The aim of this article is to highlight aspects of the relationship certain local communities, such as villages or neighbourhoods, have with their landscapes and to identify existing regulations that ...should be built upon to make these relationships sustainable. The hypothesis put forward is that the relationship between people and the landscape is constructed in the form of a "ba" or a collective place. Processes for the construction of such places are therefore presented as guiding principles for reflection. These collective places or ba can take two forms : the collective place of autonomy (jichi no ba 自治の場) and the collective place of integration (tōgō no ba 統合の場). Two case studies focus on the need to change this relationship between a local community and its landscapes through the protection of the cultural landscapes of an agricultural plateau of medium altitude. The plateau in question is the Shiraito plateau on the island of Kyūshū where the relationship between the landscape and local communities was disrupted during the disastrous Kumamoto earthquakes in 2016.
Root-associated microbial communities are very important in the adaptation of halophytes to coastal environments. However, little has been reported on microbial community structures related to ...halophytes, or on comparisons of their compositions among halophytic plant species. Here, we studied the diversity and community structure of both rhizosphere and root endosphere bacteria in two halophytic plants:
and
. We sampled the rhizosphere, the root endosphere, and bulk control soil samples, and performed bacterial 16S rRNA sequencing using the Illumina MiSeq platform to characterize the bacterial community diversities in the rhizosphere and root endosphere of both halophytes. Among the
.
samples, the richness and diversity of bacteria in the rhizosphere were higher than those in the root endosphere but were lower than those of the bulk soil. In contrast for
.
, the bulk soil, the rhizosphere, and the root endosphere all had similar bacterial richness and diversity. The number of unique operational taxonomic units within the root endosphere, the rhizosphere, and the bulk soil were 181, 366, and 924 in
.
and 126, 416, and 596 in
.
, respectively, implying habitat-specific patterns for each halophyte. In total, 35 phyla and 566 genera were identified. The dominant phyla across all samples were
and
.
was extremely abundant in the root endosphere from
.
. Beneficial bacterial genera were enriched in the root endosphere and rhizosphere in both halophytes.
,
, and
were highly abundant in
.
, whereas
and
were highly abundant in
.
A principal coordinate analysis demonstrated significant differences in the microbiota composition associated with the plant species and type of sample. These results strongly indicate that there are clear differences in bacterial community structure and diversity between
.
and
.
. This is the first report to characterize the root microbiome of
.
, and to compare the diversity and community structure of rhizosphere and root endosphere bacteria between
.
and
.
.
Inertial measurement unit (IMU)-based gait analysis systems have become popular in clinical environments because of their low cost and quantitative measurement capability. When a shank is selected as ...the IMU mounting position, an inverted pendulum model (IPM) can accurately estimate its spatial gait parameters. However, the stride-by-stride estimation of gait parameters using one IMU on each shank and the IPMs has not been validated. This study validated a spatial gait parameter estimation method using a shank-based IMU system. Spatial parameters were estimated via the double integration of the linear acceleration transformed by the IMU orientation information. To reduce the integral drift error, an IPM, applied with a linear error model, was introduced at the mid-stance to estimate the update velocity. the gait data of 16 healthy participants that walked normally and slowly were used. The results were validated by comparison with those extracted from an optical motion-capture system; the results showed strong correlation (Formula: see text) and good agreement with the gait metrics (stride length, stride velocity, and shank vertical displacement). In addition, the biases of the stride length and stride velocity extracted using the motion capture system were smaller in the IPM than those in the previous method using the zero-velocity-update. The error variabilities of the gait metrics were smaller in the IPM than those in the previous method. These results indicated that the reconstructed shank trajectory achieved a greater accuracy and precision than that of previous methods. This was attributed to the IPM, which demonstrates that shank-based IMU systems with IPMs can accurately reflect many spatial gait parameters including stride velocity.
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This study investigated endophytic nitrogen-fixing bacteria isolated from two species of yam (water yam,
Dioscorea alata
L.; lesser yam,
Dioscorea esculenta
L.) grown in nutrient-poor alkaline soil ...conditions on Miyako Island, Okinawa, Japan. Two bacterial strains of the genus
Rhizobium
, S-93
T
and S-62, were isolated. The phylogenetic tree, based on the almost-complete 16S rRNA gene sequences (1476 bp for each strain), placed them in a distinct clade, with
Rhizobium miluonense
CCBAU 41251
T
,
Rhizobium hainanense
I66
T
,
Rhizobium multihospitium
HAMBI 2975
T
,
Rhizobium freirei
PRF 81
T
and
Rhizobium tropici
CIAT 899
T
being their closest species. Their bacterial fatty acid profile, with major components of C
19 : 0
cyclo
ω
8
c
and summed feature 8, as well as other phenotypic characteristics and DNA G+C content (59.65 mol%) indicated that the novel strains belong to the genus
Rhizobium
. Pairwise average nucleotide identity analyses separated the novel strains from their most closely related species with similarity values of 90.5, 88.9, 88.5, 84.5 and 84.4 % for
R. multihospitium
HAMBI 2975
T
,
R. tropici
CIAT 899
T
,
R. hainanense
CCBAU 57015
T
,
R. miluonense
HAMBI 2971
T
and
R. freirei
PRF 81
T
, respectively; digital DNA–DNA hybridization values were in the range of 26–42 %. Considering the phenotypic characteristics as well as the genomic data, it is suggested that strains S-93
T
and S-62 represent a new species, for which the name
Rhizobium dioscoreae
is proposed. The type strain is S-93
T
(=NRIC 0988
T
=NBRC 114257
T
=DSM 110498
T
).
