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Chernozem soil is a valuable resource and contains a great diversity of microorganisms that play a global role in the process of soil formation, the species diversity of which has changed over the last five years under the influence of different agrotechnologies. For the first time, under the conditions of the Central Chernozem region, grain and fallow crop rotation, studies using the DNA-metabarcoding method were carried out to study the taxonomic structure of bacteria, fungi, cyanobacteria, and microalgae communities in the arable horizon of typical medium loamy chernozem under winter wheat cultivation. A comparative analysis of the composition of the genotypes showed significant differences in the presented level of mineral nutrition of the soil NPK (60) and NPK (100) compared with the control variant. After processing the 16S and 18S rRNA datasets, a similar trend of decreasing numbers of pro- and eukaryotic species was found from 6296 (control without MF) to 5310 with NPK (60) and to 4643 with NPK (100), respectively. The Chao1 index indicated that the expected diversity within the prokaryotic group was higher in the control without MF at 211, but decreased to 182 and 193 with NPK (60) and NPK (100) fertilizers, respectively. Analysis of the eukaryotic group revealed a 2.6- and 2.9-fold decrease in diversity by class and genus, respectively, depending on the nutritional levels in agrotechnologies, owing to the use of MF. In the prokaryotic community, Alphaproteobacteria microorganisms predominated at an amount of 14.20–14.46%, with Cyanophyceae accounting for 5.2–9.9%. The diversity of eukaryotes was smaller than the number of classes of prokaryotes; the main dominant were Zygnematophyceae 19.5–41%, Chlorophyceae occupied 10.4–15.8%. On the other hand, the doses of fertilizers used contributed to the emergence of dominant species adapted to high doses of mineral nutrients for plants. [ABSTRACT FROM AUTHOR]

Background: Invasive fungal intestinal infections are rare in pediatric patients with limited studies reported to date. Methods: Retrospective study of invasive intestinal fungal infections in pediatric patients. For fungal specification, 18S rRNA gene PCR was performed using formalin-fixed paraffin-embedded tissues. Results: A total of 19 cases from 18 patients were included (13 males, 72%) with a median age of 20 days (8 days–14 years). About 13 patients (72%) presented within 67 days of birth and 11 patients (61%) were premature and 14 patients (78%) had a significant medical history. The most common location was the jejunum/ileum (56%) followed by the right colon and terminal ileum (22%). In 10 patients, the fungal elements were seen in the mucosa with 3 extending into the submucosa, and only 3 patients showed full-thickness involvement. Tissue necrosis and angioinvasion were seen in 13 (72%) and 8 (44%) patients, respectively. Morphologically, organisms consistent with Candida spp. were seen in 17 patients and with a mucoraceous mold in 1 patient. A 18S rRNA gene sequencing performed in 18 cases identified Candida dubliniensis in 16 cases and Candida spp. in 2 cases. During the study follow-up period, 56% of the patients died. Conclusion: In our experience, most cases were due to Candida spp. and predominantly in premature infants and associated with poor outcomes. [ABSTRACT FROM AUTHOR]

Morchella spp. (true morels) are precious edible mushrooms consumed around the world, with a delicious taste, rich nutritional value, and unique healthcare effects. Various fungi and bacteria have been reported to colonize the ascocarps of Morchella, damaging their fruiting bodies and leading to serious economic losses in cultivation. The species identification of these colonizing organisms is crucial for understanding their colonization mechanisms on morels. Slime molds, which have characteristics of both "fungi" and "animals", can occasionally colonize crops and edible fungi. However, there have been no reports of dictyostelid cellular slime molds (dictyostelids) colonizing plants and fungi to date. In this study, we discovered that dictyostelids colonized the surface of one wild ascoma of Morchella in the forest of Chongqing, China, with the tissues being black and rotten. Macro- and micro-morphological observations, along with molecular phylogenetic analyses, identified the specimens investigated in this study as Dictyostelium implicatum and Morchella sp. Mel-21. The results provide new knowledge of dictyostelid colonization on organisms and contribute to the diversity of species colonizing true morels. Moreover, this is also the first report of dictyostelids distributed in Chongqing, China. This study enhances our insights into the life history and potential ecological significance of dictyostelids and updates their distribution area in China. Further research will be conducted to uncover the mechanisms behind the colonization observed in this study. [ABSTRACT FROM AUTHOR]

Summary: Vicuñas (Vicugna vicugna) are wild South American camelids (SACs) protected by law in Argentina, and information on pathogens that infect them is scarce. In this study, an adult vicuña found dead in the province of Salta was examined, and evidence of infection by Sarcocystis sp. protozoans was sought. Infection of skeletal muscles by S. aucheniae, with the production of macroscopic sarcocysts, a disease known as SAC sarcocystosis, has been described in the other three SACs - llamas, alpacas, and guanacos - but its occurrence in vicuñas has so far remained unknown. In the analyzed individual, many macroscopic cysts compatible with S. aucheniae were found upon necropsy in the muscular tissue of the neck and diaphragm. Analysis of 18 S rRNA and cytochrome c oxidase subunit 1 (cox-1) gene sequences by BLAST searches and construction of phylogenetic trees demonstrated that the etiological agent was S. aucheniae. Our results show for the first time that vicuñas act as intermediate hosts in the life cycle of this parasite. In addition, this study provides the first cox-1 sequences for S. aucheniae isolates from the four SAC species acting as intermediate hosts and suggests that this marker could be useful for genotypification of this parasite species. The impact of SAC sarcocystosis on the health, well-being, and fitness of vicuñas, and the relevance of vicuña infections in the epidemiology of S. auchaniae, remain to be elucidated. [ABSTRACT FROM AUTHOR]

Abstract In the rice agroecosystems of Southeast Asia, rice root knot nematode (Meloidogyne graminicola) significantly impairs yield, representing a major species within the ‘graminis-group’ known for its morphological similarities with other root knot nematodes (RKNs). This study delves into the variations in reproductive potential, morphology, morphometrics, and genetic diversity among thirty RKN populations in rice across three distinct agroecological zones in Jharkhand, India. Despite notable differences in reproductive potential among the populations, morphological and morphometric correlations to reproductive potential were inconclusive. However, male and juvenile morphometrics were crucial for identifying intraspecific variability. Genetic analysis utilizing five molecular markers (ITS, 18 S rRNA, D2-D3 of 28 S, COX-I, and COX-II) affirmed the populations as M. graminicola, with ITS marker revealing significant intraspecific variability. Phylogenetic analysis underscored the close relationship between M. oryzae and M. graminicola, distinct from other mitotic RKN species. Low genetic distance and nucleotide diversity, coupled with high haplotype diversity, negative Tajima’s D, and Fu’s Fs of haplotype network analysis, suggested that all M. graminicola populations are expanding. These findings highlight the urgent need for comprehensive management strategies against M. graminicola, providing valuable insights for growers, extension officials, and plant breeders to develop targeted management approaches and resistance breeding programs.

In eukaryotes, the ribosomal small subunit (40S) is composed of 18S rRNA and 33 ribosomal proteins. 18S rRNA has a special secondary structure and is an indispensable part of the translation process. Herein, a special sequence located in mammalian 18S rRNA named Poly(G)7box, which is composed of seven guanines, was found. Poly(G)7 can form a special and stable secondary structure by binding to the translation elongation factor subunit eEF1D and the ribosomal protein RPL32. Poly(G)7box was transfected into cells, and the translation efficiency of cells was inhibited. We believe that Poly(G)7box is an important translation-related functional element located on mammalian 18S rRNA, meanwhile the Poly(G)7 located on mRNA 5’ and 3’ box does not affect mRNA translation.

