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Plastic waste, especially positively buoyant polymers known as polyolefins, are a major component of floating debris in the marine environment. While plastic colonisation by marine microbes is well documented from environmental samples, the succession of marine microbial community structure over longer time scales (> > 1 month) and across different types and shapes of plastic debris is less certain. We analysed 16S rRNA and 18S rRNA amplicon gene sequences from biofilms on polyolefin debris floating in a flow-through seawater tank in Hawaii to assess differences in microbial succession across the plastic types of polypropylene (PP) and both high-density polyethylene (HDPE) and low-density polyethylene (LDPE) made of different plastic shapes (rod, film and cube) under the same environmental conditions for 1 year. Regardless of type or shape, all plastic debris were dominated by the eukaryotic diatom Nitzschia, and only plastic type was significantly important for bacterial community structure over time (p = 0.005). PE plastics had higher differential abundance when compared to PP for 20 bacterial and eight eukaryotic taxa, including the known plastic degrading bacterial taxon Hyphomonas (p = 0.01). Results from our study provide empirical evidence that plastic type may be more important for bacterial than eukaryotic microbial community succession on polyolefin pollution under similar conditions.

Standard diagnostics used in longitudinal antimalarial studies are unable to characterize the complexity of submicroscopic parasite dynamics, particularly in high transmission settings. We use molecular markers and amplicon sequencing to characterize post-treatment stage-specific malaria parasite dynamics during a 42 day randomized trial of 3- versus 5 day artemether-lumefantrine in 303 children with and without HIV (ClinicalTrials.gov number NCT03453840). The prevalence of parasite-derived 18S rRNA is >70% in children throughout follow-up, and the ring-stage marker SBP1 is detectable in over 15% of children on day 14 despite effective treatment. We find that the extended regimen significantly lowers the risk of recurrent ring-stage parasitemia compared to the standard 3 day regimen, and that higher day 7 lumefantrine concentrations decrease the probability of ring-stage parasites in the early post-treatment period. Longitudinal amplicon sequencing reveals remarkably dynamic patterns of multiclonal infections that include new and persistent clones in both the early post-treatment and later time periods. Our data indicate that post-treatment parasite dynamics are highly complex despite efficacious therapy, findings that will inform strategies to optimize regimens in the face of emerging partial artemisinin resistance in Africa.

Over three-quarters of Earth's surface exhibits extreme environments where life thrives under harsh physicochemical conditions. While prokaryotes have often been investigated in these environments, only recent studies have revealed the remarkable adaptability of eukaryotes, in particular fungi. This study explored the mycobiota of two meromictic hypersaline lakes, Ursu and Fără Fund, in Transylvania (Romania). The intrinsic and extrinsic fungal diversity was assessed using amplicon sequencing of environmental DNA samples from sediments, water columns, surrounding soils, and an associated rivulet. The fungal communities, illustrated by the 18S rRNA gene and ITS2 region, exhibited contrasting patterns between the lakes. The ITS2 region assessed better than the 18S rRNA gene the fungal diversity. The ITS2 data showed that Ascomycota was the most abundant fungal group identified in both lakes, followed by Aphelidiomycota, Chytridiomycota, and Basidiomycota. Despite similar α-diversity levels, significant differences in fungal community structure were observed between the lakes, correlated with salinity, total organic carbon, total nitrogen, and ammonium. Taxonomic profiling revealed depth-specific variations, with Saccharomycetes prevalent in Ursu Lake's deeper layers and Lecanoromycetes prevalent in the Fără Fund Lake. The functional annotation using FungalTraits revealed diverse ecological roles within the fungal communities. Lichenized fungi were dominant in Fără Fund Lake, while saprotrophs were abundant in Ursu Lake. Additionally, wood and soil saprotrophs, along with plant pathogens, were more prevalent in the surrounding soils, rivulet, and surface water layers. A global overview of the trophic relations in each studied niche was impossible to establish due to the unconnected graphs corresponding to the trophic interactions of the analyzed fungi. Plotting the unweighted connected subgraphs at the genus level suggests that salinity made the studied niches similar for the identified taxa. This study shed light on the understudied fungal diversity, distribution, and ecological functions in hypersaline environments. [ABSTRACT FROM AUTHOR]

Nematode surveys in natural environments in the Iberian Peninsula detected three unidentified Xenocriconemella populations that closely resembled the X. macrodora-species complex, but utilization of integrative taxonomy confirmed that they comprised a new taxon described in this paper as X. andreae sp. nov. Only females were detected in the new species (considered parthenogenetic) and delineated with a bare body (274–353 µm); lip region with two annuli, continuous with body delineation; second lip annulus enclosed by the first one. Flexible and thin stylet (88.0–99.0 µm), representing 30.4–47.8% of total body length. The excretory pore is positioned 2–3 annuli posterior to the level of stylet knobs, at 101.5 (87–107) µm from the lip region. Female genital tract: monodelphic, prodelphic, large, and representing 34.4–52.4% of the body length; vagina slightly ventrally curved. The anus is located at (6–9) annuli from the rear end. Tail short, conoid, and blunt round terminus. Ribosomal and mitochondrial markers (D2-D3 expansion domains of 28S, ITS , partial 18S rRNA, and COI), as well as molecular phylogenetic analyses of sequences, confirmed this new taxon, and it was clearly delineated from X. macrodora and species within the species complex (X. costaricense, X. iberica, X. paraiberica, and X. pradense). [ABSTRACT FROM AUTHOR]

Research voyages onboard RV ‘Investigator’ in 2021 (IN2021_V08) and 2022 (IN2022_V04) sampled benthic communities of seamounts off Christmas Island and Cocos (Keeling) Islands, also known as Indian Ocean Australian Territories (IOT). Over 150 specimens of the family Serpulidae collected during the voyages were deposited in the Australian Museum. The animals belonged to the filogranin genera Apomatus, Bathyvermilia, Bathyvermiloides gen. nov., Filogranula, and Protis, as well as to serpulin genera Hyalopomatus, Placostegus and Vitreotubus. In total, 12 species were identified, including three named, but very poorly known serpulids Bathyvermilia challengeri, Filogranula stellata, and Vitreotubus digeromimoi. Nine species Apomatus nishii n. sp., Bathyvermilia rolandobastidai n. sp., Bathyvermiloides juliebrockae n. sp., Protis melmackenzieae n. sp., Protis perneti n. sp., Hyalopomatus nogueirai n. sp., Hyalopomatus rossanae n. sp., Hyalopomatus suelindsayae n. sp., and Placostegus leslieharrisae n. sp. were described. All species descriptions are accompanied by DNA sequence data and their phylogenetic positions in the family Serpulidae have been assessed.

Abstract Background Trichuris spp. (whipworms) are soil-transmitted helminths distributed worldwide, parasitizing several mammalian hosts such as ruminants, primates, and rodents. Trichuris spp. is one of the most common intestinal parasites affecting both humans and animals, and it can spread directly through the fecal-oral route, resulting in severe illness and financial loss. So, this work aims to detect the frequency of Trichuris spp. in camels in Beheira Governorate, Egypt, and to identify Trichuris spp. through morphometrical studies, molecular analysis, and phylogenetic analysis. Results A total of 35 dromedaries out of 127 investigated had Trichuris spp. infection, meaning that the overall prevalence was 27.56%. The age of the camel affected the infection rate, older animals (> 5 years) having a higher prevalence of infection (24%) than animals of ages ( autumn (28.13%) > spring (25.8%) > winter (25%) indicating year-round infection. T. globulosa was identified morphometrically from camels in Beheira Governorate, Egypt. The BLAST analysis revealed the presence of T. globulosa isolate from camels using the Genbank database depending on nuclear small subunit ribosomal RNA (18s) and cytochrome b (Cytb) genes. Conclusion A high prevalence of T. globulosa was found in camels in Beheira Governorate, Egypt. This is the first report to confirm the identification of T. globulosa from camel based on morphometrical studies and molecular and phylogenetic analysis in Egypt. More thorough studies on the incidence, molecular, and genetic analysis of Trichuris spp. in Egypt are required in addition to camel control programs.

