Phylum Nematoda: feeding habits for all valid genera using a new, universal scheme encompassing the entire phylum, with descriptions of morphological characteristics of the stoma, a key, and discussion of the evidence for trophic relationships

Description of Amphimonhystrella sinica sp. nov. and Cobbia zhangi sp. nov. of the family Xyalidae (Nematoda: Monhysterida) from the Yellow Sea, China

Two new species of free-living marine nematodes belonging to the family Xyalidae are described from the Yellow Sea, China. Amphimonhystrella sinica sp. nov. is characterized by rhomboid-shaped buccal cavity, circular amphidial fovea relatively far from anterior end of body, slender L-shaped spicules with cephalated proximal end and hooked distal end, tubular gubernaculum with ventrally curved apophyses, slender tail conico-cylindrical with half cylindrical distal part. Cobbia zhangi sp. nov. is characterized by having three similar equal-sized teeth, anterior sensilla arrangement 6+10, slightly curved spicules cephalated proximally and tapered distally, gubernaculum rod-like without apophysis, tail with posterior three fourths filiform part. Updated dichotomous keys to species of Amphimonhystrella and Cobbia are given. Considering the descriptions in the present work, the two genera contain now 9 and 12 valid species, respectively; this study complemented the species diversity of nematodes in Chinese sea area.

Comparative mitochondrial genomics in Nematoda reveal astonishing variation in compositional biases and substitution rates indicative of multi-level selection

BACKGROUND

Nematodes are the most abundant and diverse metazoans on Earth, and are known to significantly affect ecosystem functioning. A better understanding of their biology and ecology, including potential adaptations to diverse habitats and lifestyles, is key to understanding their response to global change scenarios. Mitochondrial genomes offer high species level characterization, low cost of sequencing, and an ease of data handling that can provide insights into nematode evolutionary pressures.

RESULTS

Generally, nematode mitochondrial genomes exhibited similar structural characteristics (e.g., gene size and GC content), but displayed remarkable variability around these general patterns. Compositional strand biases showed strong codon position specific G skews and relationships with nematode life traits (especially parasitic feeding habits) equal to or greater than with predicted phylogeny. On average, nematode mitochondrial genomes showed low non-synonymous substitution rates, but also high clade specific deviations from these means. Despite the presence of significant mutational saturation, non-synonymous (dN) and synonymous (dS) substitution rates could still be significantly explained by feeding habit and/or habitat. Low ratios of dN:dS rates, particularly associated with the parasitic lifestyles, suggested the presence of strong purifying selection.

CONCLUSIONS

Nematode mitochondrial genomes demonstrated a capacity to accumulate diversity in composition, structure, and content while still maintaining functional genes. Moreover, they demonstrated a capacity for rapid evolutionary change pointing to a potential interaction between multi-level selection pressures and rapid evolution. In conclusion, this study helps establish a background for our understanding of the potential evolutionary pressures shaping nematode mitochondrial genomes, while outlining likely routes of future inquiry.

Description of Panagrolaimus namibiensis n. sp. (Rhabditida: Panagrolaimidae), an Anhydrobiotic Nematode from the Namib Desert of Namibia

Panagrolaimus namibiensis n. sp. was recovered and cultured from soils collected under Arthraerua leubnitziae (pencil-bush) in the Namib Desert of Namibia, one of the driest terrestrial habitats on Earth. It is described here based on morphometrics, scanning electron micrographs, light images, line drawings, and molecular data. The new species is distinguished by having a conspicuous posterior deirid, a hook-shaped stegostomal dorsal tooth, and anterior deirids and excretory pore aligned at mid-bulb. It was morphologically compared to eleven well-described species in the genus with which it shared similar labial structure (six distinct rounded lips, and low lip segments separated in pairs), conoid tail, and/or a lateral field with three incisures, including P. labiatus, P. kolymaensis, P. davidi, P. rigidus, and P. superbus. Bayesian phylogenetic analyses using SSU and LSU rDNA each placed P. namibiensis n. sp. within clades of Panagrolaimus species, although the two trees resolved its relationship to previously described species differently. Furthermore, our analyses showed the genus is not monophyletic. In a laboratory experiment, P. namibiensis n. sp. survived exposure to 0% relative humidity for 24 h, demonstrating the anhydrobiotic ability of this species that contributes to its survival in the Namib Desert.

