James G. Baldwin

Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments.

Microbial eukaryotes (nematodes, protists, fungi, etc., loosely referred to as meiofauna) are ubiquitous in marine sediments and probably play pivotal roles in maintaining ecosystem function. Although the deep-sea benthos represents one of the worlds largest habitats, we lack a firm understanding of the biodiversity and community interactions amongst meiobenthic organisms in this ecosystem. Within this vast environment, key questions concerning the historical genetic structure of species remain a mystery, yet have profound implications for our understanding of global biodiversity and how we perceive and mitigate the impact of environmental change and anthropogenic disturbance. Using a metagenetic approach, we present an assessment of microbial eukaryote communities across depth (shallow water to abyssal) and ocean basins (deep-sea Pacific and Atlantic). Within the 12 sites examined, our results suggest that some taxa can maintain eurybathic ranges and cosmopolitan deep-sea distributions, but the majority of species appear to be regionally restricted. For Operationally Clustered Taxonomic Units (OCTUs) reporting wide distributions, there appears to be a taxonomic bias towards a small subset of taxa in most phyla; such bias may be driven by specific life history traits amongst these organisms. In addition, low genetic divergence between geographically disparate deep-sea sites suggests either a shorter coalescence time between deep-sea regions or slower rates of evolution across this vast oceanic ecosystem. While high-throughput studies allow for broad assessment of genetic patterns across microbial eukaryote communities, intragenomic variation in rRNA gene copies and the patchy coverage of reference databases currently present substantial challenges for robust taxonomic interpretations of eukaryotic data sets.

A phylogenetic framework for root lesion nematodes of the genus Pratylenchus (Nematoda): Evidence from 18S and D2-D3 expansion segments of 28S ribosomal RNA genes and morphological characters.

The root lesion nematodes of the genus Pratylenchus Filipjev, 1936 are migratory endoparasites of plant roots, considered among the most widespread and important nematode parasites in a variety of crops. We obtained gene sequences from the D2 and D3 expansion segments of 28S rRNA partial and 18S rRNA from 31 populations belonging to 11 valid and two unidentified species of root lesion nematodes and five outgroup taxa. These datasets were analyzed using maximum parsimony and Bayesian inference. The alignments were generated using the secondary structure models for these molecules and analyzed with Bayesian inference under the standard models and the complex model, considering helices under the doublet model and loops and bulges under the general time reversible model. The phylogenetic informativeness of morphological characters is tested by reconstruction of their histories on rRNA based trees using parallel parsimony and Bayesian approaches. Phylogenetic and sequence analyses of the 28S D2-D3 dataset with 145 accessions for 28 species and 18S dataset with 68 accessions for 15 species confirmed among large numbers of geographical diverse isolates that most classical morphospecies are monophyletic. Phylogenetic analyses revealed at least six distinct major clades of examined Pratylenchus species and these clades are generally congruent with those defined by characters derived from lip patterns, numbers of lip annules, and spermatheca shape. Morphological results suggest the need for sophisticated character discovery and analysis for morphology based phylogenetics in nematodes.

Three-dimensional reconstruction of the amphid sensilla in the microbial feeding nematode, Acrobeles complexus (nematoda: Rhabditida)

Amphid sensilla are the primary olfactory, chemoreceptive, and thermoreceptive organs in nematodes. Their function is well described for the model organism Caenorhabditis elegans, but it is not clear to what extent we can generalize these findings to distantly related nematodes of medical, economic, and agricultural importance. Current detailed descriptions of anatomy and sensory function are limited to nematodes that recent molecular phylogenies would place in the same taxonomic family, the Rhabditidae. Using serial thin‐section transmission electron microscopy, we reconstructed the anatomy of the amphid sensilla in the more distantly related nematode, Acrobeles complexus (Cephalobidae). Amphid structure is broadly conserved in number and arrangement of cells. Details of cell anatomy differ, particularly for the sensory neurite termini. We identify an additional sensory neuron not found in the amphid of C. elegans and propose homology with the C. elegans interneuron AUA. Hypotheses of homology for the remaining sensory neurons are also proposed based on comparisons between C. elegans, Strongyloides stercoralis, and Haemonchus contortus. J. Comp. Neurol. 512:271–281, 2009.

Identification, phylogeny and phylogeography of circumfenestrate cyst nematodes (Nematoda: Heteroderidae) as inferred from analysis of ITS-rDNA.