Summary: A new species, Pratylenchus platyceriumis sp. n., was intercepted in the roots and rhizosphere of Platycerium spp. imported from Thailand. It is characterised by sexual adults with lip region containing two annuli, the lateral field with four equidistant lines, partially areolated, the female stylet (16.5-18.7 μ m) robust with broadly rounded knobs, V = (70.2-79.2), with a large oval spermatheca often full of sperm, tail subcylindrical to conoid, and terminus obliquely truncated to conical with variable mucrons or projections. Male spicules are arch-shaped, the gubernaculum trough-shaped, the tail conoid, with tip narrow and pointed and bursa striated instead of crenate. The new species is close to Pratylenchus coffeae , P. dakotaensis , P. goodeyi , P. gutierrezi , P. horti , P. morettoi , P. okinawaensis , P. panamaensis , P. pratensis , P. pseudocoffeae , P. speijeri , P. yamagutii and P. ventroprojectus , but different. Phylogenetic analyses using D2-D3 expansion domains of the 28S rRNA gene, the ITS region, the partial 18S rRNA gene and the mitochondrial cytochrome oxidase subunit I (COI) gene confirm its classification as a new species. [ABSTRACT FROM AUTHOR]

Food fraud is a problematic yet common phenomenon in the food industry. It impacts numerous sectors, including the market of edible mushrooms. Morel mushrooms are prized worldwide for their culinary and medicinal use. They represent a taxonomically complex group in which food fraud has already been reported. Among the methods to evaluate food fraud, some rely on comparisons of genetic sequences obtained from a sample to existing databases. However, the quality and usefulness of the results are limited by the type of comparison tool and the quality of the database used. The Centroid‐based approach is applied by SmartGene in a proprietary artificial intelligence‐based method for the generation of automatically curated reference databases that can be further expert curated. In this study, using sequences of the ribosomal internal transcribed spacer (ITS) of the genus Morchella (true morels), we compared this approach to the traditional pairwise alignment tool using two other databases: UNITE and Mycobank (MLST). The Centroid‐based approach using an expert‐curated database was more performant for the identification of 53 representative ITS sequences corresponding to validated species (83% accuracy, compared to 36% and 47% accuracy for UNITE and MLST, respectively). The Centroid method also revealed an inaccurate taxonomic annotation for sequences of commercial cultivars submitted to public databases. Combined with the web‐based commercial software IDNS® available at Smartgene, the Centroid‐based approach constitutes a valuable tool to ensure the quality of morel products on the market for actors of the food industry. Practical Application: The Centroid‐based approach can be used by agri‐food actors who need to identify true morels down to the species level without any prior taxonomical knowledge. These include routine laboratories of the food industry, food distributors, and public surveillance agencies. This is a reliable method that requires minimal skills and resources, therefore being particularly adapted for nonspecialists. [ABSTRACT FROM AUTHOR]

Background: Trichuris spp. (whipworms) are soil-transmitted helminths distributed worldwide, parasitizing several mammalian hosts such as ruminants, primates, and rodents. Trichuris spp. is one of the most common intestinal parasites affecting both humans and animals, and it can spread directly through the fecal-oral route, resulting in severe illness and financial loss. So, this work aims to detect the frequency of Trichuris spp. in camels in Beheira Governorate, Egypt, and to identify Trichuris spp. through morphometrical studies, molecular analysis, and phylogenetic analysis. Results: A total of 35 dromedaries out of 127 investigated had Trichuris spp. infection, meaning that the overall prevalence was 27.56%. The age of the camel affected the infection rate, older animals (> 5 years) having a higher prevalence of infection (24%) than animals of ages (< 3 years) (20%) than animals of ages (3–5 years) (19.14%). According to season: Trichuris spp. showed a unique pattern in camels in different seasons: summer (31.25%) > autumn (28.13%) > spring (25.8%) > winter (25%) indicating year-round infection. T. globulosa was identified morphometrically from camels in Beheira Governorate, Egypt. The BLAST analysis revealed the presence of T. globulosa isolate from camels using the Genbank database depending on nuclear small subunit ribosomal RNA (18s) and cytochrome b (Cytb) genes. Conclusion: A high prevalence of T. globulosa was found in camels in Beheira Governorate, Egypt. This is the first report to confirm the identification of T. globulosa from camel based on morphometrical studies and molecular and phylogenetic analysis in Egypt. More thorough studies on the incidence, molecular, and genetic analysis of Trichuris spp. in Egypt are required in addition to camel control programs. [ABSTRACT FROM AUTHOR]

Summary: Four criconematid populations were uncovered in three avocado orchards in Homestead region, Miami-Dade County, Florida, USA, with three of them in relatively high densities. Two of the populations were identified as Criconema mutabile (Taylor, 1936) Raski & Luc, 1985 and Mesocriconema basili (Jairajpuri, 1964) Loof & De Grisse, 1989, whereas the other two populations were identified as Criconemoides sp. and Ogma sp. The identification of the nematodes was based on morphological analysis and C. mutabile was also confirmed based on the 28S rRNA gene. The molecular data of M. basili (18S and 28S rRNA genes) are presented for the first time and phylogenetic trees based on the genes are provided illustrating the relationships of M. basili with other criconematid species. This study further reports the presence of C. mutabile and M. basili for the first time in Florida, USA, and the association of the latter species with avocado rhizosphere. [ABSTRACT FROM AUTHOR]

Se reportan nuevos registros de zooplancton en el Pacífico tropical mexicano, con un énfasis particular en apendicularias. Las muestras se recolectaron entre enero de 2023 y junio de 2024 en diversas localidades utilizando redes de plancton, así como técnicas de ADN ambiental y filogenia molecular para la identificación precisa de ciertas especies. Se determinó un total de 12 nuevos registros para el Pacífico mexicano y tres registros específicos en ciertas áreas, incluyendo especies de los géneros Pseudevadne, Penilia, Appendicularia, Fritillaria y Oikopleura. Entre los hallazgos, destaca la primera caracterización molecular de Oikopleura dioica en México, revelando alta similitud genética con poblaciones japonesas, lo que subraya la distribución compartida entre la parte nororiental y noroccidental del Océano Pacífico. El nuevo registro de dos subespecies del género Fritillaria para México y el hallazgo de preferencias entre aguas oceánicas y costeras de los géneros Oikolpeura y Fritillaria. Este estudio no solo amplía el conocimiento sobre la riqueza y distribución de estos organismos en el Pacífico tropical mexicano, también proporciona una base sólida para futuras investigaciones en taxonomía, ecología y biogeografía de apendicularias y otros zoopláncteres, así como enfatizar en las posibles limitantes en el conocimiento de estos grupos. Los resultados obtenidos subrayan la necesidad de realizar estudios específicos con mayor esfuerzo de muestreo en diferentes escalas espaciales y temporales para entender mejor la biodiversidad marina de esta región. Asimismo, se recomienda el uso de técnicas moleculares para mejorar la precisión en la identificación y comprensión de la dinámica de las comunidades zooplanctónicas.

