Non-metric Multidimensional Scaling Analysis Research Articles

Soil Moisture and Litter Coverage Drive the Altitude Gradient Pattern of Soil Arthropods in a Low-Elevation Mountain

This study sought to investigate the vertical distribution pattern of the soil faunal community in a low-altitude mountain area. On 8 July 2022, a low hill was selected as the study area, and soil arthropods were collected through traps. The leaf litter, vegetation type, and distribution quantity of each sampling site were investigated while the soil faunae were collected. In addition, the soil’s physical and chemical parameters were measured. The results of a one-way ANOVA showed that there were significant differences (p < 0.05) in the soil properties, leaf litter, and plant quantities at different altitudes within the research area. A total of 1086 soil arthropods, belonging to five classes and ten orders, were collected during the study period. The dominant species of soil arthropods at different altitudes were significantly different. The dominant species in low-altitude areas were Armadillidium sp. and Aethus nigritus. However, Eupolyphaga sinensis and Philodromidae were the dominant species in high-altitude areas. The results of a non-metric multidimensional scaling (NMDS) analysis showed that the soil faunae at different altitudes were clustered into two communities: a high-altitude community and a low-altitude community. With the increase in altitude, the species richness of the soil arthropods gradually decreased, and their abundance showed a decreasing trend. A redundancy analysis (RDA) of the soil arthropods and environmental factors showed that soil moisture (p < 0.01), pH (p < 0.01) and defoliation (p < 0.05) had significant effects on the distribution of the soil fauna. The results of a Pearson correlation analysis indicated that different environmental factors had interactive effects on the distribution of the soil arthropods. The quantity and species richness of the soil arthropods in different sample lines were tested using a variance analysis. The results showed that there were significantly smaller quantities of soil arthropods in the sampling line closer to the trekking ladder. This indicates that human tourism, namely mountaineering activities, had a direct impact on the soil fauna. This study can provide a reference for and data support in the development of biodiversity conservation measures for forest parks in low mountain areas.

Validation of gavage sampling as tool for longitudinal sampling of microbiota of the mouse gastric lumen

BackgroundFecal samples are commonly used for longitudinal studies of the gut lumen microbiome to track the course of response to infection or drug treatment, but no comparable method has been evaluated for longitudinal analysis of the gastric lumen microbiome in mice. Herein, a buffer flush of the stomach with a flexible gavage needle was used to collect gastric contents at one or several time points without harming the mouse. These samples were compared to samples collected by sacrifice and dissection of the mouse stomach. Microbiota from these samples were sequenced and evaluated in two ways: the composition of samples as measured by beta diversity and the richness of samples as measured by alpha diversity. Additionally, the effect of multiple sampling every two days on these metrics were studied. DNA was extracted from each of these samples and Illumina 16S rRNA gene sequencing was performed. ResultsFirst, taxonomic richness of gavage and dissection samples was compared. A greater number of taxa was detected in gavage samples than in dissection samples. Second, taxonomic richness was analyzed over time. No significant difference in taxonomic richness was observed with repeated gavage flushes. Third, a comparison was made of the taxonomic composition of samples collected by gavage versus dissection followed by a comparison of samples collected over multiple samplings. Nonmetric multidimensional scaling analysis revealed no clear differences between collection by gavage flushing or dissection. Using weighted Unifrac and Aitchison taxonomic distances between gavage and dissection samples were not significantly different from distances between gavage samples themselves, and no significant difference was found in the taxonomic composition of mice which were sampled repeatedly. Finally, relative abundances of specific identified taxa were compared, and eleven taxa were found to differ in frequency between collection methods. Using the more stringent Analysis of Composition of Microbiomes (ANCOM), seven was found to differ. Similarly, no significant differences were uncovered using these analyses over multiple samples by gastric flush. ConclusionIn summary, the consistency of the microbiota collected by gastric flushing recommends its use for microbiome analysis of gastric fluid similar to the use of fecal sampling to study the gut lumen microbiome.

