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1. Discovery of a novel Wolbachia in Heterodera expands nematode host distribution

   https://doi.org/10.3389/fmicb.2024.1446506  

   Kaur, Taranjot; Brown, Amanda MV (September 2024, Frontiers in Microbiology)

   Bioinformatics sequence data mining can reveal hidden microbial symbionts that might normally be filtered and removed as contaminants. Data mining can be helpful to detect Wolbachia, a widespread bacterial endosymbiont in insects and filarial nematodes whose distribution in plant-parasitic nematodes (PPNs) remains underexplored. To date, Wolbachia has only been reported a few PPNs, yet nematode-infecting Wolbachia may have been widespread in the evolutionary history of the phylum based on evidence of horizontal gene transfers, suggesting there may be undiscovered Wolbachia infections in PPNs. The goal of this study was to more broadly sample PPN Wolbachia strains in tylenchid nematodes to enable further comparative genomic analyses that may reveal Wolbachia’s role and identify targets for biocontrol. Published whole-genome shotgun assemblies and their raw sequence data from 33 Meloidogyne spp. assemblies, seven Globodera spp. assemblies, and seven Heterodera spp. assemblies were analyzed to look for Wolbachia. No Wolbachia was found in Meloidogyne spp. and Globodera spp., but among seven genome assemblies for Heterodera spp., an H. schachtii assembly from the Netherlands was found to have a large Wolbachia-like sequence that, when re-assembled from reads, formed a complete, circular genome. Detailed analyses comparing read coverage, GC content, pseudogenes, and phylogenomic patterns clearly demonstrated that the H. schachtii Wolbachia represented a novel strain (hereafter, denoted wHet). Phylogenomic tree construction with PhyloBayes showed wHet was most closely related to another PPN Wolbachia, wTex, while 16S rRNA gene analysis showed it clustered with other Heterodera Wolbachia assembled from sequence databases. Pseudogenes in wHet suggested relatedness to the PPN clade, as did the lack of significantly enriched GO terms compared to PPN Wolbachia strains. It remains unclear whether the lack of Wolbachia in other published H. schachtii isolates represents the true absence of the endosymbiont from some hosts. 

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2. Stochastic Fluctuations of the Facultative Endosymbiont Wolbachia due to Finite Host Population Size

   https://doi.org/10.1002/ece3.71989  

   Graham, Jason M; Klobusicky, Joseph; Hague, Michael_T J (August 2025, Ecology and Evolution)

   ABSTRACT Many insects and other animals host heritable endosymbionts that alter host fitness and reproduction. The prevalence of facultative endosymbionts can fluctuate in host populations across time and geography for reasons that are poorly understood. This is particularly true for maternally transmittedWolbachiabacteria, which infect roughly half of all insect species. For instance, the frequencies of severalwMel‐likeWolbachia, includingwMel in hostDrosophila melanogaster, fluctuate over time in certain host populations, but the specific conditions that generate temporal variation inWolbachiaprevalence are unresolved. We implemented a discrete generation model in the new R packagesymbiontmodelerto evaluate how finite‐population stochasticity contributes toWolbachiafluctuations over time in simulated host populations under a variety of conditions. Using empirical estimates from naturalWolbachia‐Drosophilasystems, we explored how stochasticity is determined by a broad range of factors, including host population size, maternal transmission rates, andWolbachiaeffects on host fitness (modeled as fecundity) and reproduction (cytoplasmic incompatibility; CI). While stochasticity generally increases when host fitness benefits and CI are relaxed, we found that a decline in the maternal transmission rate had the strongest relative impact on increasing the size of fluctuations. We infer that non‐ or weak‐CI‐causing strains likewMel, which often show evidence of imperfect maternal transmission, tend to generate larger stochastic fluctuations compared to strains that cause strong CI, likewRi inD. simulans. Additional factors, such as fluctuating host fitness effects, are required to explain the largest examples of temporal variation inWolbachia. The conditions we simulate here usingsymbiontmodelerserve as a jumping‐off point for understanding drivers of temporal and spatial variation in the prevalence ofWolbachia, the most common endosymbionts found in nature. 

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3. The Foliar Microbiome Suggests that Fungal and Bacterial Agents May be Involved in the Beech Leaf Disease Pathosystem

   https://doi.org/10.1094/PBIOMES-12-20-0088-R  

   Ewing, Carrie J.; Slot, Jason; Benítez, María-Soledad; Rosa, Cristina; Malacrinò, Antonino; Bennett, Alison; Bonello, Enrico (January 2021, Phytobiomes Journal)

   Beech leaf disease (BLD) is a recently discovered disease that is causing severe damage to American beech (Fagus grandifolia) in northeastern North America. The recently described nematode Litylenchus crenatae subsp. mccannii was detected in BLD-affected foliage and may be associated with the disease. However, speculation on the direct role of the nematode in infection still remains. In this study, we profiled the microbial communities associated with asymptomatic, symptomatic, and naïve (control) American beech foliage by using a high-throughput sequence-based metabarcoding analysis of fungi, bacteria, phytoplasmas, and nematodes. We then used both a differential abundance analysis and indicator species analysis as well as several diversity metrics to try and discover microbes associated only with symptomatic foliage. To do so, we amplified the organism-specific phylogenetic informative regions of the 16S, 18S, and internal transcribed spacer (ITS)1 regions using Illumina MiSeq. Our results detected the amplicon sequence variant (ASV) associated with the nematode L. crenatae subsp. mccannii but in all symptom types. However, four ASVs associated with the bacterial genera Wolbachia, Erwinia, Paenibacillus, and Pseudomonas and one ASV associated with the fungal genus Paraphaeosphaeria were detected only in symptomatic samples. In addition, we identified significant differences based on symptom type in both the α- and β-diversity indices for the bacterial and fungal communities. These results suggest that L. crenatae subsp. mccannii may not be fully responsible for BLD but, rather, that other microbes may be contributing to the syndrome, including the putative nematode endosymbiont Wolbachia sp. 