Objective: This study was conducted to molecularly identify and classify Cryptosporidium spp. in fecal samples (n=150) from patients with diarrhea received at the microbiology laboratory of a private hospital in Denizli. Methods: In this study, the positivity of Cryptosporidium spp. in fecal samples was investigated using direct microscopy, Kinyoun’s acid-fast staining method, and Nested polymerase chain reaction (PCR) techniques. Positive PCR products were sequenced. Results: In the examined fecal samples of patients with diarrhea, no parasites were detected through direct microscopic examination. Using the Kinyoun acid-fast staining method, Cryptosporidium spp. was identified in 2.7% (n=4) of the samples, while Nested PCR detected it in 4.67% (n=7) of the samples. The four positive samples were sequenced using primers that amplify the 18S rRNA gene region. The sequencing results identified the isolates as C. parvum. Conclusion: Cryptosporidiosis is an important public health issue as it is a zoonotic disease caused by the Cryptosporidium parasite that can be transmitted from animals to humans. This study focuses on the molecular characterization of Cryptosporidium species detected in human fecal samples, which is significant for understanding which specific strains or species are involved in human infections. According to the findings, it is recommended that control measures be implemented to reduce the risk of exposure to Cryptosporidium in both humans and animals in Türkiye.

Sarcocystis species are prevalent in Iran and have economic and public health consequences on ani-mals and humans. The present study aimed at molecular identification of Sarcocystis spp. isolated from Iranian buffaloes in Guilan province based on 18s ribosomal RNA (18s rRNA) and cytochrome oxidase subunit I (Cox1) sequences. For this purpose, a total of 100 buffalo carcasses were sampled from four tissues (oesophagus, diaphragm, shoulder, thigh), and assessed microscopically for sarco-cysts. Samples were suspected of being infected with Sarcocystis spp. according to morphological evaluation. Amplification of 18s rRNA and Cox1 sequences were performed from DNA extracted from any detected Sarcocystis. The phylogenetic tree was plotted by Neighbor-Jinning (NJ) phylo-grams. Phylogenetic analysis of 18s rRNA and Cox1 genes showed no differences between Sarcocys-tis isolates of the same species and a low level of genetic variability was found among isolates and other Sarcocystis cruzi sequences. S. cruzi was identified as the species of Iranian buffalo in the Guilan province of Iran. This is the first study of the Cox1 gene and 18s rRNA sequences to confirm the presence of S. cruzi in Iranian buffaloes.

Amplifying small subunit (SSU) rRNA genes with universal primers in assessing microbial populations diversity, but target microorganisms are sometimes omitted due to inadequate primer coverage. Adding degenerate bases to primers can help, but existing methods are complex and time-consuming. This study introduces a user-friendly tool called "Degenerate primer 111" for adding degenerate bases to existing universal primers. By aligning one universal primer with one uncovered target microorganism's SSU rRNA gene, this tool iteratively generates a new primer, maximizing coverage for the target microorganisms. The tool was used to modify eight pairs of universal primers (515F Parada-806R Apprill, S-D-Bact-0341-b-S-17/S-D-Bact-0785-a-A-21, OP_F114-KP_R013, 27F-1492R, 341F-806R, OP_F066-KP_R013, 515F Parada-926R Quince, 616*F-1132R), and generated 29 new universal primers with increased coverage of specific target microorganisms without increasing coverage of non-target microorganisms. To verify the effectiveness of the improved primers, one set of original and improved primers (BA-515F-806R and BA-515F-806R-M1) was used to amplify DNA from the same sample, and high-throughput sequencing of the amplicons confirmed that the improved primers detected more microbial species compared to the original primers. Future researchers can use this tool to develop more personalized primers to meet their diverse microorganism detection needs. [ABSTRACT FROM AUTHOR]

Zooplankton, a crucial component of urban wetland, are one of the effective bioindicators for monitoring the feeding stocks of organisms at higher trophic levels and assessing the ecological quality of ecosystems. However, information about the characteristics of epiphytic zooplankton community structure resulted from traditional methods is limited and hindered by the large amount of detritus and sludge attached to the macrophytes. We investigated the epiphytic zooplankton communities associated with macrophytes (Vallisneria, Nymphaea, and Thalia dealbata) in a subtropical wetland using as DNA markers of the 18S rRNA gene and the mitochondrial cytochrome c oxidase subunit I (COI) gene. A total of 241 OTUs of zooplankton were obtained from COI amplicons, including 194 OTUs of Rotifera, 22 of Cladocera, and 25 of Copepoda, while only 62 OTUs of zooplankton were obtained from 18S rDNA amplicons including 34 OTUs of Rotifera and 28 of Copepoda. The zooplankton communities associated with the three macrophytes were similar, but they differed significantly from those in the open waters. However, there were no significant temporal differences among the zooplankton communities. Epiphytic zooplankton communities were dominated by littoral zooplankton such as Testudinella, Lecane, and Philodina. Microzooplankton, especially littoral species, utilize macrophytes as food sources and as refuges against predation. This further led to an increase in α and β diversity of zooplankton communities in urban wetlands. Our result suggests that the joint use of multiple molecular markers could improve the taxonomic resolution and generate a comprehensive biodiversity profile of zooplankton. [ABSTRACT FROM AUTHOR]

Sarcocystis species are prevalent in Iran and have economic and public health consequences on animals and humans. The present study aimed at molecular identification of Sarcocystis spp. isolated from Iranian buffaloes in Guilan province based on 18s ribosomal RNA (18s rRNA) and cytochrome oxidase subunit I (Cox1) sequences. For this purpose, a total of 100 buffalo carcasses were sampled from four tissues (oesophagus, diaphragm, shoulder, thigh), and assessed microscopically for sarcocysts. Samples were suspected of being infected with Sarcocystis spp. according to morphological evaluation. Amplification of 18s rRNA and Cox1 sequences were performed from DNA extracted from any detected Sarcocystis. The phylogenetic tree was plotted by Neighbor-Jinning (NJ) phylograms. Phylogenetic analysis of 18s rRNA and Cox1 genes showed no differences between Sarcocystis isolates of the same species and a low level of genetic variability was found among isolates and other Sarcocystis cruzi sequences. S. cruzi was identified as the species of Iranian buffalo in the Guilan province of Iran. This is the first study of the Cox1 gene and 18s rRNA sequences to confirm the presence of S. cruzi in Iranian buffaloes. [ABSTRACT FROM AUTHOR]

Simple Summary: The Pearl River Estuary (PRE) in China, a highly urbanized coastal area, presents a unique opportunity to study the effects of environmental changes on the phytoplankton com-munity. In September 2018, a field study was conducted to examine how the photosynthetic status and spatial distribution of these organisms varied from freshwater to oceanic waters. Dinophyta and Haptophyta were prevalent in seawater, while Chlorophyta and Cryptophyta dominated from freshwater to estuarine water. Bacillariophyta were found across all regions. Phytoplankton in the mixing zone showed signs of stress due to fluctuating environmental conditions, whereas those in freshwater and oceanic areas appeared more photosynthetically active. Human activities have in-creased nutrient levels in the estuary, leading to higher chlorophyll concentrations and more diverse phytoplankton communities upstream. Understanding these patterns helps us assess the health of coastal ecosystems, which is crucial for managing the impacts of climate change and human development on marine environments. The Pearl River Estuary (PRE) is one of the world's most urbanized subtropical coastal systems. It presents a typical environmental gradient suitable for studying estuarine phytoplankton communities' dynamics and photosynthetic physiology. In September 2018, the maximum photochemical quantum yield (Fv/Fm) of phytoplankton in different salinity habitats of PRE (oceanic, estuarine, and freshwater zones) was studied, revealing a complex correlation with the environment. Fv/Fm of phytoplankton ranged from 0.16 to 0.45, with taxa in the upper Lingdingyang found to be more stressed. Community composition and structure were analyzed using 18S rRNA, accompanied by a pigment analysis utilized as a supplementary method. Nonmetric multidimensional scaling analysis indicated differences in the phytoplankton spatial distribution along the estuarine gradients. Specificity-occupancy plots identified different specialist taxa for each salinity habitat. Dinophyta and Haptophyta were the predominant taxa in oceanic areas, while Chlorophyta and Cryptophyta dominated freshwater. Bacillariophyta prevailed across all salinity gradients. Canonical correlation analysis and Mantel tests revealed that temperature, salinity, and elevated nutrient levels (i.e., NO3−-N, PO43−-P, and SiO32−-Si) associated with anthropogenic activities significantly influenced the heterogeneity of community structure. The spatial distribution of phytoplankton, along with in situ photosynthetic characteristics, serves as a foundational basis to access estuarine primary productivity, as well as community function and ecosystem health. [ABSTRACT FROM AUTHOR]