DNA of Music: Identifying Relationships among Different Versions of the Composition Sadhukarn from Thailand, Laos, and Cambodia Using Multivariate Statistics

Sadhukarn, a sacred music composition performed ritually to salute and invite divine powers to open a ceremony or feast, is played in Thailand, Cambodia, and Laos. Different countries have unique versions, arranged based on musicians’ skills and en vogue styles. This study presents the results of multivariate statistical analyses of 26 different versions of Sadhukarn main melodies using non-metric multidimensional scaling (NMDS) and cluster analysis. The objective was to identify the optimal number of parameters for identifying the origin and relationships among Sadhukarn versions, including rhyme structures, pillar tone, rhythmic and melodic patterns, intervals, pitches, and combinations of these parameters. The data were analyzed using both full and normalized datasets (32 phrases) to avoid biases due to differences in phrases among versions. Overall, the combination of six parameters is the best approach for data analysis in both full and normalized datasets. The analysis of the ‘full version’ shows the separation of Sadhukarn versions from different countries of origin, while the analysis of the ‘normalized version’ reveals the rhyme structure, rhythmic structure, and pitch as crucial parameters for identifying Sadhukarn versions. We conclude that multivariate statistics are powerful tools for identifying relationships among different versions of Sadhukarn compositions from Thailand, Laos, and Cambodia and within the same countries of origin.

Species richness of living foraminifera in Sepetiba Bay (SE Brazil): a species checklist

AbstractThere is a gap in knowledge about the biodiversity of living foraminifera (protozoa) in Brazil, particularly in coastal environments. In Sepetiba Bay (SE Brazil), a coastal system highly impacted by anthropogenic activities, several previous studies have been carried out on foraminifera based on total (living + dead) assemblages and sub-fossil records. Thus, this study intends to analyze for the first time the species richness of living foraminifera (stained with Rose Bengal) in Sepetiba Bay. Based on the morphological characteristics, 214 living species were identified in 50 samples collected in Sepetiba Bay in May 2022. The number of living specimens was counted as 6548. Living foraminifera density was < 252 specimens per gram of sediment and the species richness (S) ranged from 15 to 61 (mean 16.9 ± 15.5) in the analyzed stations. The main taxonomic classes found were Globothalamea and Tubothalamea. The main Globothalamea taxa belonged to the genus Ammonia, with Ammonia tepida, Ammonia buzasi, and Ammonia rolshauseni standing out, as well as the Bolivina, Buliminella, and Elphidium, represented mainly by Bolivina striatula, Buliminella elegantissima, and Elphidium excavatum. A non-Metric Multidimensional Scaling (nMDS) and cluster analysis based on a presence-absence matrix and Bray–Curtis similarity index allowed the identification of two main groups of stations: 1. Located in the innermost areas of Sepetiba Bay and surrounding the mainland and Marambaia Barrier Island, at shallower depths, with lower diversity; 2. an outermost group of stations with higher diversity in areas with greater oceanic influence. Compared with previous studies, the results of this work suggest an enlargement of the “innermost” zone with less diversity towards the oceanic region of Sepetiba Bay. This work shows that even using a matrix of presence/absence of living foraminifera and species richness, it is possible to distinguish environments in coastal systems. Data based on the living foraminifera is needed to understand current biodiversity to better characterize coastal environments and carry out biomonitoring studies.

Loss of submerged macrophytes in shallow lakes alters bacterial and archaeal community structures, and reduces their co-occurrence networks connectivity and complexity.

