Analysis Of Taxonomic Diversity Research Articles

Update to Floral Diversity at Gujarat Institute of Desert Ecology (GUIDE) Campus Along with New Distribution of Salsola Oppositifolia Desf. in Kachchh

This study explores the biodiversity dynamics within the prestigious Gujarat Institute of Desert Ecology (GUIDE) campus in Bhuj, India, over the span of eight years. Fieldwork conducted during pre-monsoon and post-monsoon periods revealed a significant increase in plant species, genera, and families compared to previous assessments. The taxonomic diversity analysis revealed 239 plant species representing 180 genera and 62 families, with trees, herbs, and shrubs contributing prominently. Fabaceae appeared as the dominant family, followed by Poaceae and Malvaceae. Comparative analysis with previous studies established changes in species composition, notably an increase in tree species and a decrease in herbs. Of particular interest is the discovery of the second distribution of Salsola oppositifolia Desf. on the campus, a plant species first recorded in India in 2022 from Great Rann of Kachchh. The study highlights the crucial role of urban green spaces in supporting biodiversity. With 239 plant species thriving within the campus's urban infrastructure, this study highlights the potential of urban forestry in promotion biodiversity conservation and ecological resilience. Future research directions include exploring the ecological roles of vegetation and development public awareness about the multi-layered benefits of plants beyond oxygen production.

Cestode diversity in shrews from islands in the Sea of Japan and the Sea of Okhotsk.

A comparative analysis of taxonomic diversity on shrew cestodes among four islands in the Sea of Japan and the Sea of Okhotsk (Sakhalin, Kunashir, Hokkaido, and Moneron) was performed. Cestode species shared among the islands were identified and their host specificity was investigated. On Sakhalin Island, 33 species of the families Hymenolepididae, Dilepididae and Mesocestoididae were recorded in four shrew species (Sorex caecutiens, S. gracillimus, S. minutissimus and S. unguiculatus). In S. caecutiens, S. gracillimus, and S. unguiculatus on Kunashir Island, 22 species of the same families were found and, on Hokkaido Island, 23 species of the families Hymenolepididae and Dilepididae were recorded. On Moneron Island, three species of cestodes were registered in S. tundrensis. The Sakhalin-Hokkaido-Kunashir complex of shrew cestodes includes eastern-Palearctic, trans-Palearctic and endemic species. High endemism (~22%) of shrew tapeworms in the Sakhalin-Kunashir-Hokkaido Islands was noted as compared to continental territories. The different numbers of cestode species in S. unguiculatus (31), S. caecutiens (29), S. gracillimus (19) and S. minutissimus (1) were found. It was concluded that the cestodes species diversity of shrews of Sakhalin-Kunashir-Hokkaido depended primarily on the history of island formation, their modern physical and geographical features, the abundance of definitive and intermediate cestodes hosts and, to a lesser extent, on the size and remoteness of the islands from the mainland and the diversity of host species.

Assessment of the in situ biomethanation potential of a deep aquifer used for natural gas storage

