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Bark traits of trees often serve as a key factor determining the community structure of epiphytes. However, the extent to which barks modulate the relative importance of abiotic and biotic assembly processes of epiphytes is poorly understood. Here, using a community phylogenetic approach, we aimed to infer the assembly processes of epiphytic mosses and liverworts on tree species with varying bark traits in a temperate forest of central Japan. We observed a total of 56 moss and 35 liverwort species on 150 trees. Moss communities showed decreasing species richness and a tendency toward phylogenetic overdispersion, that is, higher phylogenetic diversity than expected by chance, in relation to increasing bark roughness and acidity. Along the same bark gradients, liverwort communities became phylogenetically clustered. Species richness of both mosses and liverworts increased with the nitrogen content of barks. The results indicate non-random assembly processes such as abiotic filtering associated with environmental harshness and microhabitat variety determined by barks. Our findings imply that bark traits modulate community assembly processes through which epiphyte diversity is maintained. [ABSTRACT FROM AUTHOR]

Premise: Biodiversity is often only measured with species richness; however, this metric ignores evolutionary history and is not sufficient for making conservation decisions. Here, we characterize multiple facets and drivers of biodiversity to understand how these relate to bioregions and conservation status in the ferns of Japan. Methods: We compiled a community data set of 1239 grid cells (20 × 20 km each) including 672 taxa based on >300,000 specimen records. We combined the community data with a phylogeny and functional traits to analyze taxonomic, phylogenetic, and functional diversity and modeled biodiversity metrics in response to environmental factors and reproductive mode. Hierarchical clustering was used to delimit bioregions. Conservation status and threats were assessed by comparing the overlap of significantly diverse grid cells with conservation zones and range maps of native Japanese deer. Results: Taxonomic richness was highest at mid‐latitudes. Phylogenetic and functional diversity and phylogenetic endemism were highest in small southern islands. Relative phylogenetic and functional diversity were high at high and low latitudes, and low at mid‐latitudes. Grid cells were grouped into three (phylogenetic) or four (taxonomic) major bioregions. Temperature and apomixis were identified as drivers of biodiversity patterns. Conservation status was generally high for grid cells with significantly high biodiversity, but the threat due to herbivory by deer was greater for taxonomic richness than other metrics. Conclusions: Our integrative approach reveals previously undetected patterns and drivers of biodiversity in the ferns of Japan. Future conservation efforts should recognize that threats can vary by biodiversity metric and consider multiple metrics when establishing conservation priorities. [ABSTRACT FROM AUTHOR]

The fern and lycophyte flora of Japan comprising 721 native taxa (including subspecies and varieties) plus 371 interspecific hybrids was reassessed using a nearly comprehensively sampled distribution map at 10 km resolution vouchered by 216,687 specimens, up-to-date cytotaxonomic information covering 74% of the taxa, and an rbcL sequence dataset covering 97.9% of the taxa. Spatial distribution of species richness and phylogenetic diversity was visualized. Apomixis was observed in 11.0% of the native taxa whose reproductive modes are known. The number of sexually reproducing polyploid taxa (n = 199) is less than sexual diploids (n = 241), and 30 of them are evidently allopolyploid, in contrast with the low number of possible autopolyploids (n = 4). Apomictic taxa were found to have smaller latitudinal ranges than sexual taxa or taxa with multiple reproductive modes. A morphological character dataset in Lucid format is provided for taxonomic identification of the native taxa. [ABSTRACT FROM AUTHOR]

Dermanyssus gallinae, the poultry red mite, is an obligatory blood-sucking ectoparasite. The genetic diversity of D. gallinae has been examined in some countries, but so far not in Asian countries. Here, we sequenced a part of the mitochondrial cytochrome oxidase subunit I (COI) and16S rRNA genes and nuclear internal transcribed spacers (ITS) region in 239 mite samples collected from 40 prefectures throughout Japan. The COI and 16S rRNA nucleotide sequences were classified into 28 and 26 haplotypes, respectively. In phylogenetic trees, the haplotypes clustered into 2 haplogroups corresponding to haplogroups A and B, which were previously reported. Haplogroups A and B were further subdivided into sub-haplogroups AJ1 and AJ2, and BJ1 and BJ2, respectively. In both trees, the sequences of haplotypes in AJ1 and BJ2 were relatively distant from those reported in other countries, while some sequences in AJ2 and BJ1 were identical to those in Europe. In addition, the ITS sequences were classified into two sequences, and both sequences were closely related to the sequences found in European countries. These findings indicate a possibility of international oversea transmission of D. gallinae. [ABSTRACT FROM AUTHOR]

Abstract: Cowpea [Vigna unguiculata (L.) Walp.] is an important legume crop and yet its rhizobia have not been well characterized in many areas. In the present study, sequence analysis of the bacterial 16S-23S rRNA internal transcribed spacer (ITS) region was performed to characterize genetically 76 indigenous cowpea rhizobia from five different geographic regions (Okinawa, Miyazaki, Kyoto, Fukushima and Hokkaido) of Japan. The sequence analysis clustered all isolates in the genus Bradyrhizobium. They were conspecific with B. japonicum, B. yuanmingense, B. elkanii and Bradyrhizobium sp., although none of them grouped with B. liaoningense, B. canariense, B. betae or B. iriomotense. B. yuanmingense was only isolated from the southern region (Okinawa) where it achieved the highest frequency of 69%. B. japonicum was predominant at Miyazaki, Fukushima and Hokkaido with more than 60% of the isolates. B. elkanii was mainly recorded in the southern (Okinawa: 31%, Miyazaki: 33%) and middle (Kyoto: 33%) regions. This species was present at a very low frequency in Fukushima and absent in Hokkaido in the northern area. Bradyrhizobium sp. like-strains were absent in the southern part (Okinawa, Miyazaki) but were concentrated either in the middle regions with 67% of Kyoto isolates and 28% of Fukushima isolates, and in the northern region with 40% of the Hokkaido isolates. This study revealed a geographical distribution of cowpea bradyrhizobia which seemed to be related to the differences in the environmental characteristics (soil type and soil pH, temperature, climate, moisture) of the different regions in Japan. [Copyright &y& Elsevier]

There is considerable interest in the factors which may explain variation in microbial community assembly processes. In this study, we investigated bacterial community assembly, phylogenetic diversity and the relative role of deterministic and stochastic processes along environmental gradients on Mt. Norikura, Japan. DNA extracted from soil samples collected at a range of elevations was PCR-amplified targeting the V3 and V4 regions of the bacterial 16S rRNA gene, and sequenced using Illumina MiSeq. We hypothesized that elevation would be a strong predictor of phylogenetic community assembly, with communities being more phylogenetically clustered towards higher elevations, due to more extreme physiological conditions. We also hypothesized a greater role of stochasticity at the highest elevations, due to more frequent soil disturbance. Contrary to our hypotheses, we found that the strength of phylogenetic clustering and the role of stochasticity were strongly related to soil pH, with phylogenetic clustering and deterministic processes being strongest at lower soil pH values. Moreover, there was no trend towards stronger influence of phylogenetic clustering and stochasticity in the upper elevations of Mt. Norikura. These results reveal an overwhelming influence of soil pH on phylogenetic community assembly of soil bacteria, even when a range of other environmental gradients are present. [ABSTRACT FROM AUTHOR]