Ribosome biogenesis is essential for protein synthesis in gene expression. Yeast eIF5B has been shown biochemically to facilitate 18S ribosomal RNA (rRNA) 3 end maturation during late-stage 40S ribosomal subunit assembly and gate the transition from translation initiation to elongation. But the genome-wide effects of eIF5B have not been studied at the single-nucleotide resolution in any organism, and 18S rRNA 3 end maturation is poorly understood in plants. Arabidopsis HOT3/eIF5B1 was found to promote development and heat stress acclimation by translational regulation, but its molecular function remained unknown. Here, we show that HOT3 is a late-stage ribosome biogenesis factor that facilitates 18S rRNA 3 end processing and is a translation initiation factor that globally impacts the transition from initiation to elongation. By developing and implementing 18S-ENDseq, we revealed previously unknown events in 18S rRNA 3 end maturation or metabolism. We quantitatively defined processing hotspots and identified adenylation as the prevalent nontemplated RNA addition at the 3 ends of pre-18S rRNAs. Aberrant 18S rRNA maturation in hot3 further activated RNA interference to generate RDR1- and DCL2/4-dependent risiRNAs mainly from a 3 portion of 18S rRNA. We further showed that risiRNAs in hot3 were predominantly localized in ribosome-free fractions and were not responsible for the 18S rRNA maturation or translation initiation defects in hot3. Our study uncovered the molecular function of HOT3/eIF5B1 in 18S rRNA maturation at the late 40S assembly stage and revealed the regulatory crosstalk among ribosome biogenesis, messenger RNA (mRNA) translation initiation, and siRNA biogenesis in plants.

Nematodes play a vital ecological role in soil and marine ecosystems, but there is limited information about their dietary diversity and feeding habits. Due to methodological challenges, the available information is based on inference rather than confirmed observations. The lack of correct dietary requirements also hampers rearing experiments. To achieve insight into the prey of mononchid nematodes, this study employed high-throughput Illumina paired-end sequencing using universal eukaryotic species 18S primers on 10 pooled mononchid nematode species, namely Mylonchulus brachyuris, M. brevicaudatus, Mylonchulus sp., Clarkus parvus, Prionchulus sp. M. hawaiiensis, M. sigmaturellus, M. vulvapapillatus, Anatonchus sp. and Miconchus sp. The results indicate that mononchids are associated with a remarkable diversity of eukaryotes, including fungi, algae, and protists. While the metabarcoding approach, first introduced here for mononchids, proved to be a simple and rapid method, it has several limitations and crucial methodological challenges that should be addressed in future studies. Ultimately, such methods should be able to evaluate the dietary complexity of nematodes and provide a valuable avenue for unraveling the dietary requirements of previously unculturable nematodes. This can contribute to the methodology of understanding their feeding habits and contributions to ecosystem dynamics.

BackgroundWe have previously found that, in the pathogenic yeast Candida albicans, 18S and 25S ribosomal RNA components, containing more than one phosphate on their 5'-end were resistant to 5'-monophosphate requiring 5' → 3″ exonuclease. Several lines of evidence pointed to RNAP II as the enzyme producing them.ResultsWe now show the production of such 18S and 25S rRNAs in Saccharomyces cerevisiae that have been permanently switched to RNAP II (due to deletion of part of RNAP I upstream activator alone, or in combination with deletion of one component of RNAP I itself). They contain more than one phosphate at their 5'-end and an anti-cap specific antibody binds to them indicating capping of these molecules. These molecules are found in RNA isolated from nuclei, therefore are unlikely to have been modified in the cytoplasm.ConclusionsOur data confirm the existence of such molecules and firmly establish RNAP II playing a role in their production. The fact that we see these molecules in wild type Saccharomyces cerevisiae indicates that they are not only a result of mutations but are part of the cells physiology. This adds another way RNAP II is involved in ribosome production in addition to their role in the production of ribosome associated proteins.

The study of the epitranscriptome has thus far focused largely on mRNA methylation. Recent human genetics studies suggest that methylation of ribosomal RNA also contributes to brain development and cognition. In particular, the m6A modification at the A-1832 position of the 18S rRNA is installed by METTL5. Mutations or deletions of Mettl5 in humans and mice, respectively, cause abnormal translation and gene expression that in turn mediates stem cell behaviors such as differentiation. In this review, we provide an overview of the current knowledge of the methyltransferase METTL5, as well as the molecular biology surrounding m6A on rRNA and how it regulates cell behavior.

Pratylenchus penetrans is one of the world’s most common and destructive root-lesion nematodes and can parasitize more than 400 plant species. P. penetrans has been reported to cause serious damage to artichokes in several countries, such as Greece, Brazil, and France. Until now, there have been no reports of P. penetrans associated with artichokes in Vietnam. In this study, we recorded this species in artichoke fields in Lam Dong province, Vietnam with an average density of 50 nematodes/100g of soil (frequency of appearance at 64.7%). This nematode was associated with symptoms such as yellowing leaves, stunt, and root necrosis of artichokes in Vietnam, indicating its high damaging potential and a need for suitable control strategies. The identification of this species in our study was confirmed by morphology, morphometric data, and molecular characterization of 18S and 28S rRNA regions. Our study also provides the first molecular data of P. penetrans in Vietnam. The inclusion of molecular data for P. penetrans in Vietnam represents a significant contribution to the scientific community and a pivotal advancement in addressing nematode-related challenges in agriculture. This dataset serves as an invaluable reference for various molecular-focused endeavors, including but not limited to molecular identification, pathogenicity studies, and the development of effective management strategies.

Hemiurid digeneans conspecific with Stomachicola muraenesocis Yamaguti, 1934 (the type species of the genus Stomachicola Yamaguti, 1934) were collected from the stomach of the daggertooth pike conger Muraenesox cinereus (Forsskål) off the Persian Gulf of Iran. This study aimed to provide a detailed characterization of Stom. muraenesocis, including measurements, illustrations and scanning electron microscopy (s.e.m.) representations. Comparisons with the original and previous descriptions revealed morphological and metrical variations in several features (i.e. body size and shape, arrangement of reproductive organs, soma to ecsoma length ratio, position of genital opening, number of vitelline tubules and extension of uterine coils) between Stom. muraenesocis from different hosts and localities. This study presents the first molecular sequence data associated with the small (18S) and large (28S) subunit nuclear ribosomal RNA genes (rDNA) for Stom. muraenesocis. Phylogenetic analyses of the 18S dataset placed Stom. muraenesocis as sister lineage to a clade formed of a group of species of Lecithaster Lühe, 1901 (Lecithasteridae Odhner, 1905). In contrast, phylogenetic analyses based on the 28S consistently recovered a sister relationship between Stom. muraenesocis and representatives of the Hemiuridae Looss, 1899. Further comprehensive phylogenetically based classification in light of morphology and taxonomic history of the Hemiuridae and Lecithasteridae is required to infer phylogenetic affinities and historical biogeography of Stomachicola. A comprehensive list of previously reported species of Stomachicola together with their associated hosts, localities and morphometric data is provided.

Specimens of the sandhopper Orchestoidea tuberculata (Amphipoda; Talitridae) collected from sandy beaches in south-central Chile, were found to be parasitized by juvenile mermithids, constituting the first record of a mermithid infecting a marine amphipod in Chile. A morphological description of juveniles is provided. Sequence analyses based on mitochondrial COI and nuclear 18S rDNA of the mermithids showed extremely low genetic variation. Phylogenetic analyses indicate that the mermithid is more closely related to Hexamermis agrotis, which parasitize Coleoptera, than to Thaumamermis zealandica, which parasitizes New Zealand confamilial talitrid amphipods.