In response to the challenges of sustainable development and the H2 sector, it is foreseeable that H2 will be stored into geological storage, such as deep aquifers. However, CO2 evolves in deep aquifers because it may be naturally present there; it may also be a constituent of the stored gas mix, or could even be voluntarily stored in the context of the fight against global warming. Autochthonous microorganisms can consume them as sources of energy and carbon (methanogens, (homo)-acetogens and sulfate-reducers). This was already demonstrated in a previous experiment (Haddad 2022) and under operating conditions (Lobodice, Czech Republic ; Smigan 1990). Understanding these mechanisms and quantifying them appear necessary to assess the modifications generated by this type of microorganisms on the properties of the gas. The methanogenesis reaction (CO2 gas + 4H2 gas → CH4 gas + 2H2O liquid) induces a lowering of pressure, since 5 gas molecules are transformed into a single gas molecule: CH4 (water being condensed at subsurface conditions). In situ biomethanation technique could represent a potential on several scales larger than conventional catalytic or biological methanation reactors, due to the very large reservoir volumes involved. Biomethanation in geological reservoirs would enable us to reduce our consumption of fossil fuels, so as not to emit more CO2, while meeting the growing energy needs of a region and ensuring its independence from hydrocarbon-producing countries. A deep aquifer already used as UGS was selected for this study. Formation waters from 17 control wells in this aquifer (Fig. 1) were sampled to assess the potential activity of indigenous methanogenic populations, as well as sulfate-reducers. Despite relatively low sulfate concentrations for a deep aquifer (0.025-1.35 mM), sulfate reducers were found at all sites targeting and quantifying the dsrB gene, which is characteristic of this metabolic group (between 1.8∙101 ±2.0x100 and 1.3∙104 ±2.0∙103 dsrB gene copy numbers.mL-1). In contrast, methanogenic archaea based on the mcrA gene quantification were detected at only 10 of the 17 sites (up to 4.3∙102 ±8.3∙101 mcrA gene copy numbers.mL-1). The choice was made to focus the rest of the study on 7 of these 10 sites. The potential for methanogenesis was assessed on cultural tests with formation water alone or supplemented with calcite (CaCO3), a mineral present in the formation. Results indicate that initial times and controls are controlled by the sulfate variable, since the latter was not consumed by sulfate-reducers. Biotic trials in the presence of calcite and H2/CO2 (abiotic controls and final times) are logically characterized by higher concentrations of calcite, bicarbonate and calcium, but this is not the case for trials in the presence of H2 alone. We therefore deduce that methanogenesis took place mainly via gaseous CO2, but that without the latter, calcite was a source of carbon for lithoautotrophs. Cultures incubated with H2 as the sole gas phase have the highest methane concentrations, logically associated with the lowest sulfate concentrations (consumed by sulfate-reducers), the lowest Eh (probably due to the presence of sulfides) and more alkaline pH values up to 10 (which may have led to precipitation of carbonate and calcium ions). All the sites studied showed sulfate consumption and methane production. Analysis of taxonomic diversity (MiSeq; 16S rRNA gene V4-V5) showed the dominance of three genera of sulfate-reducers with Thermodesulfovibrio-Desulfovibrio-Desulfotomaculum and methanogenic populations belonging to the Methanobacterium genus. These initial results show a strong potential of in situ biomethanation for the deep aquifer studied. All these experiments were carried out at near-atmospheric pressure, and the results still need to be confirmed and refined in the laboratory under conditions that simulate real-life conditions as closely as possible (rock, pressure, nature of gases).

Avian Taxonomic and Functional Diversity in Contrasting Habitats: A Comparative Study of Urban and Remote Forests in Arusha, Tanzania

Urbanisation globally transforms landscapes, impacting biodiversity significantly. In Arusha, Tanzania, rapid urban expansion accentuates the interplay between urbanisation and avian biodiversity. This study investigates urbanisation's influence on avian communities in two contrasting forested habitats: the urban "Themi River Forest" and the remote "Lake Duluti Forest." We explore taxonomic and functional avian diversity, elucidating underlying mechanisms. Taxonomic diversity analysis reveals "Lake Duluti Forest" with slightly higher species richness and "Themi River Forest" with a more even species distribution, reflecting urbanisation's influence. This aligns with global trends indicating reduced urban species richness due to habitat fragmentation. The urban forest, however, demonstrates avian adaptability to urbanised landscapes. Functional diversity analysis uncovers "Lake Duluti Forest" with greater functional richness, indicating a wider array of ecological roles. In contrast, "Themi River Forest" maintains comparable functional evenness, suggesting ecological balance despite urbanisation. Both forests exhibit distinct ecological niches, highlighting avian community flexibility. These findings hold significance for avian conservation and urban planning in Arusha and similar urbanising regions. Higher taxonomic diversity in remote forests underscores conservation importance. The urban forest showcases avian adaptability, emphasising green spaces in urban planning. Long-term conservation should protect both urban and remote forests, integrating strategies for avian habitat preservation and connectivity. This study advances understanding of urbanisation, forest type, and avian biodiversity's intricate relationship, offering insights for effective conservation in evolving urban landscapes

EasyAmplicon: An easy-to-use, open-source, reproducible, and community-based pipeline for amplicon data analysis in microbiome research.

