Studies of host-associated microbes are critical for advancing our understanding of ecology and evolution across diverse taxa and ecosystems. Nematode worms are ubiquitous across most habitats on earth, yet little is known about host-associated microbial assemblages within the phylum. Free-living nematodes are globally abundant and diverse in marine sediments, with species exhibiting distinct buccal cavity (mouth) morphologies that are thought to play an important role in feeding ecology and life history strategies. Here, we investigated patterns in marine nematode microbiomes, by characterizing host-associated microbial taxa in 281 worms isolated from a range of habitat types (deep-sea, shallow water, methane seeps, Lophelia coral mounds, kelp holdfasts) across three distinct geographic regions (Arctic, Southern California and Gulf of Mexico). Microbiome profiles were generated from single worms spanning 33 distinct morphological genera, using a two-gene metabarcoding approach to amplify the V4 region of the 16S ribosomal RNA (rRNA) gene targeting bacteria/archaea and the V1-V2 region of the 18S rRNA gene targeting microbial eukaryotes. Contrary to our expectations, nematode microbiome profiles demonstrated no distinct patterns either globally (across depths and ocean basins) or locally (within site); prokaryotic and eukaryotic microbial assemblages did not correlate with nematode feeding morphology, host phylogeny or morphological identity, ocean region or marine habitat type. However, fine-scale analysis of nematode microbiomes revealed a variety of novel ecological interactions, including putative parasites and symbionts, and potential associations with bacterial/archaeal taxa involved in nitrogen and methane cycling. Our results suggest that in marine habitats, free-living nematodes may utilize diverse and generalist foraging strategies that are not correlated with host genotype or feeding morphology. Furthermore, some abiotic factors such as geographic region and habitat type do not appear to play an obvious role in structuring host-microbe associations or feeding preferences.

The significance of symbioses between eukaryotic hosts and microbes extends from the organismal to the ecosystem level and underpins the health of Earth’s most threatened marine ecosystems. Despite rapid growth in research on host-associated microbes, from individual microbial symbionts to host-associated consortia of significantly relevant taxa, little is known about their interactions with the vast majority of marine host species. We outline research priorities to strengthen our current knowledge of host–microbiome interactions and how they shape marine ecosystems. We argue that such advances in research will help predict responses of species, communities, and ecosystems to stressors driven by human activity and inform future management strategies.

Concerted evolution is often assumed to be the evolutionary force driving multi-family genes, including those from ribosomal DNA (rDNA) repeat, to complete homogenization within a species, although cases of non-concerted evolution have been also documented. In this study, sequence variation of 28S and ITS ribosomal RNA (rRNA) genes in the genus Cephalenchus is assessed at three different levels, intragenomic, intraspecific, and interspecific. The findings suggest that not all Cephalenchus species undergo concerted evolution. High levels of intraspecific polymorphism, mostly due to intragenomic variation, are found in Cephalenchus sp1 (BRA-01). Secondary structure analyses of both rRNA genes and across different species show a similar substitution pattern, including mostly compensatory (CBC) and semi-compensatory (SBC) base changes, thus suggesting the functionality of these rRNA copies despite the variation found in some species. This view is also supported by low sequence variation in the 5.8S gene in relation to the flanking ITS-1 and ITS-2 as well as by the existence of conserved motifs in the former gene. It is suggested that potential cross-fertilization in some Cephalenchus species, based on inspection of female reproductive system, might contribute to both intragenomic and intraspecific polymorphism of their rRNA genes. These results reinforce the potential implications of intragenomic and intraspecific genetic diversity on species delimitation, especially in biodiversity studies based solely on metagenetic approaches. Knowledge of sequence variation will be crucial for accurate species diversity estimation using molecular methods.

Filenchus annulatus is redescribed and males are characterised for the first time based on a population found in Northem Khorasan province, Iran. New morphological characterisation is based on light and scanning electron microscopy. In addition, molecular analyses based on 18S and 28S genes are included to test monophyly of the genus. Females from the Iranian population have a spermatheca typically filled with sperm. Generally males are similar to females, ranging from 306 to 426 ßm long. Spicules are arcuate, cephalated and 11.5-14.0 ßm long, the gubernaculum is minute and trough-shaped and the caudal alae are adanal. Phylogenetic analyses differed in results depending on the gene used: 28S gene strongly supports Filenchus as monophyletic whereas 18S shows Filenchus as polyphyletic. In both gene phytogenies, F annulatus is placed as a sister taxon of F quartus from Wyoming, USA. Although sequence divergence between these two species is only 3 base pairs and 1 base pair for 28S and 18S genes, respectively, strong morphological differences support their species status. Relationships between Filenchus and other Tylenchidae genera are also gene dependent. Such differences in tree topologies and branch support are related to the number of Filenchus species used in the analyses (greater for 18S gene) and gene resolution (greater for 28S gene). Molecular phytogenies also suggest that other Tylenchidae genera {i.e., Fsilenchus, Cephalenchus and Futylenchus) belong to separate clades, as is also suggested by some morphology-based classifications. The inclusion of more taxa and perhaps additional genes is needed further to clarify Filenchus relationships and further to test its monophyly.