Some 134 ITS rRNA gene sequences for circumfenestrate cyst nematodes and two sequences for non-cyst nematodes of the family Heteroderidae, of which 46 were newly obtained, were analysed by phylogenetic and phylogeographic methods. Sequence and phylogenetic analysis combined with known morphological, biological and geographical data allowed the identification, amongst samples original to this study, of several belonging to known valid species as well as others that might be new species. The phylogenetic analysis revealed six major clades for circumfenestrate cyst nematodes: i) Globodera from South and North America; ii) Globodera from Europe, Asia, Africa and Oceania; iii) Paradolichodera; iv) Punctodera; v) Cactodera; and vi) Betulodera. Monophylies of Punctodera, Cactodera and Betulodera were highly supported. The Betulodera clade occupied a basal position on all trees. Phylogeographic analysis suggested a North American origin of Punctoderinae with possible further long distance dispersal to South America, Africa and other regions. Molecular data supported synonymisation of G. achilleae with G. millefolii and of G. hypolysi with G. artemisiae. PCR-RFLP diagnostic profiles for some Globodera and Cactodera species are given. Problems of diagnostics for Globodera species using PCR with specific primers are discussed.

Microsporidia-nematode associations in methane seeps reveal basal fungal parasitism in the deep sea

The deep sea is Earths largest habitat but little is known about the nature of deep-sea parasitism. In contrast to a few characterized cases of bacterial and protistan parasites, the existence and biological significance of deep-sea parasitic fungi is yet to be understood. Here we report the discovery of a fungus-related parasitic microsporidium, Nematocenator marisprofundi n. gen. n. sp. that infects benthic nematodes at methane seeps on the Pacific Ocean floor. This infection is species-specific and has been temporally and spatially stable over 2 years of sampling, indicating an ecologically consistent host-parasite interaction. A high distribution of spores in the reproductive tracts of infected males and females and their absence from host nematodes intestines suggests a sexual transmission strategy in contrast to the fecal-oral transmission of most microsporidia. N. marisprofundi targets the hosts body wall muscles causing cell lysis, and in severe infection even muscle filament degradation. Phylogenetic analyses placed N. marisprofundi in a novel and basal clade not closely related to any described microsporidia clade, suggesting either that microsporidia-nematode parasitism occurred early in microsporidia evolution or that host specialization occurred late in an ancient deep-sea microsporidian lineage. Our findings reveal that methane seeps support complex ecosystems involving interkingdom interactions between bacteria, nematodes, and parasitic fungi and that microsporidia parasitism exists also in the deep-sea biosphere.

Resolving phylogenetic incongruence to articulate homology and phenotypic evolution: a case study from Nematoda.

Modern morphology-based systematics, including questions of incongruence with molecular data, emphasizes analysis over similarity criteria to assess homology. Yet detailed examination of a few key characters, using new tools and processes such as computerized, three-dimensional ultrastructural reconstruction of cell complexes, can resolve apparent incongruence by re-examining primary homologies. In nematodes of Tylenchomorpha, a parasitic feeding phenotype is thus reconciled with immediate free-living outgroups. Closer inspection of morphology reveals phenotypes congruent with molecular-based phylogeny and points to a new locus of homology in mouthparts. In nematode models, the study of individually homologous cells reveals a conserved modality of evolution among dissimilar feeding apparati adapted to divergent lifestyles. Conservatism of cellular components, consistent with that of other body systems, allows meaningful comparative morphology in difficult groups of microscopic organisms. The advent of phylogenomics is synergistic with morphology in systematics, providing an honest test of homology in the evolution of phenotype.

Comparative, three-dimensional anterior sensory reconstruction of Aphelenchus avenae (nematoda: Tylenchomorpha).

The anterior sensory anatomy (not including amphids) of the nematode Aphelenchus avenae (Tylenchomorpha) has been three‐dimensionally reconstructed from serial, transmission electron microscopy thin sections. Models, showing detailed morphology and spatial relationships of cuticular sensilla and internal sensory receptors, are the first computerized reconstruction of sensory structures of a Tylenchomorpha nematode. Results are analyzed with respect to similarly detailed reconstructions of Rhabditida outgroup nematodes, Acrobeles complexus (Cephalobomorpha) and Caenorhabditis elegans (Rhabditomorpha). Homologies identified in A. avenae demonstrate the general conservation of the anterior sensory system between freeliving nematodes and the largely plant parasitic Tylenchomorpha. A higher degree of similarity is shown between A. avenae and A. complexus, with common features including: the presence of a second, internal outer labial dendrite (OL1); a second cephalic dendrite in the female (CEP2/CEM); an accessory process loop of inner labial dendrite 1; and terminus morphology and epidermal associations of internal sensory receptors BAG and URX. Unique to A. avenae is a pair of peripheral, lateral neurons of unknown homology but with axial positions and intercellular relationships nearly identical to the “posterior branches” of URX in A. complexus. Knowledge of homologies and connectivity of anterior sensory structures provides a basis for expansion of the experimental behavioral model of C. elegans to the economically important nematodes of Tylenchomorpha. J. Comp. Neurol. 517:616–632, 2009.