Bacteria and archaea are important components in shallow lake ecosystems and are crucial for biogeochemical cycling. While the submerged macrophyte loss is widespread in shallow lakes, the effect on the bacteria and archaea in the sediment and water is not yet widely understood. In this study, 16S rRNA gene sequencing was used to explore the bacteria and archaea in samples taken from the sediment and water in the submerged macrophyte abundant (MA) and submerged macrophyte loss (ML) areas of Caohai Lake, Guizhou, China. The results showed that the dominant bacterial phyla were Proteobacteria and Chloroflexi in the sediment; the dominant phyla were Proteobacteria, Actinobacteriota, and Bacteroidota in the water. The dominant archaea in sediment and water were the same, in the order of Crenarchaeota, Thermoplasmatota, and Halobacterota. Non-metric multidimensional scaling (NMDS) analyses showed that bacterial and archaeal community structures in the water were significantly affected by the loss of submerged macrophytes, but not by significant changes in the sediment. This suggests that the loss of submerged macrophytes has a stronger effect on the bacterial and archaeal community structures in water than in sediment. Furthermore, plant biomass (PB) was the key factor significantly influencing the bacterial community structure in water, while total nitrogen (TN) was the main factor significantly influencing the archaeal community structure in water. The loss of submerged macrophytes did not significantly affect the alpha diversity of the bacterial and archaeal communities in either the sediment or water. Based on network analyses, we found that the loss of submerged macrophytes reduced the connectivity and complexity of bacterial patterns in sediment and water. For archaea, network associations were stronger for MA network than for ML network in sediment, but network complexity for archaea in water was not significantly different between the two areas. This study assesses the impacts of submerged macrophyte loss on bacteria and archaea in lakes from microbial perspective, which can help to provide further theoretical basis for microbiological research and submerged macrophytes restoration in shallow lakes.

Variation in traditional knowledge of culturally important macromycete species among three indigenous communities of Oaxaca, Mexico

BackgroundFor centuries, wild mushrooms have been a forest resource of significant cultural value in several ethnic groups worldwide. In Mexico, extensive traditional knowledge on the use of fungal resources has been developed and deeply rooted. Mexico is the second country in the world in which the most species of wild mushroom are consumed, and it is considered a pioneer in ethnomycology. Nonetheless, there are still many indigenous groups in this country that have not been studied from an ethnomycological approach. The present study aimed to record the traditional knowledge on wild mushrooms in three indigenous groups of the state of Oaxaca, Mexico, and assess the variation in this knowledge within and across the studied groups.MethodsThe data were recorded from April to October 2022 within three communities belonging to the indigenous groups Chatino, Chontal, and Chinanteco. Through 84 interviews, information related to their knowledge of wild mushrooms was obtained. The cultural significance index of wild edible mushrooms was calculated for each community. Regression analyses, analysis of variance and covariance, t test, and non-metric multidimensional scaling analysis were performed to assess the distribution of traditional knowledge in the communities.ResultsA total of 32 culturally important mushroom species were recorded for the three indigenous groups (30 edible, 2 medicinal); 23 used by Chatinos, 16 by Chontales, and 6 by Chinantecos. Only Chatinos and Chinantecos use wild mushrooms in medicine. The cultural significance of wild edible mushrooms differed among groups. Traditional knowledge about wild mushrooms declines when the level of schooling increases and age decreases, especially in the Chatino group. This knowledge distributes more homogeneously in the Chontal and Chinanteco groups. Their age determines the difference in knowledge between men and women.ConclusionDocumenting how traditional knowledge differs among ethnic groups is relevant for preserving cultural and biological diversity. Factors such as level of schooling and age can affect traditional knowledge of wild mushrooms, but the effects of these factors vary within and across communities. Conducting studies encompassing a broader range of variables is of interest for a better understanding of the human–mushroom relationship.

Effect of Application Rates of N and P Fertilizers on Soil Nematode Community Structure in Mollisols

Long-term application of chemical fertilizer poses an environmental threat to belowground ecosystems. However, the impact of nitrogen (N) or phosphorus (P) fertilizers on soil biodiversity and the conditions of soil food web remains largely unknown. Soil nematodes are the most abundant multicellular soil animals and serve as excellent bioindicators of soil. Here, we investigated soil nematode communities and food web structure in a long-term experiment with different application rates of N and P fertilizers in northeast China. The application of N and P fertilizers increased the abundance of bacterivores but suppressed the abundance of omnivores and predators. The abundance of bacterivores exhibited an increasing trend, while that of omnivores and predators showed a decreasing trend with increasing rates of N and P fertilizers. Plant parasites displayed a decreasing trend in response to N fertilizer, but not to P fertilizer. N and P fertilizers also altered nematode functional guild composition, with N fertilizer increasing the abundance of Ba1, and P fertilizer increasing the abundance of Fu2 and Ba3. Nonmetric multidimensional scaling (NMDS) analysis revealed apparent successions of nematode communities from no fertilizer soils to high rates of N or P fertilizer soils at both the genus and functional guild levels. Furthermore, N and P fertilizers resulted in different nematode communities. In terms of nematode food web indices, N fertilizer increased the enrichment index (EI) but reduced the channel index (CI) and structure index (SI), whereas P fertilizer only reduced the SI value. High rates of N and P fertilizers increased the respired carbon of bacterivores but reduced the respired carbon of predators. Mantel tests revealed significant correlations between soil properties and the community composition of both fungivores and omnivores. Among all soil properties, available phosphorus (AP) had the greatest influence on the community structure of soil nematodes. Our findings indicate that N fertilizer has a powerful effect on nematode food web structure, while P fertilizer exerts a stronger effect on soil nematode community composition.

