Two new species of Promonhystera Wieser, 1956 (Nematoda: Monhysterida: Xyalidae) from the South China Sea.

Two new species of free-living marine nematodes from the littoral sediment of the South China Sea are described as Promonhystera papilla sp. nov. and Promonhystera fluctispicula sp. nov. Both new species are characterized by striated cuticle; circular amphideal fovea; anterior sensilla in two circles, inner labial sensilla setiform; funnel-shaped buccal cavity; elongated spicules and conico-cylindrical tail. P. papilla sp. nov. is different from all known species of the genus by longer body length (more than 2.1mm versus less than 1.5 mm in other species), longer spicules (sp/a.b.d. = 4.14.6 versus 2.7) and males with three papilliform precloacal supplements and one small postcloacal papilla (versus absence) and gubernaculum boot-shaped. P. fluctispicula sp. nov. is similar to P. tricuspidata Wieser, 1956 in having similar waved spicules but differs from the latter species by tail conico-cylindrical (versus conical) and simple plate-like gubernaculum without tooth (versus gubernaculum with four distal teeth).

Testing the effectiveness of different wash protocols to remove body surface contaminants in invertebrate food web studies.

Molecular gut content analysis via diagnostic PCR or high-throughput sequencing (metabarcoding) of consumers allows unravelling of feeding interactions in a wide range of animals. This is of particular advantage for analyzing the diet of small invertebrates living in opaque habitats such as the soil. Due to their small body size, which complicates dissection, microarthropods are subjected to whole-body DNA extraction-step before their gut content is screened for DNA of their food. This poses the problem that body surface contaminants, such as fungal spores may be incorrectly identified as ingested food particles for fungivorous species. We investigated the effectiveness of ten methods for body surface decontamination in litter-dwelling oribatid mites using Steganacarus magnus as model species. Furthermore, we tested for potential adverse effects of the decontamination techniques on the molecular detection of ingested prey organisms. Prior to decontamination, oribatid mites were fed with an oversupply of nematodes (Plectus sp.) and postmortem contaminated with fungal spores (Chaetomium globosum). We used diagnostic PCR with primers specific for C. globosum and Plectus sp. to detect contaminants and prey, respectively. The results suggest that chlorine bleach (sodium hypochloride, NaClO, 5%) is most efficient in removing fungal surface contamination without significantly affecting the detection of prey DNA in the gut. Based on these results, we provide a standard protocol for efficient body surface decontamination allowing to trace the prey spectrum of microarthropods using molecular gut content analysis.

Machine learning algorithms accurately identify free-living marine nematode species.

Background: Identifying species, particularly small metazoans, remains a daunting challenge and the phylum Nematoda is no exception. Typically, nematode species are differentiated based on morphometry and the presence or absence of certain characters. However, recent advances in artificial intelligence, particularly machine learning (ML) algorithms, offer promising solutions for automating species identification, mostly in taxonomically complex groups. By training ML models with extensive datasets of accurately identified specimens, the models can learn to recognize patterns in nematodes' morphological and morphometric features. This enables them to make precise identifications of newly encountered individuals. Implementing ML algorithms can improve the speed and accuracy of species identification and allow researchers to efficiently process vast amounts of data. Furthermore, it empowers non-taxonomists to make reliable identifications. The objective of this study is to evaluate the performance of ML algorithms in identifying species of free-living marine nematodes, focusing on two well-known genera: Acantholaimus Allgén, 1933 and Sabatieria Rouville, 1903. Methods: A total of 40 species of Acantholaimus and 60 species of Sabatieria were considered. The measurements and identifications were obtained from the original publications of species for both genera, this compilation included information regarding the presence or absence of specific characters, as well as morphometric data. To assess the performance of the species identification four ML algorithms were employed: Random Forest (RF), Stochastic Gradient Boosting (SGBoost), Support Vector Machine (SVM) with both linear and radial kernels, and K-nearest neighbor (KNN) algorithms. Results: For both genera, the random forest (RF) algorithm demonstrated the highest accuracy in correctly classifying specimens into their respective species, achieving an accuracy rate of 93% for Acantholaimus and 100% for Sabatieria, only a single individual from Acantholaimus of the test data was misclassified. Conclusion: These results highlight the overall effectiveness of ML algorithms in species identification. Moreover, it demonstrates that the identification of marine nematodes can be automated, optimizing biodiversity and ecological studies, as well as turning species identification more accessible, efficient, and scalable. Ultimately it will contribute to our understanding and conservation of biodiversity.