It is difficult for beginners to learn and use amplicon analysis software because there are so many software tools to choose from, and all of them need multiple steps of operation. Herein, we provide a cross-platform, open-source, and community-supported analysis pipeline EasyAmplicon. EasyAmplicon has most of the modules needed for an amplicon analysis, including data quality control, merging of paired-end reads, dereplication, clustering or denoising, chimera detection, generation of feature tables, taxonomic diversity analysis, compositional analysis, biomarker discovery, and publication-quality visualization. EasyAmplicon includes more than 30 cross-platform modules and R packages commonly used in the field. All steps of the pipeline are integrated into RStudio, which reduces learning costs, keeps the flexibility of the analysis process, and facilitates personalized analysis. The pipeline is maintained and updated by the authors and editors of WeChat official account "Meta-genome."Our team will regularly release the latest tutorials both in Chinese and English, read the feedback from users, and provide help to them in the WeChat account and GitHub. The pipeline can be deployed on various platforms, and the installation time is less than half an hour. On an ordinary laptop, the whole analysis process for dozens of samples can be completed within 3 h. The pipeline is available at GitHub (https://github.com/YongxinLiu/EasyAmplicon) and Gitee (https://gitee.com/YongxinLiu/EasyAmplicon).

Diagnostic and prognostic potential of the resident non-small cell lung cancer microbiome.

The data of a comprehensive comparative study of the taxonomic composition of the resident microbiome of tumors from 26 patients with non-small cell lung cancer are presented. Analysis of taxonomic diversity revealed 10 types, 280 genera and 788 species of microorganisms. The analysis of the relative content and prognostic significance was carried out for 62 dominant genera. Differences in the relative abundance of bacteria of the genera Acinetobacter, Halomonas, and Chryseobacterium between tumor and conditionally normal lung tissue were found, but their diagnostic potential was not confirmed. The correlation analysis did not reveal any relationship between the content of various genera of bacteria and the histological type of the tumor, its localization, and the age of the patients. Differences were found in the content of the studied bacteria depending on the stage of the disease, the presence of regional metastases and tumor differentiation. The prognostic significance of bacteria of the genera Variovorax and Pseudoclavibacter in non-small cell lung cancer was established. The results obtained can be used in the development of new effective methods for the diagnosis and prognosis of non-small cell lung cancer.

Microvertebrate fauna from Gadoufaoua (Niger, Aptian, Early Cretaceous)

In the palaeogeographical context of the opening of the South Atlantic Ocean at the end of the Early Cretaceous, we document here the first microvertebrate fauna recorded from the Aptian deposits of Gadoufaoua, Niger. A systematic study of the fauna has resulted in a significant expansion of the existing faunal list and increase our knowledge of the palaeobiodiversity of the Gadoufaoua fossil site. Some taxa were previously recorded (lungfishes, crocodilians, chelonians, etc.), but several new taxa are described here for the first time, including the first occurrence of a stem-boreosphenidan mammal in Africa for this time-interval. In addition, chondrichthyans, pterosaurs and lissamphibians are documented. The analysis of taxonomic diversity and preservation of the fossils confirms a floodplain depositional environment (more precisely channel-type), in a higher velocity flow regime than previously thought based on studies of the macrofauna. To confirm the depositional environment inferred by the state of preservation of the fossils, a preliminary comparison with the fauna of similar age from the Santana Formation (Brazil) has been undertaken. The hypothesis of a communication between Africa and South America during the Aptian, as had already been demonstrated based on studies of the macrofauna, is strengthened.