Comparative analysis of Deinagkistrodon acutus venom from Taiwan and China utilizing chromatographic, electrophoretic, and bioinformatic approaches, along with ELISA employing a monospecific antivenom

Deinagkistrodon acutus is a medically important pitviper inhabiting mainly South China and Taiwan. The hemorrhagic effects of its envenoming are compatible to its venom, which is abundant in metalloproteases (svMPs) and C-type lectin-like proteins. In this study, we investigated geographic variations in the venom of D. acutus collected from Taiwan and four Mainland Chinese provinces: Fujian, Jiangxi, Anhui, and Hunan. The variations were assessed through high-performance liquid chromatography, non-metric multidimensional scaling analysis, gel electrophoresis, and enzyme-linked immunosorbent assay (ELISA) with a monospecific antivenom (DaMAV) generated against the Taiwanese D. acutus venom, and discussed based on venom-protein sequences in databases and literature related to D. acutus venom. Additionally, the cross-reactivity of DaMAV against Crotalus horridus and Calloselasma rhodostoma venoms was investigated. We noted differential abundances of D. acutus venom metalloproteases, C-type lectin-like proteins, and phospholipase A2, along with point mutations and selective expression of serine protease isoforms. The ELISA results revealed that the venom from Taiwan was more reactive toward Taiwanese DaMAV than the four Mainland Chinese venoms, consistent with chromatographic profile differences, whereas C. horridus venom presented moderate cross-reactivity with DaMAV. The observed immunoreactivities of these venom with DaMAV can be attributed to the high prevalence of their PIII-svMPs, which are the dominant antigens, and the conservation of PIII-svMP epitopes.

Benthic and Planktonic Microalgae Community in Probolinggo Beach

Microalgae, micro-sized plant organisms, play a crucial role in aquatic ecosystems. While many microalgae inhabit substrates or the bottom of water bodies, several types are planktonic. This study aimed to identify the types and abundance of microalgae in both sediment and water column habitats, as well as to analyse the environmental factors influencing their abundance. The research encompasses observations of water quality factors, microalgae abundance, relative abundance, diversity index, evenness index, and dominance index. Statistical analyses were using non-metric multidimensional scaling (NMDS) and Canonical Correspondence Analysis (CCA). The study was conducted in May-June 2022, with bi-weekly sampling at three points within each location for two months. Microalgae identified in the coastal area of Probolinggo belong to the Bacillariophyceae, Cyanophyceae, and Chlorophyceae classes. The highest microalgae abundance in sediment habitat was 58,472 ind/cm2, while in the water column was 4,118 ind/l. Diversity, evenness, and dominance indices in both sediment and water column habitats ranged from 1.93 to 2.61, 0.88 to 0.98, and 0.09 to 0.10, respectively. NMDS and CCA analyses indicate a graphical representation of the Bacillariophyceae class, demonstrating its prevalence across all sites.