Acrospermales represent one of the least studied lineages of Dothideomycetes and are characterized by diverse ecological strategies, including saprotrophic, epiphytic, fungicolous, lichenicolous, and bryophilous lifestyles. The order is composed of two teleomorphic genera, Acrospermum and Oomyces, and five anamorphic genera of unclear relationships. The objectives of the study were to establish the phylogenetic position of Acrospermum species collected from lichens in the tropical forest of Bolivia and to infer the evolution of the lichenicolous lifestyle in Acrospermales. Our results reveal that the examined specimens from Bolivia represent a new species, A. bolivianum, which is well characterized by its phylogenetic distinctness, morphological characteristics, and host selection. The new species is the first lichenicolous member of Acrospermum and forms a well-supported clade sister to the bryophilous Acrospermum adeanum. The evolution of lifestyles, concluded by phylogenetic analyses and ancestral state reconstructions, indicated that the saprotrophic lifestyle is ancestral to Acrospermales. This corresponds to their close relationship to other saprotrophic lineages of Dothideomycetes and indicates that the wide spectrum of nutritional strategies, currently observed in Acrospermales, may be a result of more recent shifts in their ecology. Our results also suggest that the lichenicolous lifestyle in Acrospermales appeared independently at least two times. Lichenicolous species are represented in our data set by Acrospermum bolivianum and Gonatophragmium physciae, which evolved from lichenicolous and plant-parasite ancestors, respectively. The genus Oomyces, represented by O. carneoalbus, was included for the first time in the phylogenetic analysis and showed a sister relationship to the remaining taxa of Acrospermales. [ABSTRACT FROM AUTHOR]

Tardigrades are rarely included in large biodiversity surveys, mainly because of the impracticalities that follow larger sampling and identification of these microscopic animals. Consequently, there is a lack of data on their biogeographical distribution. Here, we analyse environmental DNA sequences of eutardigrades obtained with a metabarcoding protocol on Danish soil samples collected during a national biodiversity project (Biowide). Specifically, we aimed to investigate the applicability of the V4 region (~400 bp) of the 18S rRNA marker gene to assign taxonomy to 96 eutardigrade molecular operational taxonomic units (MOTUs), using three different methods (alignment-, tree- and phylogeny-based methods). Tardigrade reference libraries are currently suffering from insufficient taxon coverage, in some cases challenging the interpretation of data based on similarity searches. This can, to some extent, be accounted for by supplementing identification with algorithms that incorporate a backbone phylogeny and infer models of evolution. Together, the present findings suggest that the V4 region of the 18S rRNA gene offers a promising tool to identify unknown MOTUs of eutardigrades to genus or family level and can, in some cases, be used to assign to species level. [ABSTRACT FROM AUTHOR]

Two known species of the genus Sporonchulus, namely S. ibitiensis and S. vagabundus, collected from natural areas of Vietnam, are characterized, including descriptions and illustrations of both species, as well as SEM observations and molecular (18S-, 28S rDNA) analyses of S. ibitiensis. The identity of the two species is discussed, with detailed comparison with previously known populations. The taxonomy of the genus is updated, presenting a diagnosis, list of species, key to their identification, and a compendium of their main morphometrics. An integrative analysis, combining morphological data with a cladistic approach and the first molecular study for a representative of Sporonchulus, better supports a narrow relationship of this genus with Mononchidae than with Mylonchulidae members, however further research should be conducted to elucidate its phylogeny. [ABSTRACT FROM AUTHOR]

Ivanovcestus yakiae gen. et sp. nov. was collected from specimens of the batoid Sympterygia bonapartii from waters off Río Negro and Buenos Aires Provinces, in the Argentine Sea. Ivanovcestus gen. nov. is assigned to the Rhinebothriidea for their possession of facially loculated bothridia borne on stalks and a cirrus covered by spinitriches. The new genus is unique in the arrangement of loculi and septa on the distal bothridial surface. The molecular analysis based on 18S and 28S rDNA of two specimens of the new species identified Ivanovcestus gen. nov. as a member of the family Escherbothriidae, with our study representing the first record of this family in the Argentine Sea. The proposed new genus requires a new amended diagnosis for the Escherbothriidae, to include a new pattern of loculi and septa for the distal bothridial surface, as well as a new host. In addition, the present study proposes to transfer two species of Rhinebothrium , originally described parasitizing the skate Sympterygia lima in the Chilean Sea (i.e., Rhinebothrium chilensis and Rhinebothrium leiblei), to Ivanovcestus gen. nov. Examination of the original descriptions and type material revealed several morphological characters that justify the relocation of both species to the new genus. [ABSTRACT FROM AUTHOR]

The spread of nonindigenous species by shipping is a large and growing global problem that harms coastal ecosystems and economies and may blur coastal biogeographical patterns. This study coupled eukaryotic environmental DNA (eDNA) metabarcoding with dissimilarity regression to test the hypothesis that ship‐borne species spread homogenizes port communities. We first collected and metabarcoded water samples from ports in Europe, Asia, Australia and the Americas. We then calculated community dissimilarities between port pairs and tested for effects of environmental dissimilarity, biogeographical region and four alternative measures of ship‐borne species transport risk. We predicted that higher shipping between ports would decrease community dissimilarity, that the effect of shipping would be small compared to that of environment dissimilarity and shared biogeography, and that more complex shipping risk metrics (which account for ballast water and stepping‐stone spread) would perform better. Consistent with our hypotheses, community dissimilarities increased significantly with environmental dissimilarity and, to a lesser extent, decreased with ship‐borne species transport risks, particularly if the ports had similar environments and stepping‐stone risks were considered. Unexpectedly, we found no clear effect of shared biogeography, and that risk metrics incorporating estimates of ballast discharge did not offer more explanatory power than simpler traffic‐based risks. Overall, we found that shipping homogenizes eukaryotic communities between ports in predictable ways, which could inform improvements in invasive species policy and management. We demonstrated the usefulness of eDNA metabarcoding and dissimilarity regression for disentangling the drivers of large‐scale biodiversity patterns. We conclude by outlining logistical considerations and recommendations for future studies using this approach. [ABSTRACT FROM AUTHOR]

Specimens of the sandhopper Orchestoidea tuberculata (Amphipoda; Talitridae) collected from sandy beaches in south-central Chile, were found to be parasitized by juvenile mermithids, constituting the first record of a mermithid infecting a marine amphipod in Chile. A morphological description of juveniles is provided. Sequence analyses based on mitochondrial COI and nuclear 18S rDNA of the mermithids showed extremely low genetic variation. Phylogenetic analyses indicate that the mermithid is more closely related to Hexamermis agrotis , which parasitize Coleoptera, than to Thaumamermis zealandica , which parasitizes New Zealand confamilial talitrid amphipods. [Display omitted] • First record of a mermithid infecting a semiterrestrial amphipod in Chile. • Sandhopper Orchestoidea tuberculata were found parasitized by juvenile mermithids. • Sequences analyzed by COI and 18S showed extremely low genetic variation. • Phylogenetic analyses indicate that the mermithid is close to parasites that inhabit in Coleoptera than those which parasitized to confamilial talitrids. [ABSTRACT FROM AUTHOR]