The addition effects of polymeric materials on natural environments have been mainly evaluated in terms of the relationships between culturable polymer-degrading microorganisms and/or their secreted ...enzymes and target materials. In this study, we applied metagenome analysis to better understand the change in unculturable microorganismal biodiversity in the four different river samples by using poly (3-hydroxybutyrate) P(3HB), a well-studied biodegradable polymer. An inverse relationship between the number of microorganisms and the weight of P(3HB) was observed for all the river samples, while no changes were observed for nondegradable polyethylene. Based on statistical analysis (Chao1 index), the microbial consortia exhibited reduced diversity and tended to converge to similar microbial communities among three of the river samples. This suggests a tight relationship between the biodegradation of P(3HB) and bacterial consortium structure in the river environments. Interestingly, metagenomic sequences corresponding to bacteria that have already been identified as culturable P(3HB) degraders were detected, suggesting a close relationship between the unculturable community and the culturable community. The metagenomic analysis has provided us useful insights into the dynamic changes in the microbial community in the river samples and is applicable for various combinations of environments and biopolymers.
•The change in diversity of microorganisms in the river samples by using P(3 HB).•The relationship between degradation of P(3HB) and bacterial consortium.•The dynamic changes in a mode of convergence of microbial community were observed.•This effect would be caused by increase of bacteria assimilating of P(3HB) degraded.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
The unicellular alga Cyanidioschyzon merolae has a simple cellular structure; each cell has one nucleus, one mitochondrion, one chloroplast and one peroxisome. This simplicity offers unique ...advantages for investigating organellar proliferation and the cell cycle. Here, we describe CZON-cutter, an engineered clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system for simultaneous genome editing and organellar visualization. We engineered a C. merolae strain expressing a nuclear-localized Cas9-Venus nuclease for targeted editing of any locus defined by a single-guide RNA (sgRNA). We then successfully edited the algal genome and visualized the mitochondrion and peroxisome in transformants using fluorescent protein reporters with different excitation wavelengths. Fluorescent protein labeling of organelles in living transformants allows us to validate phenotypes associated with organellar proliferation and the cell cycle, even when the edited gene is essential. Combined with the exceptional biological features of C. merolae, CZON-cutter will be instrumental for investigating cellular and organellar division in a high-throughput manner. This article has an associated First Person interview with the first author of the paper.
Selective identification of men with clinically significant prostate cancer (sPC) is a pivotal issue. Development of a risk model for detecting sPC based on the prostate imaging reporting and data ...system (PI-RADS) for bi-parametric magnetic resonance imaging (bpMRI) and clinical parameters in a Japanese cohort is expected to prove beneficial. We retrospectively analyzed clinical parameters and bpMRI findings from 773 biopsy-naïve patients between January 2011 and December 2016. A risk model was established using multivariate logistic regression analysis and presented on a nomogram. Discrimination of the risk model was compared using the area under the receiver operating characteristic curve. Statistical differences between the predictive model and clinical parameters were analyzed using DeLong test. sPC was detected in 343 men (44.3%). Multivariate logistic regression analysis to predict sPC revealed age (P = 0.002), log prostate-specific antigen (P < 0.001), prostate volume (P < 0.001) and PI-RADS scores (P < 0.001) as significant contributors to the model. Area under the curve was higher for the risk model (0.862), than for age (0.646), log prostate-specific antigen (0.652), prostate volume (0.697) or imaging score (0.822). DeLong test results also showed that the novel risk model performed significantly better than those parameters (P < 0.05). This novel risk model performed significantly better compared with PI-RADS scores and other parameters alone, and is thus expected to prove beneficial in making decisions regarding biopsy on suspicion of sPC.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Since DNA information was first used in taxonomy, barcode sequences such as the internal transcribed spacer (ITS) region have greatly aided fungal identification; however, a barcode sequence alone is ...often insufficient. Thus, multi-gene- or whole-genome-based methods were developed. We previously isolated Basidiomycota yeasts classified in the Trichosporonales. Some strains were described as Cutaneotrichosporon cavernicola and C. spelunceum, whereas strain HIS471 remained unidentified. We analysed the genomes of these strains to elucidate their taxonomic relationship and genetic diversity. The long-read-based assembly resulted in chromosome-level draft genomes consisting of seven chromosomes and one mitochondrial genome. The genome of strain HIS471 has more than ten chromosome inversions or translocations compared to the type strain of C. cavernicola despite sharing identical ITS barcode sequences and displaying an average nucleotide identity (ANI) above 93%. Also, the chromosome synteny between C. cavernicola and the related species, C. spelunceum, showed significant rearrangements, whereas the ITS sequence identity exceeds 98.6% and the ANI is approximately 82%. Our results indicate that the relative evolutionary rates of barcode sequences, whole-genome nucleotide sequences, and chromosome synteny in Cutaneotrichosporon significantly differ from those in the model yeast Saccharomyces. Our results revealed that the relative evolutionary rates of nucleotide sequences and chromosome synteny are different among fungal clades, likely because different clades have diverse mutation/repair rates and distinct selection pressures on their genomic sequences and syntenic structures. Because diverse syntenic structures can be a barrier to meiotic recombination and may lead to speciation, the non-linear relationships between nucleotide and synteny diversification indicate that sequence-level distances at the barcode or whole-genome level are not sufficient for delineating species boundaries.
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ABSTRACT
First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping early-career researchers promote themselves alongside ...their papers. Naoto Tanaka is first author on ‘ CZON-cutter – a CRISPR-Cas9 system for multiplexed organelle imaging in a simple unicellular alga’, published in JCS. Naoto conducted the research described in this article while at Yamato Yoshida's lab at Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Japan. He is now a Master's student in the lab of Kakutani Tetsuji at the same institution investigating the evolution and role of epigenetic mechanisms, such as histone modifications, in photosynthetic eukaryotes.
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