New evidence of nematode-endosymbiont bacteria coevolution based on one new and one known dagger nematode species of Xiphinema americanum-group (Nematoda, Longidoridae)

The evolution of entomopathogeny in nematodes

Understanding how parasites evolved is crucial to understand the host and parasite interaction. The evolution of entomopathogenesis in rhabditid nematodes has traditionally been thought to have occurred twice within the phylum Nematoda: in Steinernematidae and Heterorhabditidae families, which are associated with the entomopathogenic bacteria Xenorhabdus and Photorhabdus, respectively. However, nematodes from other families that are associated with entomopathogenic bacteria have not been considered to meet the criteria for "entomopathogenic nematodes." The evolution of parasitism in nematodes suggests that ecological and evolutionary properties shared by families in the order Rhabditida favor the convergent evolution of the entomopathogenic trait in lineages with diverse lifestyles, such as saprotrophs, phoretic, and necromenic nematodes. For this reason, this paper proposes expanding the term "entomopathogenic nematode" considering the diverse modes of this attribute within Rhabditida. Despite studies are required to test the authenticity of the entomopathogenic trait in the reported species, they are valuable links that represent the early stages of specialized lineages to entomopathogenic lifestyle. An ecological and evolutionary exploration of these nematodes has the potential to deepen our comprehension of the evolution of entomopathogenesis as a convergent trait spanning across the Nematoda.

A new species of Xiphinema americanum group (Nematoda: Longidoridae) from Iran, with additional data on three known species

One new and three known species of the genus Xiphinema from the rhizosphere of fruit trees and rose shrubs in East Azarbaijan province, Iran, are presented based on the morphological, morphometric and molecular characters. The new species is distinguished by its 2.0-2.1 mm long body, relatively flattened lip region with 8.7-10.0 µm width, set off from body contour by a deep constriction, odontostyle 82.5-88.0 µm long, V = 52-54, reproductive system didelphic-amphidelphic with symbiotic bacteria in the reflexed ovaries, tail conoid, dorsally convex with rounded to slightly subdigitate tip (42.0-43.5 µm long, c = 61-65, c' = 1.6-1.8), and males unknown. The new species, X. babaii sp. n., looks very close to X. californicum, and is regarded as its cryptic species, being separated from it using some morphological differences. Their separation was further corroborated using molecular data. Three known species belonging to the Xiphinema americanum group namely X. primum, X. pachtaicum and X. simile were also collected during present study, and new data were provided for them. Xiphinema simile is a new record for the Iran's nematode fauna. Molecular phylogenetic studies using partial sequences of 28S rRNA gene D2-D3 fragments were performed, and the phylogenetic relationships of the new species were discussed.

Assessment of Physicochemical, Microbiological and Toxicological Hazards at an Illegal Landfill in Central Poland

This study aimed to assess the physicochemical, microbiological and toxicological hazards at an illegal landfill in central Poland. The research included the analysis of airborne dust (laser photometer), the number of microorganisms in the air, soil and leachate (culture method) and the microbial diversity in the landfill environment (high-throughput sequencing on the Illumina Miseq); the cytotoxicity (PrestoBlue) and genotoxicity (alkaline comet assay) of soil and leachate were tested. Moreover, an analysis of UHPLC-Q-ToF-UHRMS (ultra-high-performance liquid chromatography-quadrupole-time-of-flight ultrahigh-resolution mass spectrometry) was performed to determine the toxic compounds and microbial metabolites. The PM₁ dust fraction constituted 99.89% and 99.99% of total dust and exceeded the threshold of 0.025 mg m⁻³ at the tested locations. In the air, the total number of bacteria was 9.33 × 10¹–1.11 × 10³ CFU m⁻³, while fungi ranged from 1.17 × 10² to 4.73 × 10² CFU m⁻³. Psychrophilic bacteria were detected in the largest number in leachates (3.3 × 10⁴ to 2.69 × 10⁶ CFU mL⁻¹) and in soil samples (8.53 × 10⁵ to 1.28 × 10⁶ CFU g⁻¹). Bacteria belonging to Proteobacteria (42–64.7%), Bacteroidetes (4.2–23.7%), Actinobacteria (3.4–19.8%) and Firmicutes (0.7–6.3%) dominated. In the case of fungi, Basidiomycota (23.3–27.7%), Ascomycota (5.6–46.3%) and Mortierellomycota (3.1%) have the highest abundance. Bacteria (Bacillus, Clostridium, Cellulosimicrobium, Escherichia, Pseudomonas) and fungi (Microascus, Chrysosporium, Candida, Malassezia, Aspergillus, Alternaria, Fusarium, Stachybotrys, Cladosporium, Didymella) that are potentially hazardous to human health were detected in samples collected from the landfill. Tested leachates and soils were characterised by varied cyto/genotoxins. Common pesticides (carbamazepine, prometryn, terbutryn, permethrin, carbanilide, pyrethrin, carbaryl and prallethrin), quaternary ammonium compounds (benzalkonium chlorides), chemicals and/or polymer degradation products (melamine, triphenylphosphate, diphenylphtalate, insect repellent diethyltoluamide, and drugs (ketoprofen)) were found in soil and leachate samples. It has been proven that the tested landfill is the source of the emission of particulate matter; microorganisms (including potential pathogens) and cyto/genotoxic compounds.