The role of microbe-microplastic associations in marine Nematode feeding behaviors

Fauna across many taxa and trophic levels have been shown to consume microplastics (MPs) in experiments, providing evidence that supports field-based gut content assessments. Multiple explanations exist regarding why fauna consume MPs, one of which posits that microbial growth on MPs may facilitate faunal ingestion. However, laboratory assessments on the reasons why MPs are consumed remain limited. Here, we assessed if the presence of microbes on MPs altered marine nematode feeding behaviors across current and potential future concentrations of MPs in a local system. We used a microcosm experiment in which field-collected sediment was spiked with bacterially treated or untreated fluorescent plastic microbeads (1.0-5.0 μm) in concentrations of 102, 104, and 106 per microcosm, representing local and potential future concentrations of MPs. Ingestion by the dominant interstitial fauna was investigated after 0, 3, and 7 days using bright field microscopy. Nematodes were the only fauna across microcosms that consumed MPs, but this consumption was variable and there were no apparent trends across exposure time, bacterial treatment, or MP concentration. There were also no genera- or feeding-type-specific trends in the number of MPs consumed, though four of the top five nematode genera that consumed MPs were pollution-tolerant genera. Our study demonstrates that microbe-MP associations do not drive marine nematodes to eat MPs, especially at local field concentrations. While there were no trends across any of the nematode genera in our study, we recognize that unrealistic MP concentrations in other studies may provide alternative explanations for nematode consumption of MPs.

Nematode community structures in the presence of wastewater treatment plant discharge

Wastewater treatment plants (WWTPs) represent major point sources of pollution in coastal systems, affecting benthic ecosystems. In the present study, we assessed the potential role that WWTPs have in shaping nematode communities and established baseline knowledge of free-living nematode community structures in St. Andrew Bay, Florida. Sediment samples were collected from four sites representing areas of WWTP outflow and areas with no apparent outflow, during the winter and summer. Nematode communities across sites were significantly different, and the differences were strongly associated with the distance to the nearest WWTP. While the communities were not different along transects at each site, nor across seasons, community dissimilarity across sites was high, implying strong contrasts throughout the bay system. Dominance of tolerant, opportunistic genera and Ecological Quality Status assessments suggest that the system is stressed by organic enrichment, possibly linked to the WWTPs. Our results suggest that knowledge on the life-history of dominant genera is imperative to assess the ecological quality of a benthic system, in addition to taxonomic and functional metrics. Considering the value of marine nematodes as bioindicators, more work should be done to monitor temporal variability in nematode communities in this system as future infrastructure changes alter its dynamics.

Nematode mitochondrial metagenomics: A new tool for biodiversity analysis

DNA barcoding approaches have greatly increased our understanding of biodiversity on the planet, and metabarcoding is widely used for classifying members of the phylum Nematoda. However, loci typically utilized in metabarcoding studies are often unable to resolve closely related species or are unable to recover all taxa present in a sample due to inadequate PCR primer binding. Mitochondrial metagenomics (mtMG) is an alternative approach utilizing shotgun sequencing of total DNA to recover the mitochondrial genomes of all species present in samples. However, this approach requires a comprehensive reference database for identification and currently available mitochondrial sequences for nematodes are highly dominated by sequences from the order Rhabditida, and excludes many clades entirely. Here, we analysed the efficacy of mtMG for the recovery of nematode taxa and the generation of mitochondrial genomes. We first developed a curated reference database of nematode mitochondrial sequences and expanded it with 40 newly sequenced taxa. We then tested the mito-metagenomics approach using a series of nematode mock communities consisting of morphologically identified nematode species representing various feeding traits, life stages, and phylogenetic relationships. We were able to identify all but two species through the de novo assembly of COX1 genes. We were also able to recover additional mitochondrial protein coding genes (PCGs) for 23 of the 24 detected species including a full array of 12 PCGs from five of the species. We conclude that mtMG offers a potential for the effective recovery of nematode biodiversity but remains limited by the breadth of the reference database.