Spatiotemporal Variation Analyses of Water Quality, Fish Ecological Guilds, and the Longitudinal Connectivity in Musim Stream

The main objectives of this study were to analyze the spatiotemporal variations of water quality, fish ecological guilds and longitudinal connectivity in the weirs of Musim Stream. Fish were collected at 44 sites during spring and fall seasons for the analysis of trophic guilds, tolerance guilds, and the ecological stream health, based on FAI model. Total 33 species were observed in the stream and the dominant species were <i>Zacco platypus</i> and <i>Squalidus qracilis majimae</i>. Mean values of BOD and COD, as an indicator of organic matter pollution, showed high in the drought spring and low in fall (post-monsoon season). Also, TP showed same pattern with the BOD and COD pattern. The hierarchical clustering, based on the fish compositions, classified as three groups (up-stream, mid-stream and the down-stream). Based on the NMDS (Non-metric Multidimensional Scaling) analysis of fish abundance, high similarity was observed between S1-S5 sites, which were consistent with the results of hierarchical cluster analysis. Fish ecological guilds in the upper stream showed a high similarity between the insectivore and sensitive species, while in the middle and lower reaches, high similarity was found between the omnivore and intermediate species. Evaluations of longitudinal connectivity, based on the structural and hydrological characteristics of the weir, indicated all disconnections by the weirs, except for S15, in the spring. Stream ecological health, based on the FAI model, was significantly (<i>p</i> < 0.05, n=37) influenced by the height of overflow (<i>Hu1</i>). Overall, our study suggests that the longitudinal connectivity, based on the weir structures, flow regime and fish swimming capacity, were blocked off by the weirs in the stream. The results provide valuable insights for securing river management strategies and served as the fundamental data for stream restoration in the future.

Comparisons of oxbow lake fish assemblages in relation to bigheaded carp establishment in the lower White River, Arkansas

BackgroundSince the late 1990s, bigheaded carps (largely silver carp [Hypophthalmichthys molitrix] but also bighead carp [H. nobilis]) have established throughout the lower Mississippi River basin. Using previously studied oxbow lakes in the lower White River basin, Arkansas, we compared current (2017, “post-carp” establishment) fish assemblages to historical (2002, “pre-carp” establishment) fish assemblages. Fish assemblages were comprehensively assessed using multiple gears, including boat electrofishing, mini-fyke nets, and experimental small-mesh gill nets.ResultsT-tests suggested that fish assemblage indices of richness, diversity, evenness, and dominance were often greater (P < 0.05) during the post-carp period as reflected by boat electrofishing and experimental gill nets. However, all indices were generally similar (P > 0.05) between the pre-carp and post-carp period with fish assemblages depicted using mini-fyke nets. Nonmetric multidimensional scaling analyses indicated that fish assemblages differed structurally between pre-carp and post-carp periods. Assemblage differences were linked to both small and large abundance changes for more than 20 species. Abundances of gizzard shad (Dorosoma cepedianum), emerald shiner (Notropis atherinoides), pugnose minnow (Opsopoeodus emiliae), crappies (Pomoxis spp.), bluegill (Lepomis macrochirus), orangespotted sunfish (L. humilis), and yellow bass (Morone mississippiensis) declined between the pre-carp and post-carp periods. Conversely, abundances of weed shiner (N. texanus), pallid shiner (Hybopsis amnis), longear sunfish (L. megalotis), buffalofishes (Ictiobus spp.), and gars (Lepisosteus spp.) generally increased during the same period.ConclusionsAlthough not possible to conclude assemblage shifts were entirely related to bigheaded carps due to the absence of an appropriate reference system where carps did not establish, the wide establishment of these carps is one of the most pervasive changes to have occurred in the lower White River ecosystem during the past two decades. Thus, it is probable to conclude that post-carp establishment observations from this study were at least, in part, attributable to bigheaded carp establishment. Impacts of further range expansions by bigheaded carps in the White River and other lower Mississippi River sub-basins are unclear, though this study suggests probable effects on native fish assemblages, underscoring the need for further research and monitoring.