Phytobacter diazotrophicus from Intestine of Caenorhabditis elegans Confers Colonization-Resistance against Bacillus nematocida Using Flagellin (FliC) as an Inhibition Factor

Symbiotic microorganisms in the intestinal tract can influence the general fitness of their hosts and contribute to protecting them against invading pathogens. In this study, we obtained isolate Phytobacter diazotrophicus SCO41 from the gut of free-living nematode Caenorhabditis elegans that displayed strong colonization-resistance against invading biocontrol bacterium Bacillus nematocida B16. The colonization-resistance phenotype was found to be mediated by a 37-kDa extracellular protein that was identified as flagellin (FliC). With the help of genome information, the fliC gene was cloned and heterologously expressed in E. coli. It could be shown that the B. nematocida B16 grows in chains rather than in planktonic form in the presence of FliC. Scanning Electronic Microscopy results showed that protein FliC-treated B16 bacterial cells are thinner and longer than normal cells. Localization experiments confirmed that the protein FliC is localized in both the cytoplasm and the cell membrane of B16 strain, in the latter especially at the position of cell division. ZDOCK analysis showed that FliC could bind with serine/threonine protein kinase, membrane protein insertase YidC and redox membrane protein CydB. It was inferred that FliC interferes with cell division of B. nematocidal B16, therefore inhibiting its colonization of C. elegans intestines in vivo. The isolation of P. diazotrophicus as part of the gut microbiome of C. elegans not only provides interesting insights about the lifestyle of this nitrogen-fixing bacterium, but also reveals how the composition of the natural gut microbiota of nematodes can affect biological control efforts by protecting the host from its natural enemies.

'Candidatus Xiphinematincola pachtaicus' gen. nov., sp. nov., an endosymbiotic bacterium associated with nematode species of the genus Xiphinema (Nematoda, Longidoridae)

An intracellular bacterium, strain IAST, was observed to infect several species of the plant-parasitic nematode genus Xiphinema (Xiphinema astaregiense, Xiphinema incertum, Xiphinema madeirense, Xiphinema pachtaicum, Xiphinema parapachydermum and Xiphinema vallense). The bacterium could not be recovered on axenic medium. The 16S rRNA gene sequence of IAST was found to be new, being related to the family Burkholderiaceae, class Betaproteobacteria. Fungal endosymbionts Mycoavidus cysteinexigens B1-EBT (92.9 % sequence identity) and 'Candidatus Glomeribacter gigasporarum' BEG34 (89.8 % identity) are the closest taxa and form a separate phylogenetic clade inside Burkholderiaceae. Other genes (atpD, lepA and recA) also separated this species from its closest relatives using a multilocus sequence analysis approach. These genes were obtained using a partial genome of this bacterium. The localization of the bacterium (via light and fluorescence in situ hybridization microscopy) is in the X. pachtaicum females clustered around the developing oocytes, primarily found embedded inside the epithelial wall cells of the ovaries, from where they are dispersed in the intestine. Transmission electron microscopy (TEM) observations supported the presence of bacteria inside the nematode body, where they occupy ovaries and occur inside the intestinal epithelium. Ultrastructural analysis of the bacterium showed cells that appear as mostly irregular, slightly curved rods with rounded ends, 0.8-1.2 µm wide and 2.5-6.0 µm long, possessing a typical Gram-negative cell wall. The peptidoglycan layer is, however, evident only occasionally and not detectable by TEM in most cells. Another irregularly occurring shell surrounding the endosymbiont cells or the cell clusters was also revealed, probably originating from the host cell membrane. Flagella or spore-like cells do not occur and the nucleoid is diffusely distributed throughout the cell. This endosymbiont is transmitted vertically through nematode generations. These results support the proposal of IAST as a new species, although its obligate intracellular and obligate endosymbiont nature prevented isolation of a definitive type strain. Strain IAST is therefore proposed as representing 'Candidatus Xiphinematincola pachtaicus' gen. nov., sp. nov.