The ITS‐2‐rRNA has been particularly useful for nematode metabarcoding but does not resolve all phylogenetic relationships, and reference sequences are not available for many nematode species. This is a particular issue when metabarcoding complex communities such as wildlife parasites or terrestrial and aquatic free‐living nematode communities. We have used markerDB to produce four databases of distinct regions of the rRNA cistron: the 18S rRNA gene, the 28S rRNA gene, the ITS‐1 intergenic spacer and the region spanning ITS‐1_5.8S_ITS‐2. These databases comprise 2645, 254, 13,461 and 10,107 unique full‐length sequences representing 1391, 204, 1837 and 1322 nematode species, respectively. The comparative analysis illustrates the complementary value but also reveals a better representation of Clade III, IV and V than Clade I and Clade II nematodes in each case. Although the ITS‐1 database includes the largest number of unique full‐length sequences, the 18S rRNA database provides the widest taxonomic coverage. We also developed PrimerTC, a tool to assess primer sequence conservation across any reference sequence database, and have applied it to evaluate a large number of previously published rRNA cistron primers. We identified sets of primers that currently provide the broadest taxonomic coverage for each rRNA marker across the nematode phylum. These new resources will facilitate more comprehensive metabarcoding of nematode communities using either short‐read or long‐read sequencing platforms. Further, PrimerTC is available as a simple WebApp to guide or assess PCR primer design for any genetic marker and/or taxonomic group beyond the nematode phylum. [ABSTRACT FROM AUTHOR]

Protists are a diverse and understudied group of microbial eukaryotic organisms especially in terrestrial environments. Advances in molecular methods are increasing our understanding of the distribution and functions of these creatures; however, there is a vast array of choices researchers make including barcoding genes, primer pairs, PCR settings, and bioinformatic options that can impact the outcome of protist community surveys. Here, we tested four commonly used primer pairs targeting the V4 and V9 regions of the 18S rRNA gene using different PCR annealing temperatures and processed the sequences with different bioinformatic parameters in 10 diverse soils to evaluate how primer pair, amplification parameters, and bioinformatic choices influence the composition and richness of protist and non-protist taxa using Illumina sequencing. Our results showed that annealing temperature influenced sequencing depth and protist taxon richness for most primer pairs, and that merging forward and reverse sequencing reads for the V4 primer pairs dramatically reduced the number of sequences and taxon richness of protists. The data sets of primers that targeted the same 18S rRNA gene region (e.g., V4 or V9) had similar protist community compositions; however, data sets from primers targeting the V4 18S rRNA gene region detected a greater number of protist taxa compared to those prepared with primers targeting the V9 18S rRNA region. There was limited overlap of protist taxa between data sets targeting the two different gene regions (80/549 taxa). Together, we show that laboratory and bioinformatic choices can substantially affect the results and conclusions about protist diversity and community composition using metabarcoding. [ABSTRACT FROM AUTHOR]

The coastal area of Qinhuangdao, particularly the Changli Gold Coast Nature Reserve, is experiencing ecological degradation and frequent Harmful Algal Blooms (HABs). This study focuses on the changing phytoplankton communities in these coastal waters, examining them from both a macroscopic and microscopic perspective. Utilizing microscopy, molecular techniques, and pigment analysis, seasonal shifts were observed, with diatoms predominating in June and July, and dinoflagellates in August. Our morphological examination enabled the classification of 89 species into four distinct groups. The species Paralia sulcata and Pseudo-nitzschia pungens were most abundant in early summer, while Tripos furca, a dinoflagellate, dominated in August. This indicates a shift in phytoplankton communities due to environmental factors such as phosphate deficiency and high nitrogen/phosphorus ratios. Additionally, the study notes the impact of reduced river runoff and reintroduction of scallop farming contributing to nitrogen-rich eutrophication in August. Molecular analysis revealed a disparity between microscopic observations and the prevalence of Teleaulax blooms during early summer. Elevated concentrations of TN and DOC, coupled with limited water exchange, emerged as primary factors contributing to their occurrence. Sediment analysis revealed a high diversity but low abundance of dinoflagellates in August, with a significant presence of harmful species. The study highlights the shift from diatoms to harmful dinoflagellate populations, exacerbated by eutrophication and pollution, leading to HABs. These findings provide a theoretical basis for understanding toxic algal blooms and are crucial for environmental agencies in developing strategies to protect and sustainably develop offshore environments. [ABSTRACT FROM AUTHOR]

So far, Rubrioxytricha guamensis Kumar et al. 2018 is known only from the type locality, namely Guam, USA. Recently, another isolate was recorded from a freshwater habitat in China that is 3500 km from the type locality. Its morphology and molecular phylogeny were investigated using live observation, protargol staining and ribosomal gene sequencing methods. The morphology of the present isolate of R. guamensis corresponds well with that of the type population despite a broad range of morphometric data in the Chinese population. Conspecificity of the two populations is supported by 99.9% 18S rRNA gene sequence similarity. Phylogenetic analysis reveals that these two populations of R. guamensis group together and cluster within the genus. The present study contributes to understanding the wide distribution of the species and helps to circumscribe the species. [ABSTRACT FROM AUTHOR]

Cyanobacterial mats are commonly reported as hotspots of microbial diversity across polar environments. These thick, multilayered microbial communities provide a refuge from extreme environmental conditions, with many species able to grow and coexist despite the low allochthonous nutrient inputs. The visibly dominant phototrophic biomass is dependent on internal nutrient recycling by heterotrophic organisms within the mats; however, the specific contribution of heterotrophic protists remains little explored. In this study, mat community diversity was examined along a latitudinal gradient (55–83°N), spanning subarctic taiga, tundra, polar desert, and the High Arctic ice shelves. The prokaryotic and eukaryotic communities were targeted, respectively, by V4 16S ribosomal RNA (rRNA) and V9 18S rRNA gene amplicon high-throughput sequencing. Prokaryotic and eukaryotic richness decreased, in tandem with decreasing temperatures and shorter seasons of light availability, from the subarctic to the High Arctic. Taxonomy-based annotation of the protist community revealed diverse phototrophic, mixotrophic, and heterotrophic genera in all mat communities, with fewer parasitic taxa in High Arctic communities. Co-occurrence network analysis identified greater heterogeneity in eukaryotic than prokaryotic community structure among cyanobacterial mats across the Canadian Arctic. Our findings highlight the sensitivity of microbial eukaryotes to environmental gradients across northern high latitudes. [ABSTRACT FROM AUTHOR]