Review of Euchromadorinae (Nematoda: Chromadorida) with description of a new species of Trochamus Boucher & De Bovée, 1971 from the Sundarban, India.

Diagnostic characters for all 11 valid genera of Euchromadorinae are presented with taxonomic key on the basis of morphology of male copulatory apparatus, cuticular pattern, amphideal fovea, and buccal onchia. The key to the species of Trochamus spp. is also constructed with the description of T. timmi sp. n. from the mud-flat of Sundarban, India. The newly described species is different from other Trochamus spp. on the basis of the appearance of lateral differentiation of cuticle, long curved spicule, simple gubernaculum and the presence of pre-cloacal modification in male.

Descriptions of Leptolaimus sinensis sp. nov. and Perspiria brevicaudata sp. nov. (Nematoda) from the Yellow Sea, China.

Two new free-living marine nematodes which were collected at silt beach of Rizhao along the Yellow Sea are identified here as Leptolaimus sinensis sp. nov. and Perspiria brevicaudata sp. nov. Leptolaimus sinensis sp. nov. is characterized by annulated cuticle with lateral alae, 2 µm in width; buccal cavity cylindrical; cephalic setae 2 µm long; amphidial fovea unispiral, circular in outline; six to seven evenly spaced tubular precloacal supplements and 23-29 continuous alveolar supplements extending from cloaca to level of the base of buccal cavity; spicules slender, slightly arcuate; gubernaculum with dorso-caudal apophysis; tail conico-cylindrical, about 6 times cloacal body diameter in males and elongated in females, about 9 times anal body diameter in length. Perspiria brevicaudata sp. nov. is characterized by having four cephalic setae and four cervical setae; small buccal cavity with dorsal tooth and minute ventral tooth; amphidial fovea unispiral, looking like double circle in outline, surrounded partially by cuticle striations; spicules arcuate with ventral velum, handle-like proximally and tapered distally; gubernaculum plate-shaped, without apophysis; twelve winged precloacal supplements present. Updated identification keys for group of Leptolaimus species characterized by the presence of both alveolar and tubular precloacal supplements and for species of Perspiria are also given.

Two new species of Cyatholaimidae (Nematoda: Chromadorida) from the Southeastern Brazilian coast with emphasis on the pore complex and lateral pore-like structures.

Cyatholaimidae is a common and diverse family of mainly marine nematodes, potentially, with a large number of species to be discovered. The taxonomy of the group is marked by a lack of information about the evolutionary history of the characters and of detailed descriptions of morphological structures that may be taxonomically relevant. Two new species of the family are described from a sublittoral region in Southeastern Brazil, emphasizing the importance of the distribution and morphology of pore complex and pore-like structures present on the cuticle. The taxonomic importance of the cuticle ornamentation and spicule shape for the Biarmifer species, as well as the precloacal supplements structures of Pomponema species, are discussed. Biarmifer nesiotes sp. nov. differs from other species of the genus by the presence of eight longitudinal rows of pore complex on the cuticle and by the shape of the copulatory structure. Pomponema longispiculum sp. nov. differs from the most similar species, P. stomachor Wieser, 1954, by the smaller number of turns of the amphidial fovea, the shorter tail and the beginning of the cuticle lateral differentiation (3/4 of the pharynx length vs. end of the pharynx, respectively). We also obtained the SSU rDNA sequence from Pomponema longispiculum sp. nov., which is closely related to Pomponema sp. (MN250093) by about 91%. Updated tabular keys to species identification of each genus (Biarmifer and Pomponema) are included, containing morphometric data, characters related to cuticle ornamentation, and copulatory structures.

Three new free-living marine nematode species of the family Comesomatidae from Mangrove wetlands in Jinmen County, Taiwan.