Diversity and phylogenetic relationships within the spiral nematodes of Helicotylenchus Steiner, 1945 (Tylenchida: Hoplolaimidae) as inferred from analysis of the D2-D3 expansion segments of 28S rRNA gene sequences

The spiral nematodes of the genus Helicotylenchus are globally distributed and associated with the root system of diverse groups of plants in cultivated and uncultivated areas. Several species are considered serious parasites of crops. The identification of many Helicotylenchus species is not always reliable, in part because many species share very similar diagnostic characters and high intraspecific variation. To verify species identification of geographically distant populations of Helicotylenchus , we tested monophyly of some classical morphospecies and studied their phylogenetic relationships; specifically, we conducted sequence and phylogenetic analysis of 89 sequences of the D2-D3 expansion segments of 28S rRNA gene sequences from 54 Helicotylenchus isolates, including species identified as H. brevis , H. digonicus , H. dihystera , H. labiodiscinus , H. leiocephalus , H. martini , H. multicinctus , H. platyurus , H. pseudorobustus and H. vulgaris , together with three outgroup taxa. Phylogenetic analysis distinguished nine highly or moderately supported major clades within Helicotylenchus. Using the molecular approach we were able to confirm congruence with morphologicalbased identification of samples of H. dihystera and H. multicinctus . However, sequence and phylogenetic analysis using Bayesian inference and maximum parsimony analysis showed that isolates collected in different countries and morphologically identified as H. pseudorobustus , H. digonicus or H. vulgaris were each representative of several different and, sometimes, unrelated lineages. Further detailed comparative morphometrics and morphological studies will help to elucidate if there is some misidentification or if putative species actually comprise a complex of cryptic species. Molecular analysis also revealed that 14 samples were classified as representatives of 11 unidentified species. Molecular characterisation of known Helicotylenchus species especially, using samples collected from type localities, is needed for future reliable identification of species of this genus.

Apratylenchus vietnamensis gen. n., sp. n. and A. binhi gen. n., sp. n., sedentary Pratylenchidae (Nematoda: Tylenchida) from coffee in Vietnam, with proposal of Apratylenchinae subfam. n.

Apratylenchinae subfam. n. is proposed within the Pratylenchidae to include Apratylenchus gen. n. and two new species, A. vietnamensis gen. n., sp. n. and A. binhi gen. n., sp. n., from coffee plantations in Vietnam. Apratylenchus gen. n. is distinguished by the presence of transverse rows of cuticular tubercles on the annuli and by sexual dimorphism in which the males are stout and cylindrical, but mature sedentary females are club-shaped. The sedentary females are broadest in the posterior third although narrowing posterior to the vulva (V >= 85%). The female cephalic region is low and dome-shaped with all labial sectors fused to one another and the oral disc and the pharyngeal glands overlap the intestine ventrally. Males have a weak stylet with reduced knobs and a conical tail with a blunt terminus, arcuate spicules and a non-protrusible gubernaculum. Apratylenchus vietnamensis gen. n., sp. n. is characterised by a sedentary mature female with a 368-515 mu m long club-shaped body, cephalic region low, dome shaped with three annuli, body annuli bearing a single or double row of refractive tubercles, stylet 17.0-19.9 mu m long, V = ca 88-92, spermatheca filled with sperm and males known, if rarely found, in the type population. Males have a weak, 15 mu m long stylet with reduced knobs, 16 mu m spicules, a non-protrusible gubernaculum and low bursa. It differs from A. binhi gen. n., sp. n., the only other nominal species of the new genus, by longer female body (368-515 vs 326-364 mu m), longer distance from anterior end to anus (353-512 vs 310-348 mu m) and longer stylet (17.0-19.9 vs 14.7-16.9 mu m). In addition, the spermatheca is filled with round sperm vs empty in A. binhi gen. n., sp. n. and the cuticle has less densely spaced and less pronounced tubercles. D2/D3 sequences of the 28 rDNA gene clearly support the separation of Apratylenchus gen. n. from other Pratylenchidae and further distinguish the two new species from each other.

Cervidellus sonorensis n. sp. (Nematoda: Cephalobidae) from the desert of Anza-Borrego, CA, USA

Cervidellus sonorensis n. sp. is described from sand near the roots of creosote bush ( Larrea tridentata ) from Anza-Borrego Desert State Park, CA, USA. It is distinguished from others in the genus by the combination of a greatly distended, guitar-shaped corpus and the morphology of the lips and labial probolae. Distinctive features include a large pharyngeal metacorpus with a double swelling, a knob-like ledge at the base of each labial probola and lips with five filamentous tines, the most apical of which are those closest to the primary axil. One male individual was discovered in this parthenogenetic species. Characters used to diagnose C. sonorensis n. sp. are not definitive with respect to other genera and are probably plesiomorphic or convergent in light of DNA-based phylogenetic hypotheses. The position of C. sonorensis n. sp. and morphologically close congeners in relation to species of Nothacrobeles and Paracrobeles is discussed.