High-throughput amplicon sequencing of nematode communities has the potential to increase our understanding of nematode community ecology. A current constraint to the widespread implementation of amplicon sequencing is the lack of sequence databases with consistent taxonomic naming schemes. Focusing on 18S sequence data, we developed NemaTaxa, a manually curated database that can be used with QIIME and mothur analysis platforms. Nematode 18S sequence data were downloaded from NCBI, from which both Nematoda universal primers NF1 and 18Sr2b aligned. Taxonomic strings were trimmed to include only classical Linnaean lineages to genera within Nematoda; incomplete Linnaean lineages were corrected. NemaTaxa was compared with other available databases (specifically, PR2 and Silva v132) available for mothur, by comparing nematode taxonomic assignment of nematode communities collected from Oregon, Idaho, and Washington potato cropping systems. In general, NemaTaxa performed similar to PR2 in the number of contigs assigned to Nematoda. NemaTaxa resolves classification at the genus, family, and order levels while PR2 always has a portion of sequences assigned at the class level due to incomplete taxonomic strings. For example, only a small proportion of contigs (0 to 0.4%) for Chromadorea and Enoplea were unclassified using NemaTaxa compared with 5 to 80% for PR2. The Silva v132 database available in mothur is of limited use because of the greatly reduced number of nematode sequences available in the database, making classification only possible to the level of order. NemaTaxa offers an “off-the-shelf” database that can be used by nonexperts in nematology wanting to explore nematode community ecology and, therefore, will allow for inclusion of nematodes in soil ecology studies that employ amplicon sequencing for other organisms such as fungi and bacteria.

The northern Adriatic is characterised as the coldest and most productive marine area of the Mediterranean, which is due to high nutrient levels introduced by river discharges, the largest of which is the Italian Po River (at the same time also the largest freshwater input into the Mediterranean). The northern Adriatic is a very shallow marine ecosystem with ocean current patterns that result in long retention times of plankton in the area. The northern Adriatic phytoplankton biodiversity and abundance are well-studied, through many scientific and long-term monitoring reports. These datasets were based on phytoplankton morphological traits traditionally obtained with light microscopy. The most recent comprehensive eastern Adriatic phytoplankton checklist was published more than 20 years ago and is still valuable today. Since phytoplankton taxonomy and systematics are constantly being reviewed (partly also due to new molecular methods of species identification that complement classical methodologies), checklists need to be updated and complemented. Today, metabarcoding of molecular markers gains more and more importance in biodiversity research and monitoring. Here, we report the use of high throughput sequencing methods to re-examine taxonomic richness and provide updated knowledge of phytoplankton diversity in the eastern northern Adriatic to complement the standardised light microscopy method.This study aimed to report an up-to-date list of the phytoplankton taxonomic richness and phylogenetic relationships in the eastern northern Adriatic, based on sequence variability of barcoding genes resolved with advanced molecular tools, namely metabarcoding. Here, metabarcoding is used to complement standardised light microscopy to advance conventional monitoring and research of phytoplankton communities for the purpose of assessing biodiversity and the status of the marine environments. Monthly two-year net sampling targeted six phytoplankton groups including Bacillariophyceae (diatoms) and Chrysophyceae (golden algae) belonging to Ochrophyta, Dinophyceae (dinoflagellates), Cryptophyceae (cryptophytes), Haptophyta (mostly coccolithophorids) and Chlorophyta with Prasinophyceae (prasinophytes) and Chlorophyceae (protist green algae). Generated sequence data were taxonomically assigned and redistributed in two kingdoms, five classes, 32 orders, 49 families and 67 genera. The most diverse group were dinoflagellates, comprising of 34 found genera (48.3%), following by diatoms with 23 (35.4%) and coccolithophorids with three genera (4.0%). In terms of genetic diversity, results were a bit different: a great majority of sequences with one nucleotide tolerance (ASVs, Amplicon sequence variants) assigned to species or genus level were dinoflagellates (83.8%), 13.7% diatoms and 1.6% Chlorophyta, respectively. Although many taxa have not been detected that have been considered as common in this area, metabarcoding revealed five diatoms and 20 dinoflagellate genera that were not reported in previous checklists, along with a few species from other targeted groups that have been reported previously. We here describe the first comprehensive 18S metabarcode inventory for the northern Adriatic Sea.

Eukaryotic phytoplankton are responsible for at least 20% of annual global carbon fixation. Their diversity and activity are shaped by interactions with prokaryotes as part of complex microbiomes. Although differences in their local species diversity have been estimated, we still have a limited understanding of environmental conditions responsible for compositional differences between local species communities on a large scale from pole to pole. Here, we show, based on pole-to-pole phytoplankton metatranscriptomes and microbial rDNA sequencing, that environmental differences between polar and non-polar upper oceans most strongly impact the large-scale spatial pattern of biodiversity and gene activity in algal microbiomes. The geographic differentiation of co-occurring microbes in algal microbiomes can be well explained by the latitudinal temperature gradient and associated break points in their beta diversity, with an average breakpoint at 14 °C ± 4.3, separating cold and warm upper oceans. As global warming impacts upper ocean temperatures, we project that break points of beta diversity move markedly pole-wards. Hence, abrupt regime shifts in algal microbiomes could be caused by anthropogenic climate change.

Abstract Background Previous flatworm phylogenetic research has been carried out analysing 18S and 28S DNA markers. Through this methodology, Mariplanellinae subfamily has been recently re-classified as Mariplanellida status novus. This new classification implied that 3 genera belonged to Mariplanellida: Mariplanella, Lonchoplanella and Poseidoplanella. In this study, we aim to clarify some of the relationships within Rhabdocoela analysing 18S and 28S DNA markers of a total of 91 species through Maximum Likelihood and Bayesian Inference methodologies. A total of 11 species and genera, including Lonchoplanella, from the island of Sylt are included and had not previously been involved in any molecular phylogenetic analyses. Results Our phylogenetic results support Mariplanellida as an independent group within Rhabdocoela and its status as an infraorder. Our study suggests that Lonchoplanella axi belongs to Mariplanellida. Within Rhabdocoela, Haloplanella longatuba is nested within Thalassotyphloplanida, instead of Limnotyphloplanida. Within Kalyptorhynchia, the taxon Eukalyptorhynchia turned out to be paraphyletic including members of Schizorhynchia. These results also support the position of the genus Toia separate from Cicerinidae. Conclusions Lonchoplanella axi belongs to Mariplanellida, whose status as infraorder is herein confirmed. The genus Toia belongs separate from Cicerinidae. Further research is needed to clarify the phylogenetic relationships of Hoploplanella. Most of the species, genera and families included in this study with more than one terminal are monophyletic and well supported. Adding gene markers and complementary morphological studies will help to clarify those relationships that remain uncertain.