Modelling Species Richness and Functional Diversity in Tropical Dry Forests Using Multispectral Remotely Sensed and Topographic Data

Efforts to assess and understand changes in plant diversity and ecosystem functioning focus on the analysis of taxonomic diversity. However, the resilience of ecosystems depends not only on species richness but also on the functions (responses and effects) of species within communities and ecosystems. Therefore, a functional approach is required to estimate functional diversity through functional traits and to model its changes in space and time. This study aims to: (i) assess the accuracy of estimates of species richness and tree functional richness obtained from field data and Sentinel-2 imagery in tropical dry forests of the Yucatan Peninsula; (ii) map and analyze the relationships between these two variables. We calculated species richness and functional richness (from six functional traits) of trees from 87 plots of the National Forest Inventory in a semi-deciduous tropical forest and 107 in a semi-evergreen tropical forest. Species richness and functional richness were mapped using reflectance values, vegetation indices, and texture measurements from Sentinel-2 imagery as explanatory variables. Validation of the models to map these two variables yielded a coefficient of determination (R2) of 0.43 and 0.50, and a mean squared relative error of 25.4% and 48.8%, for tree species richness and functional richness, respectively. For both response variables, the most important explanatory variables were Sentinel-2 texture measurements and spectral bands. Tree species richness and functional richness were positively correlated in both forest types. Bivariate maps showed that 44.9% and 26.5% of the forests studied had high species richness and functional richness values. Our findings highlight the importance of integrating field data and remotely sensed variables for estimating tree species richness and functional richness. In addition, the combination of species richness and functional richness maps presented here is potentially valuable for planning, conservation, and restoration strategies by identifying areas that maximize ecosystem service provisioning, carbon storage, and biodiversity conservation.

Gut microbiome changes in anti-N-methyl-D-aspartate receptor encephalitis patients

BackgroundAnti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is a type of autoimmune encephalitis. The underlying mechanism(s) remain largely unknown. Recent evidence has indicated that the gut microbiome may be involved in neurological immune diseases via the "gut-brain axis". This study aimed to explore the possible relationship between anti-NMDAR encephalitis and the gut microbiome.MethodsFecal specimens were collected from 10 patients with anti-NMDAR encephalitis and 10 healthy volunteers. The microbiome analysis was based on Illumina sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. The alpha, beta, and taxonomic diversity analyses were mainly based on the QIIME2 pipeline.ResultsThere were no statistical differences in epidemiology, medication, and clinical characteristics (except for those related to anti-NMDAR encephalitis) between the two groups. ASV analysis showed that Prevotella was significantly increased, while Bacteroides was reduced in the gut microbiota of the patients, compared with the controls. Alpha diversity results showed a decrease in diversity in the patients compared with the healthy controls, analyzed by the Shannon diversity, Simpson diversity, and Pielou_E uniformity based on the Kruskal–Wallis test (P = 0.0342, 0.0040, and 0.0002, respectively). Beta diversity analysis showed that the abundance and composition of the gut microbiota was significantly different between the two groups, analyzed by weighted and unweighted UniFrac distance (P = 0.005 and 0.001, respectively).ConclusionsThe abundance and evenness of bacterial distribution were significantly lower and jeopardized in patients with anti-NMDAR encephalitis than in healthy controls. Thus, our findings suggest that gut microbiome composition changes might be associated with the anti-NMDAR encephalitis. It could be a causal agent, or a consequence.

Metagenomics Bioinformatic Pipeline.

Microbial communities' taxonomic and functional diversity has been broadly studied since sequencing technologies enabled faster and cheaper data obtainment. Nevertheless, the programming skills needed and the amount of software available may be overwhelming to someone trying to analyze these data. Here, we present a comprehensive and straightforward pipeline that takes shotgun metagenomics data through the needed steps to obtain valuable results. The raw data goes through a quality control process, metagenomic assembly, binning (the obtention of single genomes from a metagenome), taxonomic assignment, and taxonomic diversity analysis and visualization.

Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake.