Seasonal and habitat dependence of plant species, functional and phylogenetic diversity in agricultural landscapes

The biodiversity of agricultural landscapes is under significant threat, while non-agricultural habitats within these landscapes play a crucial role in biodiversity conservation. There has been limited investigation into how plant species, functional and phylogenetic diversity varies across different seasons and habitats in agricultural landscapes. Thus, we carried out a survey of the plant communities in non-agricultural habitats in China's lower Yellow River plain. We investigated the diversity features of plant functionality, phylogeny, and plant species. We compared differences in plant community structure using non-metric multidimensional scaling analysis and tested phylogenetic signal using phylogenetic methods. Our analysis of plant community and diversity characteristics revealed significant differences in plant community structure between seasons and habitats, with the season having a more significant impact. The levels of plant species, functional, and phylogenetic diversity followed a seasonal pattern, with spring seeing the highest values and autumn seeing the lowest. Woodland and hedgerow habitats had the highest levels of diversity, while field roads had the lowest. The community phylogenetic structure of non-agricultural habitats was relatively concentrated and mainly influenced by human interference and environmental filtering. These findings offer scientific support for the preservation of ecosystem services and biodiversity in agricultural landscapes.

Taking the bait: Environmental factors affecting bait retention and hook disposition in the Gulf of Maine Bottom Longline Survey

Longline fishery surveys are major contributors to groundfish species abundance estimates. Catchability is often assumed constant, but bait is lost or consumed at inconsistent rates during and across gear sets. Accounting for hook availability and gear saturation can improve abundance estimates, but these data are challenging to collect. Our objectives were to determine whether video camera systems can be used to collect these data from the Northeast Fisheries Science Center’s Gulf of Maine Bottom Longline Survey and to explore the associations between hook disposition percentages and environmental characteristics. Electronic monitoring camera systems were deployed on partner vessels during two fall and two spring seasons to capture video of gear retrieval. During post-survey review, individual hooks were recorded as one of the following hook dispositions: bait, empty hook, fish, and invertebrate. Percentages of these hook dispositions were characterized across categorical (season, day or night, and bottom substrata) and continuous (bottom temperature, bottom depth, and substrate rugosity) survey station variables. Nonmetric multidimensional scaling and logistic regression analyses revealed correlations between retained bait and low bottom temperatures, the spring season, shallow depths, rough bottom substrata, and high terrain rugosity. These characteristics were typical of shallow, inshore, and topographically variable survey strata, suggesting that catchability differs among habitat types. This information will be incorporated into catch rate models to develop standardized indices of abundance for groundfish stock assessments. This study is an example of the utility of electronic technologies to supplement on board data collection during cooperative fishery surveys.

Using morpho-anatomical characters of leaves and stems for distinguishing Bolboschoenus taxa: a case study of Serbian species

The genus Bolboschoenus has been intensively studied from the morphological, ecological and physiological aspects, however, anatomical features of stems, leaves and epidermal structures of leaves have not been investigated sufficiently yet. The main objective of this study was to compare the four Bolboschoenus species growing in Serbia at the anatomical level and to define the most important anatomical characteristics for distinguishing these species. Descriptive, nonmetric multidimensional scaling and canonical discriminant analysis of the anatomical characters of leaves, stems and epidermal structures have been conducted for these purposes. The number and position of sclerenchyma strands in the leaves, the presence of bulliform cells in the epidermis, the number of translucent cell layers under the adaxial epidermis in the midrib area of the lamina, the number of aerial cavities in leaves and stems were the most significant anatomical characters for differentiation of species. The most differentiated species was B. glaucus, while B. laticarpus occupied an intermediate position between B. maritimus and B. planiculmis, on the one hand, and B. glaucus on the other. The combination of the anatomical features of leaves and stems and the epidermal structures had a more excellent taxonomic value than these three individual groups of features individually.

The comparison of species diversity and abundance of insect natural enemies in the domesticated species of cotton using the yellow pan trap method.