Background: The northern Adriatic is characterised as the coldest and most productive marine area of the Mediterranean, which is due to high nutrient levels introduced by river discharges, the largest of which is the Italian Po River (at the same time also the largest freshwater input into the Mediterranean). The northern Adriatic is a very shallow marine ecosystem with ocean current patterns that result in long retention times of plankton in the area. The northern Adriatic phytoplankton biodiversity and abundance are well-studied, through many scientific and long-term monitoring reports. These datasets were based on phytoplankton morphological traits traditionally obtained with light microscopy. The most recent comprehensive eastern Adriatic phytoplankton checklist was published more than 20 years ago and is still valuable today. Since phytoplankton taxonomy and systematics are constantly being reviewed (partly also due to new molecular methods of species identification that complement classical methodologies), checklists need to be updated and complemented. Today, metabarcoding of molecular markers gains more and more importance in biodiversity research and monitoring. Here, we report the use of high throughput sequencing methods to re-examine taxonomic richness and provide updated knowledge of phytoplankton diversity in the eastern northern Adriatic to complement the standardised light microscopy method. New information: This study aimed to report an up-to-date list of the phytoplankton taxonomic richness and phylogenetic relationships in the eastern northern Adriatic, based on sequence variability of barcoding genes resolved with advanced molecular tools, namely metabarcoding. Here, metabarcoding is used to complement standardised light microscopy to advance conventional monitoring and research of phytoplankton communities for the purpose of assessing biodiversity and the status of the marine environments. Monthly two-year net sampling targeted six phytoplankton groups including Bacillariophyceae (diatoms) and Chrysophyceae (golden algae) belonging to Ochrophyta, Dinophyceae (dinoflagellates), Cryptophyceae (cryptophytes), Haptophyta (mostly coccolithophorids) and Chlorophyta with Prasinophyceae (prasinophytes) and Chlorophyceae (protist green algae). Generated sequence data were taxonomically assigned and redistributed in two kingdoms, five classes, 32 orders, 49 families and 67 genera. The most diverse group were dinoflagellates, comprising of 34 found genera (48.3%), following by diatoms with 23 (35.4%) and coccolithophorids with three genera (4.0%). In terms of genetic diversity, results were a bit different: a great majority of sequences with one nucleotide tolerance (ASVs, Amplicon sequence variants) assigned to species or genus level were dinoflagellates (83.8%), 13.7% diatoms and 1.6% Chlorophyta, respectively. Although many taxa have not been detected that have been considered as common in this area, metabarcoding revealed five diatoms and 20 dinoflagellate genera that were not reported in previous checklists, along with a few species from other targeted groups that have been reported previously. We here describe the first comprehensive 18S metabarcode inventory for the northern Adriatic Sea. [ABSTRACT FROM AUTHOR]

The gut microbiome is a microbial ecosystem which expresses 100 times more genes than the human host and plays an essential role in human health and disease pathogenesis. Since most intestinal microbial species are difficult to culture, next generation sequencing technologies have been widely applied to study the gut microbiome, including 16S rRNA, 18S rRNA, internal transcribed spacer (ITS) sequencing, shotgun metagenomic sequencing, metatranscriptomic sequencing and viromic sequencing. Various software tools were developed to analyze different sequencing data. In this review, we summarize commonly used computational tools for gut microbiome data analysis, which extended our understanding of the gut microbiome in health and diseases.

In May–June 2017 an expedition on board RV Investigator sampled benthic communities along the lower slope and abyss of Australia’s eastern margin from off mid-Tasmania to the Coral Sea. Over 200 annelids of the family Serpulidae collected during the voyage were collected and deposited in the Australian Museum in Sydney. Among them there was a new species of the poorly known abyssal (3754–4378 m) genus Spirodiscus. Serpulids typically build cylindrical calcareous tubes attached to hard substrates. Until now, only three serpulid species inhabiting free-lying polygonal tubes were reported from the deep sea: Spirodiscus grimaldii Fauvel, 1909 with quadrangular spirally coiled tubes, Bathyditrupa hovei Kupriyanova, 1993 with quadrangular tusk-shaped tubes, and Spirodiscus groenlandicus (McIntosh, 1877) with octagonal tusk-shaped tubes. The new species, S. ottofinamusi sp. nov. has very characteristic thin tusk-shaped unattached fluted tubes similar to those found in S. groenlandicus, but it differs by the details of collar, thoracic tori and abdominal chaetae. Morphologically, it has a pinnulated opercular peduncle and flat geniculate abdominal chaetae like filogranin serpulids but lacks thoracic Apomatus chaetae like serpulins. The first DNA sequences of this mysterious taxon places the new species within the filogranins in sister group relationship with Chitinopoma serrula.

BackgroundWe have previously reported 18S and 25S ribosomal RNA molecules in Candida albicans resistant to processive 5' → 3' exonuclease, appearing as cells approached stationary growth phase. Initial analysis pointed to extra phosphate(s) at their 5'- end raising the possibility that they were newly transcribed. Here we report on additional experiments exploring this possibility and try to establish which of the RNA polymerases may be transcribing them.ResultsOligo-ligation and primer extension again showed the presence of extra phosphate at the 5'-end of the reported processing sites for both 18S and 25S ribosomal RNA components. Inhibition of Pol I with BMH-21 increased the presence of the molecules. Quantitation with an Agilent Bioanalyzer showed that resistant 18S and 25S molecules are primarily produced in the nucleus. Utilizing an RNA cap specific antibody, a signal could be detected on these molecules via immunoblotting; such signal could be eliminated by decapping reaction. Both the cap specific antibody and eIF4E cap-binding protein, increased fold enrichment upon quantitative amplification. Antibodies specific for the RNA Polymerase II c-terminal domain and TFIIB initiator factor showed the presence of Pol II on DNA sequences for both 18S and 25S molecules in chromatin precipitation and qPCR assays. Rapamycin inhibition of TOR complex also resulted in an increase of resistant 18S and 25S molecules.ConclusionsThese data raise the possibility of a role for RNA Polymerase II in the production of 18S and 25S molecules and indicate that efforts for more direct proof may be worthwhile. If definitively proven it will establish an additional role for RNA Polymerase II in ribosomal production.

The DNA taxonomy of six species of the annelid family Lumbrineridae collected from the Clarion-Clipperton Zone (CCZ) in the Central Pacific, an area of potential mining interest for polymetallic nodules, is presented. Lumbrinerids are an ecologically important and understudied annelid family within the deep sea, with many species still undescribed. This study aims to document the taxonomy and biodiversity of the CCZ using specimens collected from the UK-1, OMS, and NORI-D exploration contract areas and Areas of Particular Environmental Interest. Species were identified through a combination of morphological and molecular phylogenetic analysis. We present informal species descriptions associated with voucher specimens, accessible through the Natural History Museum (London) collections, to improve future taxonomic and biodiversity studies of this region. Five taxa in this study had no morphological or genetic matches within the literature and therefore are possibly new to science, but their suboptimal morphological preservation prevented the formalisation of new species. The most abundant taxon Lumbrinerides cf. laubieri (NHM_0020) was compared with the holotype of Lumbrinerides laubieri Miura, 1980 from the deep Northeast Atlantic. Currently no reliable morphological characters separating the Pacific and Atlantic specimens have been found and molecular data from the Atlantic specimens was not available. [ABSTRACT FROM AUTHOR]

Background: Previous flatworm phylogenetic research has been carried out analysing 18S and 28S DNA markers. Through this methodology, Mariplanellinae subfamily has been recently re-classified as Mariplanellida status novus. This new classification implied that 3 genera belonged to Mariplanellida: Mariplanella, Lonchoplanella and Poseidoplanella. In this study, we aim to clarify some of the relationships within Rhabdocoela analysing 18S and 28S DNA markers of a total of 91 species through Maximum Likelihood and Bayesian Inference methodologies. A total of 11 species and genera, including Lonchoplanella, from the island of Sylt are included and had not previously been involved in any molecular phylogenetic analyses. Results: Our phylogenetic results support Mariplanellida as an independent group within Rhabdocoela and its status as an infraorder. Our study suggests that Lonchoplanella axi belongs to Mariplanellida. Within Rhabdocoela, Haloplanella longatuba is nested within Thalassotyphloplanida, instead of Limnotyphloplanida. Within Kalyptorhynchia, the taxon Eukalyptorhynchia turned out to be paraphyletic including members of Schizorhynchia. These results also support the position of the genus Toia separate from Cicerinidae. Conclusions: Lonchoplanella axi belongs to Mariplanellida, whose status as infraorder is herein confirmed. The genus Toia belongs separate from Cicerinidae. Further research is needed to clarify the phylogenetic relationships of Hoploplanella. Most of the species, genera and families included in this study with more than one terminal are monophyletic and well supported. Adding gene markers and complementary morphological studies will help to clarify those relationships that remain uncertain. [ABSTRACT FROM AUTHOR]