Freshwater lakes present an ecological border between humans and a variety of host organisms. The present study was designed to evaluate the microbiota composition and distribution in Dal Lake at Srinagar, India. The non-chimeric sequence reads were classified taxonomically into 49 phyla, 114 classes, 185 orders, 244 families and 384 genera. Proteobacteria was found to be the most abundant bacterial phylum in all the four samples. The highest number of observed species was found to be 3097 in sample taken from least populated area during summer (LPS) whereas the summer sample from highly populated area (HPS) was found most diverse among all as indicated by taxonomic diversity analysis. The QIIME output files were used for PICRUSt analysis to assign functional attributes. The samples exhibited a significant difference in their microbial community composition and structure. Comparative analysis of functional pathways indicated that the anthropogenic activities in populated areas and higher summer temperature, both decrease functional potential of the Lake microbiota. This is probably the first study to demonstrate the comparative taxonomic diversity and functional composition of an urban freshwater lake amid its highly populated and least populated areas during two extreme seasons (winter and summer).

Utilization of species checklist data in revealing the spatial distribution of fish diversity.

Marine fish species checklists from six Chinese coastal waters were combined for the analysis of taxonomic diversity. The Genus-Family index (G-F index) ranged between 0.39 and 0.84, which generally indicated a decreasing trend with increasing latitude, with the exception of the southernmost area. Average taxonomic distinctness showed a slight increasing trend from northern to central study areas, but whether the taxonomic distinctness indices represent a latitudinal gradient of biodiversity requires further study. The multivariate analysis revealed a distinct latitudinal variation in fish assemblages. These results indicate that species checklist data are helpful in understanding the diversity distribution of fish species in the coastal zone. The potential of a species inventory should be exploited to fully understand biodiversity.

Diversity of Polyketide Synthases and Nonribosomal Peptide Synthetases Revealed Through Metagenomic Analysis of a Deep Oligotrophic Cave.

Caves are considered to be extreme and challenging environments. It is believed that the ability of microorganisms to produce secondary metabolites enhances their survivability and adaptiveness in the energy-starved cave environment. Unfortunately, information on the genetic potential for the production of secondary metabolites, such as polyketides and nonribosomal peptides, is limited. In the present study, we aimed to identify and characterize genes responsible for the production of secondary metabolites in the microbial community of one of the deepest caves in the world, Krubera-Voronja Cave (43.4184 N 40.3083 E, Western Caucasus). The analysed sample materials included sediments, drinkable water from underground camps, soil and clay from the cave walls, speleothems and coloured spots from the cave walls. The type II polyketide synthases (PKSs) ketosynthases α and β and the adenylation domains of nonribosomal peptide synthetases (NRPSs) were investigated using a metagenomic approach. Taxonomic diversity analysis showed that most PKS sequences could be attributed to Actinobacteria followed by unclassified bacteria and Acidobacteria, while the NRPS sequences were more taxonomically diverse and could be assigned to Proteobacteria, Actinobacteria, Cyanobacteria, Firmicutes, Chloroflexi, etc. Only three putative metabolites could be predicted: an angucycline group polyketide, a massetolide A-like cyclic lipopeptide and a surfactin-like lipopeptide. The absolute majority of PKS and NRPS sequences showed low similarity with the sequences of the reference biosynthetic pathways, suggesting that these sequences could be involved in the production of novel secondary metabolites.

Analysis of Oribatid Fauna of the East European Tundra with First Reported Data of Subpolar Urals

This study presents data on the oribatid mite fauna of the Subpolar Urals for the first time. Observations were made in the Lembekoyu River valley and 35 species of oribatid mites from 24 genera and 21 families were found. The analysis of taxonomic diversity and distribution of East European tundra oribatid mite species is presented based on available literature and the author’s own research findings. The taxonomic list includes 163 species from 81 genera and 45 families. Ceratozetidae (15 species), Crotoniidae (14 species), Oppiidae (12 species), Suctobelbidae (12 species), Damaeidae (9 species), Brachychthoniidae (8 species), Phthiracaridae (5 species), Humerobatidae (5 species), Achipteriidae (5 species), Punctoribatidae (5 species), and Galumnidae (5 species) are the leading families, comprising more than 58% of all species. The zoogeographical structure of the fauna is dominated by widely distributed Holarctic, cosmopolitan, and semi-cosmopolitan species. The share of Palaearctic species is 23%. The specificity of the fauna of East European tundra manifests itself in the small group of Arctic species, both in the mainland tundra and on the Arctic islands. A complex of arctic-boreal species, widely distributed in the Eurasian sector of the Arctic, is distinguished.