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4. A continental-scale survey of Wolbachia infections in blue butterflies reveals evidence of interspecific transfer and invasion dynamics

   Shastry, V.; Bell, K. L.; Buerkle, C. A.; Fordyce, J. A.; Forister, M. L.; Gompert, Z.; Lebeis, S. L.; Lucas, L. K.; Marion, Z. H.; Nice, C. C. (August 2022, Genes genomes genomics)

   Infections by maternally inherited bacterial endosymbionts, especially Wolbachia, are common in insects and other invertebrates but infec- tion dynamics across species ranges are largely under studied. Specifically, we lack a broad understanding of the origin of Wolbachia infec- tions in novel hosts, and the historical and geographical dynamics of infections that are critical for identifying the factors governing their spread. We used Genotype-by-Sequencing data from previous population genomics studies for range-wide surveys of Wolbachia pres- ence and genetic diversity in North American butterflies of the genus Lycaeides. As few as one sequence read identified by assembly to a Wolbachia reference genome provided high accuracy in detecting infections in host butterflies as determined by confirmatory PCR tests, and maximum accuracy was achieved with a threshold of only 5 sequence reads per host individual. Using this threshold, we detected Wolbachia in all but 2 of the 107 sampling localities spanning the continent, with infection frequencies within populations ranging from 0% to 100% of individuals, but with most localities having high infection frequencies (mean 1⁄4 91% infection rate). Three major lineages of Wolbachia were identified as separate strains that appear to represent 3 separate invasions of Lycaeides butterflies by Wolbachia. Overall, we found extensive evidence for acquisition of Wolbachia through interspecific transfer between host lineages. Strain wLycC was confined to a single butterfly taxon, hybrid lineages derived from it, and closely adjacent populations in other taxa. While the other 2 strains were detected throughout the rest of the continent, strain wLycB almost always co-occurred with wLycA. Our demographic modeling suggests wLycB is a recent invasion. Within strain wLycA, the 2 most frequent haplotypes are confined almost exclusively to separate butterfly taxa with haplotype A1 observed largely in Lycaeides melissa and haplotype A2 observed most often in Lycaeides idas localities, consistent with either cladogenic mode of infection acquisition from a common ancestor or by hybridization and accompanying mutation. More than 1 major Wolbachia strain was observed in 15 localities. These results demonstrate the utility of using resequencing data from hosts to quan- tify Wolbachia genetic variation and infection frequency and provide evidence of multiple colonizations of novel hosts through hybridiza- tion between butterfly lineages and complex dynamics between Wolbachia strains. 

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5. Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes

   https://doi.org/10.3389/fmicb.2022.867392  

   Weyandt, Nicholas; Aghdam, Shiva A.; Brown, Amanda M. (April 2022, Frontiers in Microbiology)

   Wolbachia is a widespread endosymbiont of insects and filarial nematodes that profoundly influences host biology. Wolbachia has also been reported in rhizosphere hosts, where its diversity and function remain poorly characterized. The discovery that plant-parasitic nematodes (PPNs) host Wolbachia strains with unknown roles is of interest evolutionarily, ecologically, and for agriculture as a potential target for developing new biological controls. The goal of this study was to screen communities for PPN endosymbionts and analyze genes and genomic patterns that might indicate their role. Genome assemblies revealed 1 out of 16 sampled sites had nematode communities hosting a Wolbachia strain, designated w Tex, that has highly diverged as one of the early supergroup L strains. Genome features, gene repertoires, and absence of known genes for cytoplasmic incompatibility, riboflavin, biotin, and other biosynthetic functions placed w Tex between mutualist C + D strains and reproductive parasite A + B strains. Functional terms enriched in group L included protoporphyrinogen IX, thiamine, lysine, fatty acid, and cellular amino acid biosynthesis, while dN/dS analysis suggested the strongest purifying selection on arginine and lysine metabolism, and vitamin B6, heme, and zinc ion binding, suggesting these as candidate roles in PPN Wolbachia . Higher dN/dS pathways between group L, w Pni from aphids, w Fol from springtails, and w CfeT from cat fleas suggested distinct functional changes characterizing these early Wolbachia host transitions. PPN Wolbachia had several putative horizontally transferred genes, including a lysine biosynthesis operon like that of the mitochondrial symbiont Midichloria , a spirochete-like thiamine synthesis operon shared only with w CfeT, an ATP/ADP carrier important in Rickettsia , and a eukaryote-like gene that may mediate plant systemic acquired resistance through the lysine-to-pipecolic acid system. The Discovery of group L-like variants from global rhizosphere databases suggests diverse PPN Wolbachia strains remain to be discovered. These findings support the hypothesis of plant-specialization as key to shaping early Wolbachia evolution and present new functional hypotheses, demonstrating promise for future genomics-based rhizosphere screens. 

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