Vegetables are important preventive foods and are useful for maintaining health and preventing diseases and some fungi, such as Penicillium spp., Aspergillus spp. and Fusarium spp. grown on vegetables and contaminated it. Therefore, the aim of the study was to isolation and identification of fungi contaminating different types of vegetables infected with rot collected from local markets of Duhok city/Iraq, and Molecular identification of Aspergillus nidulans using Polymerase Chain Reactions (PCR), by Design of the primer, Extraction of DNA, Nucleotide sequencing of amplified pieces using DNA sequencing which was done at Psomagene sequencing company (Maryland/USA) and The phylogenetic tree was constructed by bootstrap (100X) analysis using the MEGA-11 software. Results referred to all vegetable samples under study contaminated with different genera of fungi, green bell pepper contaminated with Rhizopus stolonifer in (43.2%), Aspergillus nidulans was isolated from red bell pepper in (19.2%), while it was the most frequent isolates from eggplant, pumpkin, cucumber and cauliflower in percentage of 43.3%, 46.8%, 31.5% and 58.9% respectively. According to morphological and microscopic identification A. nidulans was chosen for molecular study because of its high frequency in most vegetable samples. Molecular identification of A. nidulans using 18 S rRNA, a pair of specialized primers (ITS1) and (ITS2) was adopted. In electrophoresis on agarose gel at a concentration of 2%, the results showed a package size of 600 bp. belonging to Aspergillus nidulans, and identical results were obtained for the isolate with the standard isolates installed in the Basic Local Alignment Search Tool (BLAST) program database. The evolutionary relationship was found between the local isolate in this study and the one registered in NCBI under the name Aspergillus nidulans HAA78. The isolate Aspergillus nidulans HAA78 was 100% identical to the isolate Aspergillus nidulans strain ATCC (10074). It was concluded that all vegetables isolated from local markets of Duhok City,Iraq were contaminated with many genera of fungi. The molecular identification of the main and most common fungi collected from these vegetables was Aspergillus nidulans. The study would help understand the important role of molecular identification in addition to Manual methods in identifying fungi. [ABSTRACT FROM AUTHOR]

Species of Haemogregarina are blood parasites known to parasitise vertebrate hosts, including fishes (Haemogregarina sensu lato) and freshwater turtles (Haemogregarina sensu stricto). Their vectors, include gnathiid isopods and leeches, respectively. In turtles, Haemogregarina balli has the best-characterized life cycle in the genus. However, no studies in Brazil have suggested a possible vector for any species of Haemogregarina from freshwater turtles. Therefore, in the present study, we provide insights into a leech vector based on specimens found feeding on two species of freshwater turtles, Podocnemis unifilis and Podocnemis expansa, using morphological and molecular data. In 2017 and 2019, freshwater turtles were collected in Goiás State, Brazil. Hosts were inspected for ectoparasites and leeches were collected from two specimens of P. expansa and nine specimens of P. unifilis. Leeches were subsequently identified as members of the genus Unoculubranchiobdella. Leech histological slides revealed haemogregarine-like structures, similar to post-sporogonic merogony, found near the gills and within the posterior sucker. Molecular analysis of the haemeogregarines resulted in the identification of three species of Haemogregarina: Haemogregarina embaubali, Haemogregarina goianensis, and Haemogregarina brasiliana. Therefore, our findings, based on morphology and DNA data suggest leeches of the genus Unoculubranchiondella as vectors for at least three species of Haemogregarina from Brazilian turtles. [ABSTRACT FROM AUTHOR]

In the present study, tissue samples (tongue, esophagus and heart) were investigated from dromedary camels of India for identification and characterization of Sarcocystis spp. using histopathology, PCR and gene sequencing. Genomic DNA extracted from these tissue samples was used for PCR amplification of the cytochrome c oxidase subunit I gene (cox1) of Sarcocystis spp. and the partial sequence of small subunit ribosomal RNA (18S rRNA) gene of the S. cameli. The PCR products were purified, sequenced and analyzed using bioinformatics tools. Based on phylogenetic analysis of the cox1 gene, the sequences of the present study clustered with those of S. cameli, hosted by dromedary camels of Iraq and a close association was observed with S. masoni hosted by dogs and alpacas of China. Until now, there are no 18S rRNA sequences of S. cameli available in GenBank and this is the first study recording 18S rRNA sequences of S. cameli which were grouped with S. masoni from alpaca of China and guanaco and llama of Argentina in phylogenetic analysis. These findings could be useful for further studies on the characterization through molecular epidemiology, genetic diversity and host specificity of S. cameli. [ABSTRACT FROM AUTHOR]

The speciose scarinine clade of coral reef parrotfishes display significant variation in trophic cranial morphology, yet are often described as generalist herbivores. The hypothesis that many parrotfishes target micro-photoautotrophs is a new framework within which to clarify parrotfish diets. Here, we investigate the dietary targets of Scarus rubroviolaceus using the feeding substrata extraction method and then compare the results to fourteen other syntopic parrotfish species. Scarus rubroviolaceus were followed on snorkel until repeated biting was observed. A 22 mm × 20 mm core was extracted around the bite. We identified and quantified the bite core biota by scraping the top 1 mm from bite cores for microscopy and 16S/18S small subunit rRNA metabarcoding. Filamentous cyanobacteria density on S. rubroviolaceus bite cores did not differ from the other fourteen parrotfish species, Calothrix (Nostocales) being the most frequently observed filamentous cyanobacteria for all fifteen parrotfish species. The 18S metabarcoding analysis detected the encrusting, endolithic sponge taxon Clionaida in the S. rubroviolaceus bite cores. We investigated the possibility of spongivory across all fifteen parrotfish species including an analysis of sponge-associated microbiota detected on the bite cores. This revealed a new axis of trophic partitioning with varying levels of spongivory amongst the fifteen Indo-Pacific parrotfish species. The bite cores of Cetoscarus ocellatus, Chlorurus spilurus, Chlorurus microrhinos, Scarus frenatus and S. rubroviolaceus particularly indicated spongivory. Our findings develop our understanding of parrotfish diet and provide further evidence that parrotfishes are specialized feeders and partition benthic trophic resources. [ABSTRACT FROM AUTHOR]

Current knowledge of the microbiota of soda pans of the Carpathian Basin focuses mainly on diatoms. In studying six soda pans in Vojvodina (Serbia), we aimed to gain deeper insights into the diatom community by using not only traditional microscopic analysis but also high-throughput sequencing of the 18S rRNA gene. In addition, this study aimed to evaluate bacterial communities in these soda pans for the first time using the 16S rRNA gene marker. Although similar numbers of diatom taxa were found using both approaches, a significant discrepancy in species composition was found. The genus Nitzschia was one of the most represented and numerous genera according to the morphological and molecular analyses, but with lower diversity according to the molecular data, with the sequences mostly unassigned. Another major discrepancy was noticed with taxon Halamphora veneta, the results of metabarcoding showed high abundance in almost all soda pans, while microscopy detected it as very low. Diverse communities of aerobic and anaerobic bacteria were detected in the studied soda pans, such as Proteobacteria, Bacteroidota, Actinobacteria, Bacillaceae, and Peptoclostridium. According to current knowledge, harsh environmental conditions and habitat homogeneity regulate diatom and bacteria community composition and enable the survival of taxa with predominantly high ecophysiological plasticity. Finally, uncovering the structure of the microbial community as the first phase in developing an efficient tool to assess the ecological status of these fragile ecosystems is an essential step towards their conservation. [ABSTRACT FROM AUTHOR]