Изменение таксономического разнообразия мезонаселения почв в диапазоне экологических условий северного макросклона хребта Хамар-Дабан

Landscape-ecological analysis of taxonomic diversity and structure of soil invertebrates’ community in the geosystems of the Hamar-Daban Region was carried out on the main levels: local (biogeocenotic), topological (facies) and regional. The paper considers regularities of transformation of communities’ structure in landscape-zonal range under the influence of natural conditions: phytocenotic (peculiarities of vegetation), edaphical and climatic (hydrothermal regime of the soil) and anthropogenic factors. On the models groups: Сarabidae, Staphylinidae, Elateridae, Formicidae altitudinal changes of community' structure have been traced; in all landscape-high-rise complexes (in species composition and abundance of species) was revealed forest preference. The main trend of changes in taxonomic diversity of invertebrate’s communities is a decrease in the species number in the gradient of an increase of climate aridity, and strengthening of the hypothermal character and anthropogenic pressure. Peculiarities of structures invertebrate’s communities and their changes due to the climate change and anthropogenic impacts can serve as one of diagnostic criteria of soil conditions and can be used for estimation of landscapes’ transformation and monitoring.

Microbial Community of Umkhei Thermal Lake (Baikal Rift Zone) in the Groundwater Discharge Zone

The diversity and functional activity of the microbial community of the bottom sediments and water of the thermal alkaline Umkhei Lake (Baikal Rift Zone), which was formed as a result of groundwater discharge, has been studied. The lake water is shown to be thermal hydrocarbonate–sulphate–sodium water of the Kuldur type. Lake sediments are characterized by higher temperatures and greater saturation with microelements. A comparative analysis of the species abundance of the microbial community of water and bottom sediments shows high indices of diversity in all layers of sediments, while the diversity in water is low. An analysis of taxonomic diversity reveals the predominance of the members of Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Chloroflexi phyla in the community of water and bottom sediments. The presence of bacteria with various metabolic pathways of substance and energy transformation in both production and destruction processes is determined. The sequences belonging to the genus Hydrogenophaga (class β-Proteobacteria, phylum Proteobacteria), which is an indicator of the deep geochemical processes of hydrogen production, are found in the bottom layers of sediments. The rates of microbial processes of photosynthesis, dark assimilation of CO2, sulfate reduction, and methanogenesis are determined to characterize the functional activity. The main part of the organic-matter production in water is found to be formed as a result of the activity of chemolithoautotrophic prokaryotes. In the microbial community, the producers synthesize organic matter using volcanogenic carbon dioxide enriched in the heavy isotope (δ13C). An analysis of the rates of terminal processes indicates that sulfate reduction is the main process.

Soil microbiome in chronosequence of spoil heaps of Kursk Magnetic Anomaly

The physicochemical parameters, vegetation and biodiversity of microbiomes inhabiting 10-, 35- and 50-year-old embryonic soils (technozems) formed in the mining areas of the Kursk Magnetic Anomaly (Russia) were analyzed in the current study. Analysis of taxonomic diversity was carried out by 454-pyrosequencing of the V4 variable region of the 16S rRNA gene. All points of the chronosequence were characterized by microbiomes reliably differing in taxonomic composition. The older the dump, the higher the proportion of bacteria from the phyla Actinobacteria (mostly representatives of the Solirubrobacteriaceae family), Chloroflexi and Acidobacteria in the community. In 10-year-old dumps, bacteria from the phyla Proteobacteria, Gemmatimonadetes and Bacteroides prevailed. The most pronounced changes in the community structure at the early and middle stages of microbiological succession were demonstrated by bacteria from the genus Delftia, which may indicate their active role in the processes of soil formation in this ecosystem.