Description of Longidorella (Saevadorella) caspica n. sp. (Dorylaimida: Nordiidae) from north Iran

This contribution provides the morphological and molecular identification of a new species of the genus Longidorella (Saevadorella). L. (S.) caspica n. sp., was recovered from the rhizospheric soil of grasses in Mazandaran province in the seashore of the Caspian Sea. It is characterized by females with a length of 788 to 874 μm and a cephalic region with prominent papillae; and separated from the rest of the body by a remarkable constriction, an odontostyle of 32 to 33 μm, vulva at 52.5 to 59.0%, and a tail of 33 to 38 μm with a rounded tip. Males have 32 to 35 μm long spicules of dorylaimoid form and five to seven ventral supplements ending at 48 to 55 μm distance from cloacal pair. The new species was morphologically compared with seven nominal species viz. L. (S.) arenicola, L. (S.) cuspidata, L. (S.) magna, L. (S.) perplexa, L. (S.) saadi, L. (S.) saevae, and L. (S.) tharensis. It was further compared with similar species under the subgenus Longidorella (Enchodorella) viz. L. (E.) deliblatica and L. (E.) murithi. Besides morphological studies, molecular phylogenetic studies using partial sequences of D2 to D3 expansion fragments of 28S rDNA were performed for the new species and its phylogenetic relationships with other species and genera were discussed.

Essential Amino Acid Enrichment and Positive Selection Highlight Endosymbiont's Role in a Global Virus-Vectoring Pest

Host-associated microbes display remarkable convergence in genome repertoire resulting from selection to supplement missing host functions. Nutritional supplementation has been proposed in the verrucomicrobial endosymbiont Xiphinematobacter sp., which lives within a globally widespread group of plant-parasitic nematodes that vector damaging nepoviruses to plants. Only one genome sequence has been published from this symbiont, leaving unanswered questions about its diversity, host range, role, and selective pressures within its hosts. Because its hosts are exceptionally resistant to culturing, this symbiont is best studied through advanced genomic approaches. To analyze the role of Xiphinematobacter sp. in its host, sequencing was performed on nematode communities, and then genomes were extracted for comparative genomics, gene ontology enrichment tests, polymorphism analysis, de Bruijn-based genome-wide association studies, and tests of pathway- and site-specific selection on genes predicted play a role in the symbiosis. Results showed a closely clustered set of Xiphinematobacter isolates with reduced genomes of ∼917 kbp, for which a new species was proposed. Symbionts shared only 2.3% of genes with outgroup Verrucomicrobia, but comparative analyses showed high conservation of all 10 essential amino acid (EAA) biosynthesis pathways plus several vitamin pathways. These findings were supported by gene ontology enrichment tests and high polymorphisms in these pathways compared with background. Genome-wide association analysis confirmed high between-species fixation of alleles with significant functional enrichment for EAA and thiamine synthesis. Strong positive selection was detected on sites within these pathways, despite several being under increased purifying selection. Together, these results suggest that supplementation of EAAs missing in the host diet may drive this widespread symbiosis.IMPORTANCE Xiphinematobacter spp. are distinctly evolved intracellular symbionts in the phylum Verrucomicrobia, which includes the important human gut-associated microbe Akkermansia muciniphila and many highly abundant free-living soil microbes. Like Akkermansia sp., Xiphinematobacter sp. is obligately associated with the gut of its hosts, which in this case consists of a group of plant-parasitic nematodes that are among the top 10 most destructive species to global agriculture, by vectoring plant viruses. This study examined the hypothesis that the key to this symbiont's stable evolutionary association with its host is through provisioning nutrients that its host cannot make that may be lacking in the nematode's plant phloem diet, such as essential amino acids and several vitamins. The significance of our research is in demonstrating, using population genomics, the signatures of selective pressure on these hypothesized roles to ultimately learn how this independently evolved symbiont functionally mirrors symbionts of phloem-feeding insects.