India is the world's largest cotton producer and the only country that grows all four cultivated cotton species. There have been very few studies on the diversity and abundance of natural enemies of cotton insect pests in these cultivated cotton species. Therefore, the current study (2016-2018) was conducted to assess the diversity and abundance of natural enemies that cultivated cotton species harbour. Phule Dhanwantari, Suraj, Suvin, RCH-2, and DCH-32 were the five genotypes used in the study, each with a distinct genetic background. Using the adiv 2.0.1 and vegan R packages, we identified significant differences in natural enemies in terms of species diversity, richness, evenness, and abundance. Analysis of Similarity (ANOSIM) and Non-metric Multidimensional Scaling (NMDS) indicated substantial differences in the natural enemy community structure among the examined genotypes. A total of 17,279 natural enemies were collected and identified across genotypes from seven predatory families and five parasitoid families. The percentage share of these natural enemy families across genotypes and years, in descending order, is Coccinellidae (28.23%) < Tachinidae (19.23%) < Braconidae (12.68%) < Chrysopidae (11.65%) < Chalcididae (9.41%) < Aphelinidae (6.33%) < Pentatomidae (3.29%) < Ichneumonidae (2.37%) < Syrphidae (2.33%) < Vespidae (1.81%) < Asilidae (1.79%) < Geocoridae (0.89%). Coccinellidae, Tachinidae, Braconidae, Chrysopidae, Chalcididae, and Aphelinidae are the six major families that account for more than 85% of all recorded natural enemies. These six families have a higher percentage share in Phule Dhanwantary (90%) compared to the other genotypes. The conservation and better utilization of these natural enemies are crucial for the ecological and safe management of insect pests in the cotton ecosystem.

Implication of abandoned post‐quarry sites on avifauna composition for strategic landscape restoration in Ndarugu, Kiambu, Kenya

AbstractAbandoned post‐quarry sites have potentiality to be remodeled into natural‐wilderness areas, a desire especially in rapidly urbanizing and transforming landscapes. However, paucity of ecological information on post‐quarry sites limits nature‐based restoration, especially in the sub‐Saharan tropical landscape. This study investigated avifauna composition of post‐quarry sites in Ndarugu, Kenya, relative to non‐quarried sites for conservation role prioritization. Birds were censused in 166 point count stations using the fixed‐radius distance method. Land use land cover types within each point provided the variables for explaining bird occurrence. Observed bird species were classified into functional guilds, avifaunal composition assessed, and bird data subjected to multivariate analysis. In total 158 species, 128 in post‐quarry and 123 in non‐quarried sites, were recorded. Bush‐ and forest‐related species were dominant, constituting over 55% of total observed birds, in both site categories. Six wetland‐related species were detected only in quarried sampling sites. Mann–Whitney statistical tests returned a significant effect of land use category on bird species richness, abundance, and diversity, all higher in post‐quarried than in non‐quarried sites (p &lt; 0.05). Emergent natural shrubs, quarry cliffs, and cultivated farms were most influential to bird community structuring. Nonmetric multidimensional scaling and cluster analysis revealed four functional groups of birds whose species richness increased with number of post‐quarried sampling sites in a cluster. Unique physical features of post‐quarry sites and emergent vegetation types, can be partially mimicked in nature‐oriented rehabilitation planning for long‐term social and ecological benefits.

Ecological connectivity analysis based on the fish community in Jeongan Stream

This study focused on the longitudinal connectivity analysis, based on fish communities in the aspect of spatial variations of 34 sites from upstream to downstream. The Fish Assessment Index (FAI), based on ecological guilds and species composition, was applied to compare the ecological health among the sampling sites. The total number of 35 fish species, were sampled during the study period with dominant species of &lt;i&gt;Zacco platypus&lt;/i&gt; (35.4%) and &lt;i&gt;Zacco koreanus&lt;/i&gt; (11.8%). Cluster analysis showed that all sites were categorized as 4 distinct group communities (A, B, C, D). Non-metric multidimensional scaling analysis showed distinct difference between upstream (A, B) and downstream groups (C, D). Indicator Value Analysis (IndVal method), conducted to identify indicator species within each group, indicated that the species favoring upstream environments Rhynchocypris oxycephalus for the Group A and Iksookimia koreensis for the Group B. In contrast, the analysis indicated that the species with a preference for downstream habitats Pseudogobio esocinus for the Group C and Carassius auratus for the Group D. Ecological health, based on the FAI scores, showed a declining pattern toward the downstream, along with an increasing proportion of tolerant species and omnivores within the fish community. Overall these findings suggest the compositions of fish communities, as four groups, were modified by the weir structures and organic matter, nutrient pollutions.