One new species of Racovitzaibathynella Serban and Coineau, 1994 and one of Cteniobathynella Schminke, 1973 of the order Bathynellacea Chappuis, 1915 (family Parabathynellidae Noodt, 1065) are described from Benin in West Africa. These represent the first records of Bathynellacea species in Benin following a broad sampling throughout the country. Two species of the genus Racovitzaibathynella are known from South Africa and one is known from Chad and Israel. Specimens of Racovitzaibathynella beninensis Camacho and Lagnika sp. n. and Cteniobathynella boutini Camacho and Lagnika sp. n. have a unique combination of morphological characters and several shared generic features. Racovitzaibathynella beninensissp. n. has a six-segmented antennule with three aesthetascs on segment five; a five-segmented antenna; concave labrum; mandible with only three teeth on the distal endite; no epipod on thoracopods I to III; plumose setae on the exopod of thoracopods I to VII; female thoracopod VIII distal-end bilobed, and two plumose setae on the endopod of the uropod. Cteniobathynella boutinisp. n. has a six-segmented antennula; five-segmented antenna; no epipod on thoracopods I to III; endopod on ThVIII of males as exopod, and five setae on the endopod of the uropod. To complement the morphological description of the two new species, a phylogenetic analysis based on the 18S ribosomal RNA (rRNA) gene was performed to infer their phylogenetic position within the family Parabathynellidae. The phylogenetic reconstruction shows an Afrotropical clade, which includes the new African species, and is clearly distinct from the European, Australian and Asiatic clades. [ABSTRACT FROM AUTHOR]

Coccidiosis is an intestinal protozoan disease that affects the poultry industry worldwide. The severity of this disease varies depending on the identity of the infectious agents. Therefore, this study was carried out to identify the Eimeria species that affect broiler chickens, Gallus gallus domesticus, through morphological and molecular phylogenetic analyses. Twenty‐five faecal samples were collected from the broiler chickens in a commercial poultry farm in Riyadh (Saudi Arabia). Using the floatation technique, faeces were examined microscopically for the Eimeria occurrence. Identification of Eimeria species was performed based on morphological criteria and molecular tools (DNA amplification for the partial small subunit ribosomal RNA (18S rRNA), internal transcribed spacer (ITS)‐1, and mitochondrial cytochrome c oxidase I (COI) genes. In this study, 32% (8 out of 25) of collected samples were found to be positive for coccidiosis. After sporulation in potassium dichromate (K2Cr2O7), the sporulated oocysts were observed as ovoid and measured 18.37–23.19 µm (19.87) long and 15.07–18.67 µm (16.46) wide, with the anterior location of a polar granule and absence of micropyle. These Eimeria oocysts were assumed to size and shape characteristics of Eimeria acervulina. Molecular analysis was conducted on the sequences of the polymerase chain reaction products from the three genes studied (18S rRNA, ITS‐1, and COI). At the three genes, results showed that the resultant sequences clustered with E. acervulina from different regions confirming morphological description. This study highlighted the importance of molecular techniques to detect avian Eimeria species more than the traditional morphology‐based tool to optimise the appropriate anticoccidial strategies for long‐term control in the studied area. [ABSTRACT FROM AUTHOR]

Background: Granulomas in pediatric liver biopsies (GPLB) are rare with the largest pediatric cohort reported over 25 years ago. Methods: Single-center retrospective study of GPLB. Results: Seventeen liver biopsies from 16 patients with granulomas were identified (9 boys, 56%) with a median age of 13 years (range: 1–18) for which the most common indication was the presence of a nodule/mass (47%). Significant comorbidities were seen in 13 patients (81%) and included: liver transplant (25%), history of a neoplasm (25%), autoimmune hepatitis (6%), Crohn disease (6%), bipolar disorder (6%), severe combined immunodeficiency (6%), and sickle cell disease (6%). Eleven patients were taking multiple medications at the time of biopsy. Granulomas were more commonly pan-acinar (11 cases) followed by subcapsular (4 cases), portal (1 case), and periportal (1 case). Necrosis was seen in 10 cases (59%). GMS stain was positive in 2 cases for Histoplasma -like yeast; microbiological cultures were negative in all cases (no: 4). A 18S and 16S rRNA gene sequencing performed in 15 cases revealed only 1 with a pathogenic microorganism, Mycobacterium angelicum. Conclusion: In our experience, GPLB are heterogenous with only 3 cases having an identifiable infectious etiology and many of the remaining cases being associated to multiple medications, suggesting drug-induced liver injury as possible etiology. [ABSTRACT FROM AUTHOR]

Abstract Background members of the genus Sarcocystis are intracellular obligate protozoan parasites classified within the phylum Apicomplexa and have an obligate heteroxenous life cycle involving two hosts. A more comprehensive understanding of the prevalence and geographic range of different Sarcocystis species in marine ecosystems is needed globally and nationally. Hence, the objective of this study was to document the incidence of Sarcocystis infection in sharks within the aquarium ecosystem of Egypt and to identify the species through the characterization of the SSU rDNA gene. Methods All organs of the mako shark specimen underwent macroscopic screening to detect the existence of a Sarcocystis cyst. Ten cysts were collected from the intestine and processed separately to extract the genomic DNA. The polymerase chain reaction (PCR) was accomplished by amplifying a specific 18S ribosomal RNA (rRNA) gene fragment. Subsequently, the resulting amplicons were subjected to purification and sequencing processes. Results Macroscopic examination of the mako shark intestinal wall sample revealed the presence of Sarcocystis cysts of various sizes and shapes, and sequencing of the amplicons from Sarcocystis DNA revealed a 100% nucleotide identity with the sequence of Sarcocystis tenella recorded from sheep in Iran; The mako shark sequence has been deposited in the GeneBank with the accession number OQ721979. This study presents the first scientific evidence demonstrating the presence of the Sarcocystis parasite in sharks, thereby documenting this specific marine species as a novel intermediate host in the Sarcocystis life cycle. Conclusions This is the first identification of Sarcocystis infection in sharks, and we anticipate it will be an essential study for future screenings and establishing effective management measures for this disease in aquatic ecosystems.

The purpose of the research is isolation, identification, and analysis of ASV (Amplicon Sequence Variant) types of Cryptosporidia spp. in pigs in the Vologda Region of the Russian Federation.Materials and methods. The research has been conducted in the Russian Federation for the first time. The research was conducted on pig farms in the Vologda Region of the Northwestern Federal District of the Russian Federation from January to October 2023. Feces were taken from piglets of various age groups, as well as milking sows. The samples were studied using the equipment of the resource center “Genomic Technologies, Proteomics and Cell Biology” of ARRIAM. Species of the genus Cryptosporidia were identified in fecal samples using high-throughput sequencing of 18S rRNA gene fragment amplicon libraries as obtained from nested PCR followed by “denoising”, sequence combining, and restoring the original phylotypes (ASV, (Amplicon Sequence Variant)).Results and discussion. Cryptosporidia spp. species were identified in each age group studied. As a result of high-throughput sequencing of the libraries using the Illumina technology, 20 to 100 thousand nucleotide sequences (reads) were obtained for each sample after processing of which a total of 2,372 ASVs were identified. The analysis of the ASV taxonomic affiliation performed with phylogenetic analysis supplemented by an analysis using the blastn algorithm in the GenBank database showed that, in total, 10 ASVs were only present in all studied samples that had high similarity to sequences deposited in the GenBank as 18S rRNA gene fragments of Cryptosporidium scrofarum. Eight ASV types were unique and did not repeat from farm to farm. Probably, these sequences belong to local populations of C. scrofarum subspecies. Of interest is the discovery of a unique Cryptosporidium sequence of ASV8 type which is only 91.47% similar to the closest relative of the genus, which may indicate a rather distant taxonomic relationship. This type of nucleotide sequence can be further described as a new species. All identified unique ASV nucleotide sequences were deposited in GenBank.