Three new free-living marine nematodes, belonging to the genera Dorylaimopsis, Comesoma and Paracomesoma are described from the mangrove wetlands of western Taiwan Island. Dorylaimopsis jinmendaoica sp. nov. is characterized by having a cuticle with lateral differentiation of longitudinal rows of two rows of larger dots in the middle of the body, a spiral amphideal fovea with 2.52.75 turns, excretory pore anterior to nerve ring and 1721 fibriform precloacal supplements. Comesoma quattuordecimsupplementata sp. nov. is characterized by having a spiral amphideal fovea with 2.52.75 turns and 14 fibriform precloacal supplements. Paracomesoma paralissum sp. nov. is characterized by having a spiral amphideal fovea with 3.0 turns and 40 fibriform precloacal supplements. Differentiating characteristics of all known male Dorylaimopsis, Comesoma and Paracomesoma species are also given.

Two new species of Xyalidae Chitwood, 1951 (Nematoda, Monhysterida) from Chinese Sea Area.

Two new nematode species of the family Xyalidae were found in the intertidal zone of the Chinese coast, and they are described here as Daptonema sinica sp. nov. and Metadesmolaimus bulbosus sp. nov. Daptonema sinica sp. nov. is characterised by a relatively large body with a broad funnel-shaped buccal cavity; relatively long cephalic setae; a circular amphidial fovea posterior to the buccal cavity; slender spicules bending into a hook shape in the posterior half; a small plate-like gubernaculum without apophysis; and a conico-cylindrical slender tail with terminal setae. Metadesmolaimus bulbosus sp. nov. can be identified by its large buccal cavity, long cervical setae, multiple bulb-like pharyngeal muscular swellings, conico-cylindrical tail narrowing abruptly immediately posterior to the cloaca, straight clavated spicules with a broad proximal end and hooked distal end, and gubernaculum absent. An updated dichotomous key to the species of Metadesmolaimus is given.

Three new free-living marine nematode species of Subsphaerolaimus Lorenzen, 1978, Halichoanolaimus de Man, 1886 and Belbolla Andrssy, 1973 from mangrove wetlands in Taiwan.

Three new species of free-living marine nematodes belonging to the genera Subsphaerolaimus, Halichoanolaimus and Belbolla are described from the mangrove wetlands of western Taiwan Island. Subsphaerolaimus danshuiensis sp. nov. is characterized by a body length of 13451693 m, subcephalic setae 22.565.0 m long, cervical setae 16.533.0 m long, an L-shaped spicule 66.976.4 m long, and a gubernaculum with a caudally-dorsally directed apophysis 16.423.0 m long. Halichoanolaimus sicaoensis sp. nov. is characterized by an amphidial fovea with 3.53.75 turns, a conico-cylindrical tail with the cylindrical portion approximately 3/4 of the total tail length, and 1314 not equidistant papillose precloacal supplements. Belbolla forkyspicula sp. nov. is characterized by seven oesophageal bulbs, a short tail, a spicule with a proximal fork, and two winged supplements. Differentiating characteristics of the genera Subsphaerolaimus, Halichoanolaimus and Belbolla are provided. Types are deposited in the College of Fisheries, Jimei University.

Corononema vulgare sp. n. and Hofmaenneria coralis sp. n. (Nematoda, Monhysterida) from coral reefs off the coast of Vietnam.

Two new nematode species of the order Monhysterida, found in coral reefs on the coast of Vietnam, are described and illustrated. Corononema vulgare sp. n. morphology is similar to C. thai Nicholas & Stewart, 1995 but differs from it by the shorter outer labial setae, shorter tail in males, and a different shape of the guiding lateral bodies in the spicular apparatus of males. Hofmaenneria coralis sp. n. morphology is close to H. niddensis Gerlach & Meyl, 1957 and H. optata Alekseev, 1983. The new species differs from the first species by having thinner body, a shorter and less slender tail, and shorter spicules. The new species differs from H. optata in having a longer body, shorter pharynx, shorter tail, and longer outer labial setae.

Two new species of Sabatieria de Rouville, 1903 (Nematoda: Araeolaimida: Comesomatidae) from the Southern Ocean.