Composition of Essential Oils from Fruits of Peucedanum longifolium and Rhizomatophora aegopodioides (Apiaceae) with Regard to Other Related Taxa—A Chemometric Approach

The aim of this work was to investigate the composition of essential oils isolated from fruits of Peucedanum longifolium, and Rhizomatophora aegopodioides (a species which was previously placed in the genus Peucedanum), as well as to compare the obtained results to those available for other previously investigated related species (including taxa which are also, according to some authors, excluded from the genus Peucedanum). Essential oils were obtained via hydrodistillation in a Clevenger-type apparatus and their composition was analyzed using GC-FID and GC-MS. To compare these data to those of previously investigated taxa, a chemometric approach was applied; the data were analyzed using multivariate statistical methods: non-metric multidimensional scaling (nMDS) and hierarchical cluster analysis. The most abundant in P. longifolium essential oil were monoterpenes (79.7%), mostly α-phellandrene (26.2%), β-phellandrene + limonene (21.0%) and myrcene (9.5%), followed by sesquiterpenes (18.3%), mostly germacrene B (9.5%). On the other hand, dominant in R. aegopodioides essential oil were non-terpenic aliphatic hydrocarbons (46.1%), mainly n-undecane (16.5%) and n-nonane (11.3%). In addition, this essential oil also contained a notable quantity of sesquiterpenes (25.1%), with (E)-sesquilavandulol being the most abundant (10.0%). The results of multivariate statistics revealed a clear separation of the essential oil composition of R. aegopodioides and P. longifolium, as well as of P. longifolium and P. officinale. The clustering of the samples of most of the taxa that do not belong to the Peucedanum in the narrow sense (sensu stricto) was also observed, which is in accordance with their recent inclusion in separate genera.

Specific gut microbiome signature predicts hepatitis B virus-related hepatocellular carcinoma patients with microvascular invasion

Background We aimed to assess differences in intestinal microflora between patients with operable hepatitis B virus-related hepatocellular carcinoma (HBV-HCC) with microvascular invasion (MVI) and those without MVI. Additionally, we investigated the potential of the microbiome as a non-invasive biomarker for patients with MVI. Methods We analyzed the preoperative gut microbiomes (GMs) of two groups, the MVI (n = 46) and non-MVI (n = 56) groups, using 16S ribosomal RNA gene sequencing data. At the operational taxonomic unit level, we employed random forest models to predict MVI risk and validated the results in independent validation cohorts [MVI group (n = 17) and non-MVI group (n = 15)]. Results β diversity analysis, utilizing weighted UniFrac distances, revealed a significant difference between the MVI and non-MVI groups, as indicated by non-metric multidimensional scaling and principal coordinate analysis. We also observed a significant correlation between the characteristic intestinal microbial communities at the genus level and their main functions. Nine optimal microbial markers were identified, with an area under the curve of 79.76% between 46 MVI and 56 non-MVI samples and 79.80% in the independent verification group. Conclusion This pioneering analysis of the GM in patients with operable HBV-HCC with and without MVI opens new avenues for treating HBV-HCC with MVI. We successfully established a diagnostic model and independently verified microbial markers for patients with MVI. As preoperative targeted biomarkers, GM holds potential as a non-invasive tool for patients with HBV-HCC with MVI.

Phenotypic Diversity and Genetic Parameters of Coffea canephora Clones

The simultaneous analysis of the maximum number of chemical elements present in plant tissues provides more comprehensive information about their chemical constitution and increases the number of characteristics for the selection process in various plant breeding programs. The objective of this study was to analyze productivity, grain yield, and concentration of chemical elements in tissues of Coffea canephora clones to study phenotypic diversity and estimate genetic parameters for use in breeding. This experiment was carried out in Manaus, Amazonas, Brazil, in randomized blocks with four replications. The concentrations of elements in various organs were quantified using total reflection X-ray fluorescence (TXRF). Genetic parameters and genetic divergence were estimated, and genotypes were clustered using the UPGMA hierarchical method and non-metric multidimensional scaling analysis. The study allowed us to differentiate the performance of the clones in terms of the absorption of essential and non-essential chemical elements for plant development and to analyze the correlation of the characteristics in the selection process. TXRF efficiently characterizes the presence and concentration of multiple elements, aiding genotype discrimination for C. canephora improvement.