In May-June 2017 an expedition on board RV Investigator sampled benthic communities along the lower slope and abyss of Australia's eastern margin from off mid-Tasmania to the Coral Sea. Over 200 annelids of the family Serpulidae collected during the voyage were collected and deposited in the Australian Museum in Sydney. Among them there was a new species of the poorly known abyssal (3754-4378 m) genus Spirodiscus. Serpulids typically build cylindrical calcareous tubes attached to hard substrates. Until now, only three serpulid species inhabiting free-lying polygonal tubes were reported from the deep sea: Spirodiscus grimaldii Fauvel, 1909 with quadrangular spirally coiled tubes, Bathyditrupa hovei Kupriyanova, 1993 with quadrangular tusk-shaped tubes, and Spirodiscus groenlandicus (McIntosh, 1877) with octagonal tusk-shaped tubes. The new species, S. ottofinamusi sp. nov. has very characteristic thin tusk-shaped unattached fluted tubes similar to those found in S. groenlandicus, but it differs by the details of collar, thoracic tori and abdominal chaetae. Morphologically, it has a pinnulated opercular peduncle and flat geniculate abdominal chaetae like filogranin serpulids but lacks thoracic Apomatus chaetae like serpulins. The first DNA sequences of this mysterious taxon places the new species within the filogranins in sister group relationship with Chitinopoma serrula. [ABSTRACT FROM AUTHOR]

X-cells were first described as an unknown cell type in northern hemisphere flatfish in 1969. Almost a decade later they were described in an Antarctic fish, the bald notothen Trematomus borchgrevinki, thus demonstrating their global distribution. Since this time, X-cells from various northern hemisphere fish species and from three other Antarctic fishes, the emerald notothen Trematomus bernacchii, the crowned notothen Trematomus scotti, and the painted notothen Nototheniops larseni have been identified as perkinsozoan parasites of the Family Xcellidae. Currently there are seven X-cell species described within this family. Here we report the morphology of X-cells isolated from the gill filaments of the bald notothen and include details of some of its division forms. Using short-read high-throughput DNA sequencing technology we have sequenced, assembled, and verified a 5347-bp region of the X-cell rRNA repeat unit that includes the complete 18S gene. In all cases, phylogenetic analyses identified this sequence as a distinct taxon and placed it among the perkinsozoan alveolates alongside other previously identified species in the X-cell family. Using a combination of morphological and genetic evidence we now describe a new X-cell genus and species, Cryoxcellia borchgrevinki gen. nov., sp. nov., from McMurdo Sound, Antarctica. [ABSTRACT FROM AUTHOR]

There is growing interest in local elimination of soil-transmitted helminth (STH) infection in endemic settings. In such settings, highly sensitive diagnostics are needed to detect STH infection. We compared double-slide Kato-Katz, the most commonly used copromicroscopic detection method, to multi-parallel quantitative polymerase chain reaction (qPCR) in 2,799 stool samples from children aged 2-12 years in a setting in rural Bangladesh with predominantly low STH infection intensity. We estimated the sensitivity and specificity of each diagnostic using Bayesian latent class analysis. Compared to double-slide Kato-Katz, STH prevalence using qPCR was almost 3-fold higher for hookworm species and nearly 2-fold higher for Trichuris trichiura. Ascaris lumbricoides prevalence was lower using qPCR, and 26% of samples classified as A. lumbricoides positive by Kato-Katz were negative by qPCR. Amplicon sequencing of the 18S rDNA from 10 samples confirmed that A. lumbricoides was absent in samples classified as positive by Kato-Katz and negative by qPCR. The sensitivity of Kato-Katz was 49% for A. lumbricoides, 32% for hookworm, and 52% for T. trichiura; the sensitivity of qPCR was 79% for A. lumbricoides, 93% for hookworm, and 90% for T. trichiura. Specificity was ≥ 97% for both tests for all STH except for Kato-Katz for A. lumbricoides (specificity = 68%). There were moderate negative, monotonic correlations between qPCR cycle quantification values and eggs per gram quantified by Kato-Katz. While it is widely assumed that double-slide Kato-Katz has few false positives, our results indicate otherwise and highlight inherent limitations of the Kato-Katz technique. qPCR had higher sensitivity than Kato-Katz in this low intensity infection setting.

Spirobranchus tetraceros (Schmarda, 1861) originally briefly described from New South Wales, Australia was later reported as a widely distributed species of Indo-Pacific origin. The species was assumed to be a highly successful invasive Lessepsian migrant to the Mediterranean via the Suez Canal. However, recently, such wide distributions have been questioned and S. tetraceros was treated as a complex of morphologically similar species. Moreover, genetic evidence proved that the species that invaded the Mediterranean originated neither in warm temperate Australia nor in the Red Sea. This study examines the taxonomic status of Spirobranchus tetraceros populations along the east coast of Australia. Given the absence of the holotype, we re-described Spirobranchus tetraceros from New South Wales, designated the neotype supported by DNA sequence data, and fixed Port Botany as the type locality. The phylogenetic analysis revealed the existence of a sympatric cryptic species with a mean genetic distance of 36% (described here as S. schmardai sp. nov.) and proved that the tropical coral-associated specimens from Queensland belong to at least two distinct species. We also suggest resurrecting the name S. multicornis Grube, 1862 for the Red Sea population of the Spirobranchus tetraceros complex. This study calls for a worldwide revision of the complex.

Paratylenchus ilicis n. sp. was found associated with holly in the Netherlands and was described based on morphology, morphometrics, rRNA and mitochondrial cox1 genes, phylogenetic relationships with other Paratylenchus species, host information and geographical distribution. This species can be morphologically diagnosed based on its light brown, slightly obese to obese females with tubercles on cuticle, lateral bands widening into an ovoid field around vulva level, stylet length of 70 μm to 100 μm, outstretched to reflexed ovary, rounded sperm-filled spermatheca, vagina opening into a thick-walled rounded space, absence of vulval flaps and vulva at 89% to 95% of body length, very short tail in all life stages, and a characteristic finger-like tail tip in juveniles (J2). The new species is morphologically closest to Cacopaurus pestis but differs based on the absence of a scutellum-like differentiation in the lateral field, the ovaries that can be outstretched or reflexed, and the finger-like tail tip in J2. Furthermore, both species were found to be molecularly distant from one another, found in different habitats, and are associated with different hosts. The high morphological similarity between Cacopaurus and Paratylenchus and our phylogenetic analyses, revealing that the former is embedded within different Paratylenchus clades and thus polyphyletic, provide new evidences for the synonymization of Cacopaurus with Paratylenchus.