Two new free-living marine nematode species of the genus Sabatieria de Rouville, 1903 are described from the Southern Ocean using morphological and molecular data. Sabatieria brevicaudata sp. nov. is characterized by body length 14761740 m, short cephalic setae, 1324% corresponding body diameter long, lateral differentiation of body cuticle with only slightly coarser punctations, spiral amphidial fovea with 3 turns, spicules arcuated and 1.31.6 cloacal body diameter long, slightly arcuated gubernacular apophyses, and twelve precloacal supplements, in the form of small pores. Sabatieria multipora sp. nov. is characterized by body length 21392324 m, short cephalic setae (47 m long, 3040% corresponding body diameter long), cuticle with lateral differentiation of distinctly coarser punctations extending from anterior edge of amphidial fovea to anterior of intestine and in the tail region, spiral amphidial fovea with 3 turns, males with spicules 1.92.0 cloacal body diameter long, seventeen fine tubular precloacal supplements with distance between adjacent supplements increasing towards anterior, and with curved gubernacular apophyses. We obtained 18S rDNA and 28S rDNA sequences from the two new species, which are both closely related to other species of Sabatieria. Our analyses also show that several genera of Comesomatidae Filipjev, 1918 do not form monophyletic clades.

A catalogue of the nematode slide collection from the late W.L. Nicholas held at National Research Collections Australia, CSIRO.

A catalogue is presented of the nematode slide collection of W.L. Nicholas, which is deposited in the National Research Collections Australia at CSIRO. This is the most extensive slide collection of free-living marine and estuarine nematodes from Australia to date, and consists of 553 putative species, collected across a wide range of Australias eastern and northern regions over the course of nearly 40 years. The collection contains mostly marine and estuarine free-living nematodes collected on coarse substrate in littoral habitats. The most abundant genera were Desmodora, Theristus, and Onyx. Most taxa were found rarely, being recorded only once, and repeated sampling at several sandy beach sites revealed only a small proportion of the fauna on more than one occasion. A significant proportion of the taxa were also found to be widespread, occurring on more than one occasion at more than one location, with Theristus sp., Onyx sp., and Viscosia sp. occurring in the greatest number of localities. The catalogue adds an additional 90 species and 160 genera to the documented fauna of Australian free-living nematodes verifiable by specimens in permanent collections. It thus provides a better framework for studying nematode biodiversity and biogeography in the region.

Description of two new species of Nematoda: Litinium macramphida sp. nov. (Oxystominidae) and Cyartonema breviseta sp. nov. (Cyartonematidae) from the Yellow Sea, China.

Two new species of Nematoda, Litinium macramphida sp. nov. and Cyartonema breviseta sp. nov. are described from the Yelllow Sea. Litinium macramphida sp. nov. is characterized by body relatively long, inner and outer labial sensilla setiform with same length, amphideal fovea large and drop-shaped with amphideal aperture ovoid, spicules short and wide, gubernaculum simple and boat shaped, two precloacal supplements, and tail conical with rounded tip. Cyartonema breviseta sp. nov. is characterized by body short and slender, four cephalic sensilla papilliform, amphideal fovea circular and large, spicules curved and sickle-shaped, gubernaculum with dorsal-caudal apophysis and posterior end anteriorly hooked, and tail conical.

Description of Bolbolaimus major sp. nov. (Nematoda), from the Yellow Sea, China and phylogenetic analysis in Microlaimidae.

Bolbolaimus major sp. nov. is described from Rizhao coast along the Yellow Sea. The new species is characterized by relatively large body size, cuticle strongly annulated, six outer labial sensilla setiform, four cephalic setae long, buccal cavity wide with one large dorsal tooth and two small subventral teeth, amphidial fovea unispiral shaped oval in males and circular in females, spicules curved with swollen proximal end, gubernaculum with anterior-hooked dorso-caudal apophysis, and tail conical with short spinneret. A phylogenetic analysis of maximum-likelihood and Bayesin inference based on rDNA sequences confirms the taxonomic position of Bolbolaimus major sp. nov. within the family Microlaimidae. Tree topology in Microlaimidae shows genus Microlaimus as polyphyletic group and genera in Microlaimidae are closely related.

Host identity is the dominant factor in the assembly of nematode and tardigrade gut microbiomes in Antarctic Dry Valley streams.