Hidden diversity of micro-eukaryotes in Lake Baikal: a metagenomic approach

We have studied the diversity and composition of communities of micro-eukaryotes from two localities: area under anthropogenic impact near the town of Baikalsk and reference area, Irinda Bay, based on high-throughput ITS2 rDNA region sequencing. High taxonomic diversity of micro-eukaryotes has been revealed in both localities studied. However, micro-eukaryotic community from the area under anthropogenic impact is depressed, compared to reference area. Analysis of taxonomic diversity has revealed that community from the area under anthropogenic impact has a trend towards a decrease in diversity. Among the detected taxa, detected Alveolata, Stramenopiles and Fungi prevailed. Sorensen index of OTUs was 65%, which indicates the similarity of communities studied by taxonomic composition. The spectrum of Alveolata and Stramenopiles taxa identified in the area under the anthropogenic impact and the reference area was similar. The main differences were revealed in spectrum of Fungi taxa.

A New Phoronid Species, Phoronis savinkini sp. n., from the South China Sea and an Analysis of the Taxonomic Diversity of Phoronida

Phoronida is a phylum of marine invertebrates with a worldwide distribution. Currently, there are 14 species of phoronids in the world fauna, but this number may increase, based on the latest research. In the present study, the morphology and microanatomy of a new phoronid species, Phoronis savinkini sp. n., from the Gulf of Tonkin in the South China Sea are studied. The new phoronid species forms highly dense populations on rocky ground covered with soft sediment at a depth of 2 m. Since the epidermal collar at the base of the tentacles is absent, we refer this species to the genus Phoronis. The lophophore is a one-coil spiral in shape. There are 154 (160) tentacles. Special reproductive glands in the lophophoral cavity are absent. Longitudinal muscle bundles are of the bushy type. The maximum number of bundles is 50. Each metanephridium has a strongly curved excretory canal and two funnels: anal (small) and oral (large). There are two giant nerves of 2–5 μm in diameter. A comparative analysis of the morphological characters used in phoronid taxonomy shows that the morphology of the new phoronid species from the South China Sea seems to be the most similar to that of Phoronis hippocrepia Wright 1856, which has two morphs, one burrowing in hard ground and the other living in soft substrates. However, there are significant morphological differences between the two species: a fundamentally different type of lophophore organization, which is the main taxonomic character in phoronids, a different type of organization of excretory organs (including the structure of the nephridial funnels), and the absence of reproductive glands in the crown of tentacles in the new species. The cladistics analysis of phoronid taxonomic diversity shows that the ecological division of phoronids into two groups (burrowing and living in soft substrates) is meaningful taxonomically as well. Burrowing and digging phoronids might have diverged long ago. The muscle type and the number of branches of the nephridial canal can be considered as the main differences between the two groups. In the present paper, the monophyly of the genus Phoronopsis and the paraphyly of the genus Phoronis are shown. Secondary simplification of Phoronis ovalis is assumed. A separate clade that includes Phoronis pallida and Phoronis embryolabi is suggested.

Proteomic Analysis of Dacryoliths from Patients with or without Topical Rebamipide Treatment

Background: A dacryolith mainly contains organic material, but its specific protein content is unknown. We observed a unique dacryolith formation in patients with long-term use of rebamipide eye drops and tried to identify the differences in protein compositions of dacryoliths from patients with or without use of rebamipide eye drops using novel proteomic analysis. Methods: Dacryolith samples were obtained from 7 patients (4 samples were without rebamipide usage, 3 were with rebamipide usage) who underwent endo-dacryocystorhinostomy or lacrimal endoscopic surgery and were subjected to protein identification and metaproteomic analysis. Results: The proteomic analysis revealed that most core proteins of dacryoliths are involved in immune and inflammatory responses and rebamipide-related proteins participated in several biological processes, including immune response, receptor-mediated endocytosis, and negative regulation of endopeptidase activity. Metaproteomic analysis of taxonomic diversity of dacryolith proteomes suggested less involvement of bacterial infections in dacryoliths from patients with long-term use of rebamipide. Conclusion: This is the first report to clinically detect the different features of dacryoliths related with long-term use of rebamipide eye drops with proteomic analysis. It is possible that lacrimal protein alteration may be accelerated by topical rebamipide treatment with less bacterial infection involvement, but this requires further study. Long-term rebamipide eye drop use may be restricted in patients with nasolacrimal duct obstruction.