Abstract Background Microbial symbioses in marine invertebrates are commonplace. However, characterizations of invertebrate microbiomes are vastly outnumbered by those of vertebrates. Protists and fungi run the gamut of symbiosis, yet eukaryotic microbiome sequencing is rarely undertaken, with much of the focus on bacteria. To explore the importance of microscopic marine invertebrates as potential symbiont reservoirs, we used a phylogenetic-focused approach to analyze the host-associated eukaryotic microbiomes of 220 animal specimens spanning nine different animal phyla. Results Our data expanded the traditional host range of several microbial taxa and identified numerous undescribed lineages. A lack of comparable reference sequences resulted in several cryptic clades within the Apicomplexa and Ciliophora and emphasized the potential for microbial invertebrates to harbor novel protistan and fungal diversity. Conclusions Microscopic marine invertebrates, spanning a wide range of animal phyla, host various protist and fungal sequences and may therefore serve as a useful resource in the detection and characterization of undescribed symbioses. Video Abstract

We used DNA metabarcoding to compare macrozoobenthic species colonization between autonomous reef monitoring structures (ARMS) and artificial seaweed monitoring systems (ASMS). We deployed both substrates in two different locations (Ría de Vigo and Ría de Ferrol, NW Iberian coast) and collected them after 6, 9, and 12 months to assess species composition of the colonizing communities through high-throughput sequencing of amplicons within the barcode region of the mitochondrial cytochrome c oxidase I (COI-5P) and the V4 domain of the 18S rRNA genes. We observed a consistently low similarity in species composition between substrate types, independently of sampling times and sites. A large fraction of exclusive species was recorded for a given substrate (up to 72%), whereas only up to 32% of species were recorded in both substrates. The shape and structural complexity of the substrate strongly affected the colonization preferences, with ASMS detecting more exclusive crustacean and gastropod species and a broader diversity of taxonomic groups (e.g., Entoprocta and Pycnogonida were detected exclusively in ASMS). We demonstrate that despite the customary use of ARMS for macrozoobenthos monitoring, by using ASMS we complemented the recovery of species and enlarged the scope of the taxonomic diversity recorded. [ABSTRACT FROM AUTHOR]

The diatom Minutocellus polymorphus is a widely studied species because it is an ideal model for toxicity tests since it grows rapidly. Although the gross morphology has been extensively described, the ultrastructural characters associated with its importance, are unknown. It is also the only species in the genus that has been documented in the North American Atlantic, but unknown on the Eastern Pacific coasts. In a collection made in Acapulco Bay, Guerrero, Mexico, cells morphologically identical to M. polymorphus were isolated. From cultures and observations in transmission electron microscope, a first description of the ultrastructure of the genus is provided, and from sequences of 18S, we confirmed its taxonomic identity as M. polymorphus. However, more detailed studies are needed to continue increasing the knowledge about the ultrastructure of diatoms on the Mexican Pacific coasts, where they are previously unknown. [ABSTRACT FROM AUTHOR]

Although diverse groups of spiders are present in tropical countries, very little attention has been given on various types of differences that exist within these groups, particularly for the groups of tropical spiders in Malaysia. The morphological and genitalia characteristics are traditionally used to identify species variants. However, in this study, a molecular approach was utilized to produce a more precise and accurate result in an effort to identify, delineate and verify the species. Mitochondria-encoded cytochrome oxidase I (COI) and nuclear-encoded 18S rRNA (18S) genes) were adopted to establish DNA bacodes for 17 species of tetragnathid spiders (Araneae, Tetragnathidae) in Malaysia. Generally, the molecular data of tetragnathid spiders was consistent with their classification based upon morphological characteristics, though species boundary of Opadometa grata and Leucauge decorate could not be resolved by 18S gene. [ABSTRACT FROM AUTHOR]

The taxonomic study of Great Amazon Reef System sponges yielded three Oceanapia -like (Phloeodictyidae, Haplosclerida) species of similar gross morphology, two preliminarily identified as O. bartschi and another as Coelocarteria (Poecilosclerida), due to the presence of common palmate isochelae. The remarkable overall similarity of all three species in gross morphology necessitated an integrative assessment of the phylogenetic affinities. A selection of haplosclerid and poecilosclerid sequences (18S and 28S rRNA) was gathered from Genbank and compared to sequences mapped to reference from metagenome of two Oceanapia -like species from the Amazon River mouth, one of which matched O. bartschi. Both Brazilian species clustered with Coelocarteria singaporensis (Singapore). These species nest in the Poecilosclerida, far from Oceanapia (sp. and isodictyiformis) and other haplosclerids (Amphimedon , Petrosia, Siphonodictyon and Xestospongia) but also far from the poecilosclerid Isodictya that is currently classified in the same family as Coelocarteria , the Isodictyidae. Specimens with chelae are named Coelocarteria alcoladoi sp. nov. herein, while those without chelae represent the other two species. One matched Inflatella bartschi (O. bartchi 's holotype, here re-examined), thereby supporting the transfer of this species to Coelocarteria. The other is proposed as C. amadoi sp. nov. and is the second known lipochelous species in this genus. The 28S phylogenies recovered Coelocarteria bartschi comb. nov. (formerly Oceanapia bartschi) in the Poecilosclerida clade that clustered with Coelocarteria spp., including the type species of this genus, C. singaporensis , with 100% support. Coelocarteria alcoladoi sp. nov., also without chelae, grouped in the same clade, thereby corroborating the classification in this genus. The clade composed of Coelocarteria spp. grouped with Cornulella sp., suggesting an affinity between these genera. Coelocarteria is currently situated within Isodictyidae and Cornulella in Acarnidae. Isodictya (Isodictyidae) grouped with Amphilectus (Esperiopsidae) with high support and is only distantly related to Coelocarteria. Acarnus (Acarnidae) grouped with Clathria , also with high support, far from Coelocarteria and Cornulella. These results suggest the polyphyletic nature of Isodictyidae and Acarnidae, for which reason we preferred to propose a new, currently monotypic family for Coelocarteria spp., Coelocarteriidae fam. nov. ZooBank: urn:lsid:zoobank.org:pub:71FDB6FD-4A5F-4180-8DA7-79EA4CB615D1 The remarkable similarity among three species of sponges from the Amazon reefs, seemingly classified in two distinct orders, necessitated an integrative assessment of the phylogenetic affinities. These species were all found to belong in a highly supported clade together with the type species of the poecilosclerid Coelocarteria (Demospongiae, Porifera). Since this clade did not nest more closely to any poecilosclerid family in particular, we propose to erect the monogeneric Coelocarteriidae fam. nov. [ABSTRACT FROM AUTHOR]

Summary: A study of coffee rhizospheres collected from six coffee fields in the Gera and Gomma districts of Jimma Zone, southwest Ethiopia, revealed the presence of 12 genera of plant-parasitic nematodes, including Belonolaimus , Criconemoides , Cryphodera , Discocriconemella , Helicotylenchus , Longidorus , Ogma , Paratylenchus , Rotylenchus , Scutellonema , Tylenchorhynchus and Xiphinema. The genera Criconemoides , Helicotylenchus , Longidorus , Paratylenchus , Tylenchorhynchus and Xiphinema were the most prevalent, detected in all soil samples with up to 1590 individuals 100 ml−1 soil for Cryphodera. Morphological and molecular analysis of three genera with higher densities revealed a single species of an unknown Cryphodera sp., Paratylenchus leptos and Tylenchorhynchus cf. zeae occurring in all soil samples. Cryphodera is reported for the first time in Africa. Molecular analyses also revealed the presence of Xiphinema citricolum and several unknown species comprising one Discocriconemella sp., one Paratylenchus sp., four Helicotylenchus spp., two Ogma spp., one Rotylenchus sp. and three Xiphinema spp. In total, 32 partial 18S, 74 D2-D3 of 28S, three ITS sequences of ribosomal DNA and 24 partial mitochondrial COI gene sequences of 16 nematode species were generated. This study demonstrates that the identities of several potentially harmful nematodes are not well known, even in relation to highly important crops such as coffee. [ABSTRACT FROM AUTHOR]