Recent work examining nematode and tardigrade gut microbiomes has identified species-specific relationships between host and gut community composition. However, only a handful of species from either phylum have been examined. How microbiomes differ among species and what factors contribute to their assembly remains unexplored. Cyanobacterial mats within Antarctic Dry Valley streams host a simple and tractable natural ecosystem of identifiable microinvertebrates to address these questions. We sampled 2 types of coexisting mats (i.e., black and orange) across four spatially isolated streams, hand-picked single individuals of two nematode species (i.e., Eudorylaimus antarcticus and Plectus murrayi) and tardigrades, to examine their gut microbiomes using 16S and 18S rRNA metabarcoding. All gut microbiomes (bacterial and eukaryotic) were significantly less diverse than the mats they were isolated from. In contrast to mats, microinvertebrates' guts were depleted of Cyanobacteria and differentially enriched in taxa of Bacteroidetes, Proteobacteria, and Fungi. Among factors investigated, gut microbiome composition was most influenced by host identity while environmental factors (e.g., mats and streams) were less important. The importance of host identity in predicting gut microbiome composition suggests functional value to the host, similar to other organisms with strong host selected microbiomes.

Chromaspirina aliapapillata sp.nov. (Nematoda, Desmodorida) from Donuzlav Bay (Crimea, Black Sea).

A new species of free-living marine nematode Chromaspirina aliapapillata sp. nov. from the Donuzlav Bay (Black Sea) is described. Chromaspirina aliapapillata sp. nov. is characterized by a slender body, buccal cavity with two dorsal teeth, spiral amphids, tail conico-cylindrical and presence of precloacal supplements. The new species differs from other known species of the genus by having two dorsal teeth and presence of 17 to 21 precloacal supplements of which one or two are cup-shaped and rest curved tubes.

Differential regulation of degradation and immune pathways underlies adaptation of the ectosymbiotic nematode Laxus oneistus to oxic-anoxic interfaces.

Eukaryotes may experience oxygen deprivation under both physiological and pathological conditions. Because oxygen shortage leads to a reduction in cellular energy production, all eukaryotes studied so far conserve energy by suppressing their metabolism. However, the molecular physiology of animals that naturally and repeatedly experience anoxia is underexplored. One such animal is the marine nematode Laxus oneistus. It thrives, invariably coated by its sulfur-oxidizing symbiont Candidatus Thiosymbion oneisti, in anoxic sulfidic or hypoxic sand. Here, transcriptomics and proteomics showed that, whether in anoxia or not, L. oneistus mostly expressed genes involved in ubiquitination, energy generation, oxidative stress response, immune response, development, and translation. Importantly, ubiquitination genes were also highly expressed when the nematode was subjected to anoxic sulfidic conditions, together with genes involved in autophagy, detoxification and ribosome biogenesis. We hypothesize that these degradation pathways were induced to recycle damaged cellular components (mitochondria) and misfolded proteins into nutrients. Remarkably, when L. oneistus was subjected to anoxic sulfidic conditions, lectin and mucin genes were also upregulated, potentially to promote the attachment of its thiotrophic symbiont. Furthermore, the nematode appeared to survive oxygen deprivation by using an alternative electron carrier (rhodoquinone) and acceptor (fumarate), to rewire the electron transfer chain. On the other hand, under hypoxia, genes involved in costly processes (e.g., amino acid biosynthesis, development, feeding, mating) were upregulated, together with the worm's Toll-like innate immunity pathway and several immune effectors (e.g., bactericidal/permeability-increasing proteins, fungicides). In conclusion, we hypothesize that, in anoxic sulfidic sand, L. oneistus upregulates degradation processes, rewires the oxidative phosphorylation and reinforces its coat of bacterial sulfur-oxidizers. In upper sand layers, instead, it appears to produce broad-range antimicrobials and to exploit oxygen for biosynthesis and development.

Inverted base composition skews and discontinuous mitochondrial genome architecture evolution in the Enoplea (Nematoda).