Red-bellied pacu (Piaractus brachypomus) is a popular exotic fish cultured globally for ornamental and human consumption purposes. In Indonesia, this fish is mainly cultured in Java, including to supply seed to other regions for the ornamental fish trade or aquaculture. Although this exotic fish in widely cultured, information on parasitic infections is negligible. Red-bellied pacus were purchased from a fish farmer and examined for monogenean parasite infection. Monogenean parasites were identified based on morphological and molecular characteristics. Histopathological examinations were performed on gills from heavily infected fish. DNA was extracted from an individual monoge-nean; 18S rRNA PCR product was sequenced and a phylogenetic tree constructed. Morphological and molecular traits identified the monogenean as Mymarothecium viatorum, the first report of the neotropical M. viatorum in this region. The parasite was most likely introduced to Indonesia through the importation of ornamental fish. This parasite had a prevalence of 79% and a mean intensity of 7.1. There was no significant correlation between the parasite abundance and the condition factor of the fish. M. viatorum was more abundant on smaller fish than on larger fish. Gill histopathology showed oedema, severe haemorrhage, and infiltration of inflammatory cells. The occurrence of these parasites could pose a serious threat to the development of red-bellied pacu culture.

The flowerhorn cichlid is a popular ornamental fish in many Asian countries. The present study reports the occurrence of Paracapillaria philippinensis (Chitwood et al., 1968), a parasitic nematode in flowerhorn cichlid (Cichlasoma sp.) from south India. The infected fish demonstrated clinical symptoms viz. dark coloration, poor appetite, lethargy, erratic swimming, and white stringy faeces. Microscopic observation of the intestinal content and faeces revealed the presence of adult worms, larvae, and unembryonated eggs. PCR amplification of eukaryotic 18S rRNA, P. philippinensis-specific SSU rRNA gene, and the subsequent sequence analysis confirmed the species identity as P. philippinensis. The generated sequences were submitted in the GenBank, NCBI, under the accession numbers, MK895507.1, MK895446.1, MW144993.1, and OR685675.1. This is the first scientific report of P. philippinensis in fish from India, and it confirms that the flowerhorn cichlid can act as a definitive host for P. philippinensis. This report alerts fish handlers and enthusiasts to undertake suitable precautionary measures while handling live flowerhorn cichlids to prevent possible transmission of P. Philippinensis, which has the potential to infect humans causing intestinal capillariasis. [ABSTRACT FROM AUTHOR]

Parasites play a pivotal role in ecosystem health, influencing human and zoonotic diseases, as well as biodiversity preservation. The genus Trypanosoma comprises approximately 500 species mostly found in wildlife animals. This study focuses on identifying trypanosomes found in the white-necked thrush (Turdus albicollis) and the yellow-legged thrush (Turdus flavipes) in the Neotropics. First, we demonstrate the utility of an 18S rDNA sequence-structure phylogeny as an alternative method for trypanosome classification, especially when gGAPDH sequences are unavailable. Subsequently, the sequence-structure phylogeny is employed to classify new trypanosome sequences discovered in wild birds, placing them within the Ornithotrypanum subgenus. This marks the first identification of Ornithotrypanum in Neotropical birds, contributing to the understanding of the distribution and ecological adaptation of avian trypanosomes. Beyond taxonomy, this study broadens our comprehension of the ecological implications of avian trypanosomes in the Neotropics, emphasizing the need for continued research in this field. These findings underscore the importance of alternative classification methods, which are essential to unravel the complex interactions between parasites, wildlife hosts, and their ecosystems. [ABSTRACT FROM AUTHOR]

Red-bellied pacu (Piaractus brachypomus) is a popular exotic fish cultured globally for ornamental and human consumption purposes. In Indonesia, this fish is mainly cultured in Java, including to supply seed to other regions for the ornamental fish trade or aquaculture. Although this exotic fish in widely cultured, information on parasitic infections is negligible. Red-bellied pacus were purchased from a fish farmer and examined for monogenean parasite infection. Monogenean parasites were identified based on morphological and molecular characteristics. Histopathological examinations were performed on gills from heavily infected fish. DNA was extracted from an individual monogenean; 18S rRNA PCR product was sequenced and a phylogenetic tree constructed. Morphological and molecular traits identified the monogenean as Mymarothecium viatorum, the first report of the neotropical M. viatorum in this region. The parasite was most likely introduced to Indonesia through the importation of ornamental fish. This parasite had a prevalence of 79% and a mean intensity of 7.1. There was no significant correlation between the parasite abundance and the condition factor of the fish. M. viatorum was more abundant on smaller fish than on larger fish. Gill histopathology showed oedema, severe haemorrhage, and infiltration of inflammatory cells. The occurrence of these parasites could pose a serious threat to the development of red-bellied pacu culture. [ABSTRACT FROM AUTHOR]

Background: Cryptosporidiosis is a disease that causes major intestinal damage in humans and animals. The causative agents of the disease are Cryptosporidium species. In newborn calves, diarrhea can lead to death, resulting in significant economic losses for the farms. Therefore, accurate, rapid, and cost-effective diagnosis of the disease is very important. Material and methods: In this study, a novel colorimetric loop-mediated isothermal amplification (LAMP) test named "Rapid-Crypto Colorimetric LAMP test" targeting Cryptosporidium spp. 18S rRNA gene was developed to detect cryptosporidiosis in the feces of newborn calves. The analytical sensitivity of the test was determined by plasmid controls. Clinical sensitivity was determined using the feces of 127 calves collected from farms in İzmir and Manisa provinces. All of the samples were also investigated with Real-Time PCR targeting the Cryptosporidium spp. COWP gene. Cross-reactivity was tested using the DNA of other parasites and bacteria. Results: According to the results, the analytical sensitivity of the "Rapid-Crypto Colorimetric LAMP test" was found as 1 copy plasmid/reaction. When the results were compared with the Real-Time PCR test, the sensitivity of the "Rapid-Crypto Colorimetric LAMP test" was 100% and the specificity was 97.4%. The test did not cross-react with other parasites and bacteria. Conclusion: The "Rapid-Crypto Colorimetric LAMP test" developed in this study provides an advantage in the diagnosis of Cryptosporidium spp. in calf stool samples since it can be applied in basic laboratories or in the field, does not require experienced personnel, and has high sensitivity. Moreover, diagnosis can be made with the naked eye without using any device. [ABSTRACT FROM AUTHOR]

The importance of sustainable bioassessment and management of coasts to maintain good trophic status is increasing due to the high anthropogenic impacts on marine ecosystems. Diatoms are one of the most important assemblages and useful tools for assessing the state of the environment due to their advantages over other organisms such as short life span and rapid reaction to environmental changes in aquatic systems. In this study, our objective was to investigate marine benthic diatoms and compare them using three different methods: light microscopy (LM), scanning electron microscopy (SEM), and molecular metabarcoding (MB). LM observations were supported by SEM; in addition, 18S rRNA metabarcoding was used to reveal the diatom flora. The results showed that the highest number of genera was observed with LM (49), followed by SEM (27) and MB (21). Eight genera were found to be common by all three methods. Although MB identified a small number of genera, it verified the presence of common taxa through a rigorous analysis. However, all the methods used gave consistent results in confirming that the diatom assemblages found along the coasts of Istanbul in the Sea of Marmara exhibited low diversity. Our results suggest that the morphological approach to the study of marine benthic diatoms can be complemented by the metabarcoding approach, which showed encouraging results, and that both approaches can be mutually supportive. [ABSTRACT FROM AUTHOR]