External and Internal Microbiomes of Antarctic Nematodes are Distinct, but More Similar to each other than the Surrounding Environment

Host-associated microbiomes have primarily been examined in the context of their internal microbial communities, but many animal species also contain microorganisms on external host surfaces that are important to host physiology. For nematodes, single strains of bacteria are known to adhere to the cuticle (e.g., Pasteuria penetrans), but the structure of a full external microbial community is uncertain. In prior research, we showed that internal gut microbiomes of nematodes (Plectus murrayi, Eudorylaimus antarcticus) and tardigrades from Antarctica's McMurdo Dry Valleys were distinct from the surrounding environment and primarily driven by host identity. Building on this work, we extracted an additional set of individuals containing intact external microbiomes and amplified them for 16S and 18S rRNA metabarcoding. Our results showed that external bacterial microbiomes were more diverse than internal microbiomes, but less diverse than the surrounding environment. Host-specific bacterial compositional patterns were observed, and external microbiomes were most similar to their respective internal microbiomes. However, external microbiomes were more influenced by the environment than the internal microbiomes were. Non-host eukaryotic communities were similar in diversity to internal eukaryotic communities, but exhibited more stochastic patterns of assembly compared to bacterial communities, suggesting the lack of a structured external eukaryotic microbiome. Altogether, we provide evidence that nematode and tardigrade cuticles are inhabited by robust bacterial communities that are substantially influenced by the host, albeit less so than internal microbiomes are.

Altitudinal Variation Influences Soil Fungal Community Composition and Diversity in Alpine-Gorge Region on the Eastern Qinghai-Tibetan Plateau

Soil fungi play an integral and essential role in maintaining soil ecosystem functions. The understanding of altitude variations and their drivers of soil fungal community composition and diversity remains relatively unclear. Mountains provide an open, natural platform for studying how the soil fungal community responds to climatic variability at a short altitude distance. Using the Illumina MiSeq high-throughput sequencing technique, we examined soil fungal community composition and diversity among seven vegetation types (dry valley shrub, valley-mountain ecotone broadleaved mixed forest, subalpine broadleaved mixed forest, subalpine coniferous-broadleaved mixed forest, subalpine coniferous forest, alpine shrub meadow, alpine meadow) along a 2582 m altitude gradient in the alpine-gorge region on the eastern Qinghai-Tibetan Plateau. Ascomycota (47.72%), Basidiomycota (36.58%), and Mortierellomycota (12.14%) were the top three soil fungal dominant phyla in all samples. Soil fungal community composition differed significantly among the seven vegetation types along altitude gradients. The α-diversity of soil total fungi and symbiotic fungi had a distinct hollow pattern, while saprophytic fungi and pathogenic fungi showed no obvious pattern along altitude gradients. The β-diversity of soil total fungi, symbiotic fungi, saprophytic fungi, and pathogenic fungi was derived mainly from species turnover processes and exhibited a significant altitude distance-decay pattern. Soil properties explained 31.27-34.91% of variation in soil fungal (total and trophic modes) community composition along altitude gradients, and the effects of soil nutrients on fungal community composition varied by trophic modes. Soil pH was the main factor affecting α-diversity of soil fungi along altitude gradients. The β-diversity and turnover components of soil total fungi and saprophytic fungi were affected by soil properties and geographic distance, while those of symbiotic fungi and pathogenic fungi were affected only by soil properties. This study deepens our knowledge regarding altitude variations and their drivers of soil fungal community composition and diversity, and confirms that the effects of soil properties on soil fungal community composition and diversity vary by trophic modes along altitude gradients in the alpine-gorge region.