Three Species of Xiphinema Americanum-group Complex (Nematoda: Longidoridae), from Lorestan Province, Iran

The dagger nematodes of the longidorids can cause diseases of various agronomic and horticultural crops, and are consisted of more than 260 valid species. In a forest survey of ecotypes of longidorid nematodes, from the root zone soil of Brant’s oak, (Quercus brantii Lindl.) and hawthorn (Crataegus aronia L.) trees, three species of Xiphinema americanum group namely Xiphinema pachtaicum, X. oxycaudatum and X. plesiopachtaicum were collected and studied based on their morphological and morphometric characters. X. pachtaicum is prevalent Xiphinema species in Iran. In this paper additional data for X. oxycaudatum and X. plesiopachtaicum species are presented. X. plesiopachtaicum is a new record for nematode fauna of Iran.

Core and Differentially Abundant Bacterial Taxa in the Rhizosphere of Field Grown Brassica napus Genotypes: Implications for Canola Breeding

Modifying the rhizosphere microbiome through targeted plant breeding is key to harnessing positive plant-microbial interrelationships in cropping agroecosystems. Here, we examine the composition of rhizosphere bacterial communities of diverse Brassica napus genotypes to identify: (1) taxa that preferentially associate with genotypes, (2) core bacterial microbiota associated with B. napus, (3) heritable alpha diversity measures at flowering and whole growing season, and (4) correlation between microbial and plant genetic distance among canola genotypes at different growth stages. Our aim is to identify and describe signature microbiota with potential positive benefits that could be integrated in B. napus breeding and management strategies. Rhizosphere soils of 16 diverse genotypes sampled weekly over a 10-week period at single location as well as at three time points at two additional locations were analyzed using 16S rRNA gene amplicon sequencing. The B. napus rhizosphere microbiome was characterized by diverse bacterial communities with 32 named bacterial phyla. The most abundant phyla were Proteobacteria, Actinobacteria, and Acidobacteria. Overall microbial and plant genetic distances were highly correlated (R = 0.65). Alpha diversity heritability estimates were between 0.16 and 0.41 when evaluated across growth stage and between 0.24 and 0.59 at flowering. Compared with a reference B. napus genotype, a total of 81 genera were significantly more abundant and 71 were significantly less abundant in at least one B. napus genotype out of the total 558 bacterial genera. Most differentially abundant genera were Proteobacteria and Actinobacteria followed by Bacteroidetes and Firmicutes. Here, we also show that B. napus genotypes select an overall core bacterial microbiome with growth-stage-related patterns as to how taxa joined the core membership. In addition, we report that sets of B. napus core taxa were consistent across our three sites and 2 years. Both differential abundance and core analysis implicate numerous bacteria that have been reported to have beneficial effects on plant growth including disease suppression, antifungal properties, and plant growth promotion. Using a multi-site year, temporally intensive field sampling approach, we showed that small plant genetic differences cause predictable changes in canola microbiome and are potential target for direct and indirect selection within breeding programs.

Data of an Iranian Population of L. proximus Sturhan & Argo, 1983, with taxonomic revision of L. israelensis Peneva, Orion, Shlevin, Bar-Eyal & Brown, 1998 (Nematoda: Longidoridae) and Proposal for a New Synonymy

The morphology and morphometric characteristics of a Longidorus population recovered from a wheat-potato field in Hamadan province, western Iran, fit well with those given for two species, L. proximus and L. israelensis. The Iranian population was characterized by 5.6 to 8.6-mm-long females having a 17 to 21-µm-wide lip region separated from the rest of the body by a shallow depression, pocket-shaped amphidial fovea with a simple base and a ventral enlargement, a guiding ring at 31 to 40 µm distance from the anterior end, 108 to 127-µm-long odontostyle, 58 to 64-µm-long odontophore, 101 to 129-µm-long pharyngeal bulb with remarkably larger dorsal gland nucleus (at 49 to 53% of the bulb length) and two smaller ventrosublateral nuclei (at 66 to 76% of the pharyngeal bulb length), four juvenile developmental stages, and a rare male. The morphological and molecular data corroborated its assignment to the species L. proximus. In molecular phylogenetic analyses using partial LSU rDNA D2-D3 sequences, the presently studied Iranian population and previously sequenced isolates of L. proximus formed a clade with L. cretensis, L. iranicus, L. pseudoelongatus, and L. closelongatus, all except L. pseudoelongatus with no available data, having the similar pharyngeal gland nuclei size and arrangement. In internal transcribed spacer 1 (ITS1) phylogeny, it formed a clade with L. sturhani and four aforementioned species. The characters delimiting the two species L. proximus and L. israelensis were discussed and a new synonymy was proposed.