A novel Eimeria sp. from a captive‐bred bilby (Macrotis lagotis Reid, 1837) has been identified in Western Australia. The bilby was bred at the Kanyana Wildlife Rehabilitation Centre, Perth, as part of the National Bilby Recovery Plan. Oocysts (n = 31) irregular blunt ellipsoidal, 17–18 × 11–12 (17.2 × 11.3); length/width (L/W) ratio 1.4–1.5 (1.5). Wall bi‐layered, 0.8–1.0 (0.9) thick, outer layer smooth, c.2/3 of total thickness. Micropyle barely discernible. Oocyst residuum is absent, but 2–3 small polar granules are present. Sporocysts (n = 31) ovoidal, 7–8 × 5–6 (7.8 × 5.7); L/W ratio 1.3–1.4 (1.4). Stieda, sub‐Stieda and para‐Stieda bodies absent or indiscernible; sporocyst residuum present, usually as an irregular body consisting of numerous granules that appear to be membrane‐bound or sometimes diffuse among sporozoites. Sporozoites vermiform with a robust refractile body. Further molecular characterization was conducted on the sporulated oocysts. At the 18S locus, it sat in a large clade of the phylogenetic tree with two isolates of Eimeria angustus from quendas (Isoodon obesulus Shaw, 1797) and the Choleoeimeria spp. It shared the highest identity with E. angustus (KU248093) at 98.84%; at the COI gene locus, it was unique and most closely related to Choleoeimeria taggarti, which is hosted by another species of marsupial, the yellow‐footed antechinus (Antechinus flavipes flavipes), with 90.58% genetic similarity. Based on morphological and molecular data, this isolate is a new species and named as Choleoeimeria yangi n. sp. [ABSTRACT FROM AUTHOR]

Assessing the ecological status of benthic habitats is important in marine ecosystem management. Sea-crossing bridges have been constructed worldwide to facilitate human travels and transactions. However, limited information is available on the ecological impacts of bridge constructions on local microeukaryotic compositions and functional shifts. In the present study, next-generation sequencing and bioinformatics analyses were performed to compare changes of microeukaryotic communities in local sediments influenced by sea-crossing bridge construction. Relatively low levels of alpha diversity and high levels of beta diversity were observed in samples influenced by bridge construction (group EG). The decreased abundance of Chloroplastida and increased abundance of Animalia in group EG suggested that engineering activities induced environmental disturbance, which impaired the ecosystem balance. LEfSe and SIMPER approaches revealed a significant abundance of ectomycorrhizal fungi in group EG, while these taxa were rare in sediments of a control group. Increased abundance and metabolic functions of these rare ectomycorrhizal fungi suggested that rare microeukaryotes should play fundamentally ecological roles in local ecosystems, especially when environmental perturbations occurred. This report is the first to address the ecological impacts of sea-crossing bridge construction on local microeukaryotic communities, which can improve our understanding of local microbial responses to marine infrastructure construction. [ABSTRACT FROM AUTHOR]

Our ability to assess biodiversity at relevant spatial and temporal scales for informing management is of increasing importance given this is foundational to identify and mitigate the impacts of global change. Collecting baseline information and tracking ecological changes are particularly important for areas experiencing rapid changes and representing data gaps such as Arctic marine ecosystems. Environmental DNA has the potential to provide such data. We extracted environmental DNA from 90 surface sediment samples to assess eukaryote diversity around Greenland and Svalbard using two separate primer pairs amplifying different sections of the 18S rRNA gene. We detected 27 different phyla and 99 different orders and found that temperature and the change in temperature explained the most variation in the community in a single linear model, while latitude, sea ice cover and change in temperature explained the most variation in the community when assessed by individual non-linear models. We identified potential indicator taxa for Arctic climate change, including a terebellid annelid worm. In conclusion, our study demonstrates that environmental DNA offers a feasible method to assess biodiversity and identifies warming as a key driver of differences in biodiversity across these remote ecosystems. [ABSTRACT FROM AUTHOR]

Understanding how biological communities are assembled is central to many ecological studies. The semi-confined nature of the Red Sea, with limited exchange of waters with other seas and strong environmental gradients, is an ideal ecosystem to investigate assembly processes of biological communities. Sampling through the water column (surface, deep chlorophyll maximum (DCM), oxygen minimum zone (OMZ), and bottom) along the latitudinal axis of the Red Sea was undertaken during cruises in 2015/2016. The composition and assembly of eukaryotic communities were assessed using high-throughput sequencing of the 18S rRNA gene. Distinct differences were noted in the composition of the eukaryotic community across the different depth layers. Dinophyceae were more prevalent in the euphotic zone (surface = 35.3%; DCM = 18.1%), while Syndiniales had the highest relative abundances in the OMZ (45.9%) and the bottom waters (52.6%). We showed that the assembly of eukaryotic communities through the water column was primarily determined by deterministic processes, especially variable selection due to different environmental conditions. The exception was between the OMZ and the bottom, where deterministic and stochastic processes were balanced with homogeneous selection and homogenizing dispersal dominating, indicating similar environmental conditions and high levels of dispersal between the layers. Across the latitudinal gradient, environmental variable selection was predominant in the euphotic zone, most likely driven by the strong environmental gradients present in the Red Sea. In the aphotic zones, homogenizing dispersal was more prevalent, especially in the OMZ. Our study highlights the contrasting assembly mechanisms governing the distribution of eukaryotic planktonic communities through the water column. [ABSTRACT FROM AUTHOR]

Simple Summary: In South Korea, the red fox (Vulpes vulpes) has been introduced and released as part of a restoration project since 2012. One of the released individuals was found dead two months after release in 2019. During necropsy, the intestinal contents were collected and oocysts of Sarcocystis sp. were found during coprological examination. PCR of the 18S rRNA gene and cox1 gene sequences was conducted, and the isolate was identified as Sarcocystis pilosa. This is the first report of this species in South Korea, implying that there were mammals that originally acted as intermediate and definitive hosts. The red fox (Vulpes vulpes) is a known host for various parasites, including numerous helminths and protozoans. Among these, certain species in the genus Sarcocystis (phylum Apicomplexa) have been documented to possess the capability to infect red foxes as definitive hosts. In South Korea, red foxes have been introduced and released as part of a re-introduction program. However, two months after its release, one of the foxes was found dead because of illegal trapping. The fox was necropsied, and a subsequent coprological study revealed oocysts of Sarcocystis sp. in the intestinal contents. The oocysts were identified as Sarcocystis pilosa based on the 18S rRNA and cytochrome c oxidase subunit 1 (cox1) gene sequences. It exhibited a 99.7–100% identity with 18S rRNA gene sequences and 99.1–99.8% identity with cox1 gene sequences from other previously reported S. pilosa samples. Additionally, it showed identities of 95.4–96.4% and 91.1–91.5% with the cox1 gene sequences of S. hjorti and S. gjerdei, while demonstrating 99.6 and 98.1% identity with the 18S rRNA gene sequences of S. hjorti and S. gjerdei, respectively. This is the first report from mainland Asia, excluding the Japanese archipelago, indicating that the life cycle of S. pilosa persists in South Korea. [ABSTRACT FROM AUTHOR]

The crab and seafood processing industry must fulfill standard requirements for sanitation, hygiene, and good manufacturing methods to ensure the safety of the products and free from foodborne bacteria. However, equipment and processing unit surfaces are challenging to clean optimally, which can cause persistent bacteria to emerge. Eliminating persistent bacteria is the latest challenge in the fish processing industry for optimal disinfection, preventing cross-contamination, and controlling foodborne outbreaks. Microbiological testing in industry has been limited to selective culture-media techniques; thus, a rapid, sensitive, accurate, and routine applicable analytical method is urgently needed. The significant reduction in the costs of high-throughput sequencing technologies supports the possibility of routine applications in the industry. This study aimed to determine the profile of the microbial community on the surface of the production room and blue-swimming crab processing unit equipment using short-read metagenomic techniques. The analysis included the stages of sampling, bacterial incubation, bacterial DNA isolation, sequencing, and bioinformatics analysis. The first important step to increase the possibility of routine adoption in the seafood industry is to reduce the cost, complexity, and time required to complete the analysis. Therefore, in this protocol, we generate a scalable, flexible, cost-effective, and auditable workflow. • Collection of bacterial samples by swabbing the surface of the equipment using a sterile cotton swab and sterile cloth, which is easy to apply and follow in the blue-swimming crab processing plant industry. • Effective and efficient sample-pooling is an important step in identifying bacterial communities by metagenomic analysis.

