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.

Abstract:Isotopic composition of leaf carbon (δ13C) and nitrogen (δ15N) is determined by biotic and abiotic factors. In order to determine the influence of leaf habit and site on leaf δ13C and δ15N in the understorey of two Atlantic forests in Brazil that differ in annual precipitation (1200 and 1900 mm), we measured these isotopes in the shaded understorey of 38 tropical tree species (20 in the 1200-mm site and 18 in the 1900-mm site). Mean site values for δ15N were significantly lower at the 1200-mm site (−1.4‰) compared with the 1900-mm site (+3.0‰), and δ13C was significantly greater in the 1200-mm site (−30.4‰) than in the 1900-mm site (−31.6‰). Leaf C concentration was greater and leaf N concentration was lower at 1200-mm than at 1900-mm. Leaf δ15N was negatively correlated with δ13C across the two sites. Leaf δ13C and δ15N of evergreen and deciduous species were not significantly different within a site. No significant phylogenetic signal for any traits among the study species was found. Overall, site differences were the main factor distinguishing traits among species, suggesting strong functional convergence to local climate and soils within each site for individuals in the shaded understorey.

We used morphological and molecular approaches to evaluate the diversity of free-living marine nematodes (order Enoplida) at four coastal sites in the Gulf of California and three on the Pacific coast of Baja California, Mexico. We identified 22 morphological species belonging to six families, of which Thoracostomopsidae and Oncholaimidae were the most diverse. The genus Mesacanthion (Thoracostomopsidae) was the most widespread and diverse. Five allopatric species, genetically and morphologically differentiated, were found in two localities in the Gulf of California (M. sp1 and M. sp2) and three in the Pacific coast (M. sp3, M. sp4 and M. sp5). Overall, we produced 19 and 20 sequences for the 18S and 28S genes, respectively. Neither gene displayed intraspecific polymorphisms, which allowed us to establish that some morphological variation was likely either ontogenetic or due to phenotypic plasticity. Although 18S and 28S phylogenies were topologically congruent (incongruence length difference test, P > 0.05), divergences between species were much higher in the 28S gene. Moreover, this gene possessed a stronger phylogenetic signal to resolve relationships involving Rhabdodemania and Bathylaimus. On the other hand, the close relationship of Pareurystomina (Enchilidiidae) with oncholaimids warrants further study. The 28S sequences (D2D3 domain) may be better suited for DNA barcoding of marine nematodes than those from the 18S rDNA, particularly for differentiating closely related or cryptic species. Finally, our results underline the relevance of adopting an integrative approach encompassing morphological and molecular analyses to improve the assessment of marine nematode diversity and advance their taxonomy.Electronic supplementary materialThe online version of this article (doi:10.1007/s00227-010-1439-z) contains supplementary material, which is available to authorized users.

Marine multicellular organisms host a diverse collection of bacteria, archaea, microbial eukaryotes, and viruses that form their microbiome. Such host-associated microbes can significantly influence the host’s physiological capacities; however, the identity and functional role(s) of key members of the microbiome (“core microbiome”) in most marine hosts coexisting in natural settings remain obscure. Also unclear is how dynamic interactions between hosts and the immense standing pool of microbial genetic variation will affect marine ecosystems’ capacity to adjust to environmental changes. Here, we argue that significantly advancing our understanding of how host-associated microbes shape marine hosts’ plastic and adaptive responses to environmental change requires (i) recognizing that individual host–microbe systems do not exist in an ecological or evolutionary vacuum and (ii) expanding the field toward long-term, multidisciplinary research on entire communities of hosts and microbes. Natural experiments, such as time-calibrated geological events associated with well-characterized environmental gradients, provide unique ecological and evolutionary contexts to address this challenge. We focus here particularly on mutualistic interactions between hosts and microbes, but note that many of the same lessons and approaches would apply to other types of interactions.

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