems, we observed substantial improvement in statistical power when we incorporated temporal patterns during incubation instead of using only endpoint data. Using maximum or minimum values of technical replicates also sometimes gave better results than averages. Incorporating chemical structural information based on fuzzy set theory could improve statistical power but only when relative color density information was considered; it was not seen when the pattern was first binarized into the presence or absence of metabolic activity. Finally, we discuss research directions to improve these approaches and offer some practical considerations for applying our methods to other datasets.
[en] Our human-dominant world can be viewed as being built up in two parts, social and ecological systems, each consisting of multi-level organizations that interact in a complex manner. However, there are knowledge gaps among those interactions. In this paper, we focus on studies filling two types of gaps in the socioecological system, some of which are case studies in the East Asia region and others are discussed in a more general context. First, we address the gaps between different levels of organizations in ecological systems, namely, (1) the importance of plant trait plasticity in bridging evolution and ecology, (2) linking primary producer diversity and the dynamics of blue carbon in coastal ecosystems in the Asia–Pacific region, and (3) research direction of climate change biology to fill the gaps across evolution, community, and ecosystem. Also included is (4) the gap between ecological monitoring programs and theories, which also addresses the potential of citizen science. Second, we illustrate the gaps between ecological and social systems through ongoing development of an ecosystem management framework, i.e., ecosystem-based disaster risk reduction. Finally, we summarize the benefits of filling the gaps for ecologists and society.