During two campaigns, one in the Kattegat (Denmark) in 2018, and the other off Namibia in 2019, the same fish baited trap was applied to catch scavenging amphipods at two stations each. The water depths in both areas were between 50 and 130 m. In addition to very few individuals of other species (Isopoda and Amphipoda), the samples consisted mainly of Scopelocheirus sp. The species from the Kattegat was identified as S. hopei. The question arises as to whether it is possible that the same species could dominate scavenging communities in sea areas more than 10,000 km apart. At first glance, the scopelocheirid amphipods of the northern and southern hemispheres appear identical, but subtle morphological and large genetic differences led to the conclusion that we are dealing with a previously undescribed species off Namibia. We have named it Scopelocheirus sossi sp. nov.

We investigated the morphology and phylogenetic relationships of novel and previously recognized Sarcocystis spp. infecting small mammals and colubrid snakes in Asia. The nuclear 18S rRNA and mitochondrial cox1 of Sarcocystis sp.1 from mangrove snakes (Boiga dendrophila) in Thailand and Sarcocystis sp.2 from a ricefield rat (Rattus argentiventer) in Sumatra were partially sequenced. Sporocysts of Sarcocystis sp.1 induced development of sarcocysts in experimentally infected rats, which showed a unique ultrastructure that was observed previously by S.P. Kan in rats from Malaysia; therefore, we describe this species as Sarcocystis kani sp. nov. Its integration into the 18S rRNA phylogeny of Sarcocystis spp. cycling between small mammals and colubrid snakes helped clarify relationships among the so-called S. zuoi-complex of molecularly cryptic species: Sarcocystis kani sp. nov., S. sp.2, S. attenuati, S. scandentiborneensis, and S. zuoi were all included in this clade. Tree topology was resolved into dichotomies congruent with the morphological disparities between the taxa. However, cox1 gene sequencing (including newly sequenced S. singaporensis and S. zamani) revealed that Sarcocystis kani, S. attenuati, and S. scandentiborneensis were identical suggesting a recent, common ancestry. To identify other distinctive features, lineage-specific molecular patterns within both genes were examined revealing that all 18S rRNA sequences of the S. zuoi – complex possess a unique, 7-nt long motif in helix 38 of domain V7 that was different in S. clethrionomyelaphis which branched off basally from the complex. Three-dimensional homology modelling of COX1 protein structure identified amino acid substitutions within the barcode area specific for the S. zuoi-complex and substantial divergence in structurally important amino acids between Sarcocystis species of snakes as definitive hosts and other lineages of the Sarcocystidae. We discuss the utility of selected genes for species delimitation of the Sarcocystis spp. under investigation, which probably evolved during recent radiations of their intermediate and definitive hosts.

Morchella spp. (true morels) are precious edible mushrooms consumed around the world, with a delicious taste, rich nutritional value, and unique healthcare effects. Various fungi and bacteria have been reported to colonize the ascocarps of Morchella, damaging their fruiting bodies and leading to serious economic losses in cultivation. The species identification of these colonizing organisms is crucial for understanding their colonization mechanisms on morels. Slime molds, which have characteristics of both “fungi” and “animals”, can occasionally colonize crops and edible fungi. However, there have been no reports of dictyostelid cellular slime molds (dictyostelids) colonizing plants and fungi to date. In this study, we discovered that dictyostelids colonized the surface of one wild ascoma of Morchella in the forest of Chongqing, China, with the tissues being black and rotten. Macro- and micro-morphological observations, along with molecular phylogenetic analyses, identified the specimens investigated in this study as Dictyostelium implicatum and Morchella sp. Mel-21. The results provide new knowledge of dictyostelid colonization on organisms and contribute to the diversity of species colonizing true morels. Moreover, this is also the first report of dictyostelids distributed in Chongqing, China. This study enhances our insights into the life history and potential ecological significance of dictyostelids and updates their distribution area in China. Further research will be conducted to uncover the mechanisms behind the colonization observed in this study.

The Pearl River Estuary (PRE) is one of the world’s most urbanized subtropical coastal systems. It presents a typical environmental gradient suitable for studying estuarine phytoplankton communities’ dynamics and photosynthetic physiology. In September 2018, the maximum photochemical quantum yield (Fv/Fm) of phytoplankton in different salinity habitats of PRE (oceanic, estuarine, and freshwater zones) was studied, revealing a complex correlation with the environment. Fv/Fm of phytoplankton ranged from 0.16 to 0.45, with taxa in the upper Lingdingyang found to be more stressed. Community composition and structure were analyzed using 18S rRNA, accompanied by a pigment analysis utilized as a supplementary method. Nonmetric multidimensional scaling analysis indicated differences in the phytoplankton spatial distribution along the estuarine gradients. Specificity-occupancy plots identified different specialist taxa for each salinity habitat. Dinophyta and Haptophyta were the predominant taxa in oceanic areas, while Chlorophyta and Cryptophyta dominated freshwater. Bacillariophyta prevailed across all salinity gradients. Canonical correlation analysis and Mantel tests revealed that temperature, salinity, and elevated nutrient levels (i.e., NO3−-N, PO43−-P, and SiO32−-Si) associated with anthropogenic activities significantly influenced the heterogeneity of community structure. The spatial distribution of phytoplankton, along with in situ photosynthetic characteristics, serves as a foundational basis to access estuarine primary productivity, as well as community function and ecosystem health.

ABSTRACT: Similarly to poultry industry, coccidiosis may cause significant economic losses also in the commercial quail industry, an emerging sector undergoing uneven development around the world. Although scant and mostly dated, the available literature reports detailed morphological and morphometric features of both oocysts and sporocysts of the Eimeria species hitherto recognized in Japanese quails, i.e. E. tsunodai, E. uzura, E. bateri, and E. fluminensis. Mixed infections are very common in the field and require an accurate differential diagnosis of diverse species of coccidia, identifying the highly pathogenic ones, in particular E. tsunodai (localized in the caeca), and E. uzura (localized in both caeca and small intestine). This goal is hampered by time-consuming laboratory procedures involving highly qualified staff and facilities, and poorly compatible with routine management practices in farmed quails. A supplemental difficulty is represented by the lack of nucleotide sequences available in GenBank. To overcome these issues, copromicroscopic and molecular analyses (amplifying the 18S rRNA region, and the internal transcribed spacers regions ITS1-5.8rRNA-ITS2) were performed on oocysts populations separately isolated from pools of 12 caecal and 12 cloacal contents collected from 240 naturally infected laying Japanese quails. Data on morphological and morphometric features of 1,000 sporulated oocysts were statistically compared, demonstrating the presence of different Eimeria species colonizing the 2 intestinal tracts. This result was also confirmed by PCR and phylogenetic analysis of the 18S rRNA gene. Overall results allowed to hypothesize the presence of E. uzura in our Japanese quails. Although a certain identification at species level was not obtained, the present study demonstrates that reasonable turnaround times of monitoring procedures performed on Japanese quail farms, shedding light on the in vivo and post-mortem differential diagnosis of coccidiosis can be achieved, and provide obvious benefits in disease understanding and control.