BACKGROUND: Within the class Enoplea, the earliest-branching lineages in the phylum Nematoda, the relatively highly conserved ancestral mitochondrial architecture of Trichinellida is in stark contrast to the rapidly evolving architecture of Dorylaimida and Mermithida. To better understand the evolution of mitogenomic architecture in this lineage, we sequenced the mitogenome of a fish parasite Pseudocapillaria tomentosa (Trichinellida: Capillariidae) and compared it to all available enoplean mitogenomes. RESULTS: P. tomentosa exhibited highly reduced noncoding regions (the largest was 98 bp), and a unique base composition among the Enoplea. We attributed the latter to the inverted GC skew (0.08) in comparison to the ancestral skew in Trichinellidae (-0.43 to -0.37). Capillariidae, Trichuridae and Longidoridae (Dorylaimida) generally exhibited low negative or low positive skews (-0.1 to 0.1), whereas Mermithidae exhibited fully inverted low skews (0 to 0.05). This is indicative of inversions in the strand replication order or otherwise disrupted replication mechanism in the lineages with reduced/inverted skews. Among the Trichinellida, Trichinellidae and Trichuridae have almost perfectly conserved architecture, whereas Capillariidae exhibit multiple rearrangements of tRNA genes. In contrast, Mermithidae (Mermithida) and Longidoridae (Dorylaimida) exhibit almost no similarity to the ancestral architecture. CONCLUSIONS: Longidoridae exhibited more rearranged mitogenomic architecture than the hypervariable Mermithidae. Similar to the Chromadorea, the evolution of mitochondrial architecture in enoplean nematodes exhibits a strong discontinuity: lineages possessing a mostly conserved architecture over tens of millions of years are interspersed with lineages exhibiting architectural hypervariability. As Longidoridae also have some of the smallest metazoan mitochondrial genomes, they contradict the prediction that compact mitogenomes should be structurally stable. Lineages exhibiting inverted skews appear to represent the intermediate phase between the Trichinellidae (ancestral) and fully derived skews in Chromadorean mitogenomes (GC skews = 0.18 to 0.64). Multiple lines of evidence (CAT-GTR analysis in our study, a majority of previous mitogenomic results, and skew disruption scenarios) support the Dorylaimia split into two sister-clades: Dorylaimida + Mermithida and Trichinellida. However, skew inversions produce strong base composition biases, which can hamper phylogenetic and other evolutionary studies, so enoplean mitogenomes have to be used with utmost care in evolutionary studies.

Onyx disparamphis sp. n. (Nematoda, Desmodorida) from South Korea with a taxonomic review of the genus.

A new free-living marine nematode Onyx disparamphis sp. n. (Nematoda, Desmodorida) is described from sandy littoral of Jeju Island, South Korea. The new species differs from all other Onyx species by the unusual amphideal fovea morphology in males (elongated loop). O. disparamphis relates to O. balochinensis, and O. brevispiculatum by having simple non-double terminal pharyngeal bulb and relatively small and straight, non-sigmoid supplementary organs, but differs from them by smaller body length, shorter cephalic setae, smaller terminal pharyngeal bulb, smaller spicules, number of supplementary organs and tail shape expressed as ratio tail length/anal diameter. The genus Onyx is revised with updated genus diagnosis, and an annotated list of 23 valid species is presented. Onyx ferox is considered species inquirenda because the species is known only from a sole immature female specimen, while within Onyx, the males provide the most important distinguishing characters such as enlarged and complicated amphids, supplementary organs and copulatory spicules. For species identification, a pictorial key consisting of illustrations of simplified icons of male heads and posterior body sections, as well as a table of the most important morphometric and numerical characters are provided. Geographical distribution and habitat specifity of Onyx species is analysed briefly.

Three new species of Microlaimus (Nematoda: Microlaimidae) from the South Atlantic.

Three new species of Microlaimus are described from the continental shelf of the Campos Basin, southwest Atlantic, Brazil. Microlaimus campiensis sp. n. differs from all other species in the presence of two anterior testes, slender spicules with enlarged proximal ends, 7-11 pre-cloacal papilliform supplements, and females with a pair of constriction structures, one on each branch of the ovary. Microlaimus alexandri sp. n. shows sexual dimorphism in the size of the amphidial fovea, which occupies 100% of the diameter of the corresponding area in the male; the buccal cavity provided with five teeth and a slightly cuticularized cuticular ring. Microlaimus vitorius sp. n. has four longitudinal-lateral rows of glands associated with small pores, one seta and three pores small pre-cloacal, and the gubernaculum has a triangular base. An amendment to the diagnosis of the genus is proposed, where the number of teeth was modified.