Variable Abundance and Distribution of Wolbachia and Cardinium Endosymbionts in Plant-Parasitic Nematode Field Populations

Both symbionts and environmental factors contribute to shape the microbiota in a pest insect, Sogatella furcifera

Introduction

Bacterial symbionts are prevalent in arthropods globally and play a vital role in the fitness and resistance of hosts. While several symbiont infections have been identified in the white-backed planthopper Sogatella furcifera, the impact of environmental factors on the microbiota within S. furcifera remains elusive.

Methods

In this study, a total of 142 S. furcifera individuals from 18 populations were collected from 14 locations across six countries (China, Thailand, Myanmar, Cambodia, Vietnam, and Laos) analyzed with 2bRAD-M sequencing, to examine the effects of symbionts on the microbiota in the S. furcifera population, as well as the vital effects of environmental factors on the bacterial communities.

Results and discussion

Based on the results, in S. furcifera, the presence of symbionts Wolbachia and Cardinium negatively influenced the abundance of other bacteria, including Enterobacter, Acinetobacter, and Lysinibacillus, while Wolbachia infection significantly decreased the diversity of the microbial community. Moreover, several environmental factors, including longitude, latitude, temperature, and precipitation, affected the abundance of symbionts and microbiota diversity in S. furcifera. These results collectively highlight the vital role of Wolbachia in S. furcifera microbiota, as well as the intricate effects of environmental factors on the bacterial communities of S. furcifera.

Wolbachia: Advancing into a Second Century

Wolbachia pipientis had its scientific debut nearly a century ago and has recently emerged as a target for therapeutic treatment of filarial infections and an attractive tool for control of arthropod pests. Wolbachia was known as a biological entity before DNA was recognized as the molecule that carries the genetic information on which life depends, and before arthropods and nematodes were grouped in the Ecdysozoa. Today, some investigators consider Wolbachia the most abundant endosymbiont on earth, given the numbers of its hosts and its diverse mutualistic, commensal, and parasitic roles in their life histories. Recent advances in molecular technologies have revolutionized our understanding of Wolbachia and its associated reproductive phenotypes. New models have emerged for its investigation, and substantial progress has been made towards Wolbachia-based interventions in medicine and agriculture. Here I introduce Wolbachia, with a focus on aspects of its biology that are covered in greater detail in subsequent chapters.

Detection and Analysis of Wolbachia in Plant-Parasitic Nematodes and Insights into Wolbachia Evolution

Since the discovery of Wolbachia in plant-parasitic nematodes (PPNs), there has been increased interest in this earliest branching clade that may hold important clues to early transitions in Wolbachia function in the Ecdysozoa. However, due to the specialized skills and equipment of nematology and the difficulty in culturing most PPNs, these PPN-type Wolbachia remain undersampled and poorly understood. To date, there are few established laboratory methods for working with PPN-type Wolbachia strains, and most research has relied on chance discovery and comparative genomics. Here, we address this challenge by providing detailed methods to assist researchers with more efficiently collecting PPNs and screen these communities, populations, or single nematodes with a newly developed PPN-type Wolbachia-specific PCR assay. We provide an overview of the typical yields and outcomes of these methods, to facilitate further targeted cultivation or experimental methods, and finally we provide a short introduction to some of the specific challenges and solutions in following through with comparative or population genomics on PPN-type Wolbachia strains.

Deep data mining reveals variable abundance and distribution of microbial reproductive manipulators within and among diverse host species

Bacterial symbionts that manipulate the reproduction of their hosts are important factors in invertebrate ecology and evolution, and are being leveraged for host biological control. Infection prevalence restricts which biological control strategies are possible and is thought to be strongly influenced by the density of symbiont infection within hosts, termed titer. Current methods to estimate infection prevalence and symbiont titers are low-throughput, biased towards sampling infected species, and rarely measure titer. Here we develop a data mining approach to estimate symbiont infection frequencies within host species and titers within host tissues. We applied this approach to screen ~32,000 publicly available sequence samples from the most common symbiont host taxa, discovering 2,083 arthropod and 119 nematode infected samples. From these data, we estimated that Wolbachia infects approximately 44% of all arthropod and 34% of all nematode species, while other reproductive manipulators only infect 1-8% of arthropod and nematode species. Although relative titers within hosts were highly variable within and between arthropod species, a combination of arthropod host species and Wolbachia strain explained approximately 36% of variation in Wolbachia titer across the dataset. To explore potential mechanisms for host control of symbiont titer, we leveraged population genomic data from the model system Drosophila melanogaster. In this host, we found a number of SNPs associated with titer in candidate genes potentially relevant to host interactions with Wolbachia. Our study demonstrates that data mining is a powerful tool to detect bacterial infections and quantify infection intensities, thus opening an array of previously inaccessible data for further analysis in host-symbiont evolution.

Distribution of Bacterial Endosymbionts of the Cardinium Clade in Plant-Parasitic Nematodes

Bacteria of the genus "Candidatus Cardinium" and related organisms composing the Cardinium clade are intracellular endosymbionts frequently occurring in several arthropod groups, freshwater mussels and plant-parasitic nematodes. Phylogenetic analyses based on two gene sequences (16S rRNA and gyrB) showed that the Cardinium clade comprised at least five groups: A, B, C, D and E. In this study, a screening of 142 samples of plant-parasitic nematodes belonging to 93 species from 12 families and two orders using PCR with specific primers and sequencing, revealed bacteria of Cardinium clade in 14 nematode samples belonging to 12 species of cyst nematodes of the family Heteroderidae. Furthermore, in this study, the genome of the Cardinium cHhum from the hop cyst nematode, Heterodera humuli, was also amplified, sequenced and analyzed. The comparisons of the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values for the strain Cardinium cHhum with regard to related organisms with available genomes, combined with the data on 16S rRNA and gyrB gene sequence identities, showed that this strain represents a new candidate species within the genus "Candidatus Paenicardinium". The phylogenetic position of endosymbionts of the Cardinium clade detected in nematode hosts was also compared to known representatives of this clade from other metazoans. Phylogenetic reconstructions based on analysis of 16S rRNA, gyrB, sufB, gloEL, fusA, infB genes and genomes and estimates of genetic distances both indicate that the endosymbiont of the root-lesion nematode Pratylenchus penetrans represented a separate lineage and is designated herein as a new group F. The phylogenetic analysis also confirmed that endosymbionts of ostracods represent the novel group G. Evolutionary relationships of bacterial endosymbionts of the Cardinium clade within invertebrates are presented and discussed.

Diversity and Regional Variation of Endosymbionts in the Green Peach Aphid, Myzus persicae (Sulzer)

The green peach aphid, Myzus persicae, is globally distributed and an important pest of many economically valuable food crops, largely due to its ability to transmit plant viruses. Almost all aphids, including M. persicae, carry the obligate symbiont Buchnera aphidicola, which provides essential amino acids that aphids cannot obtain from the phloem of plants themselves. Many aphids also harbor facultative (secondary) endosymbionts, which provide benefits under specific ecological conditions. In this study, we screened for secondary endosymbionts in M. persicae, with a particular focus on Australian populations where this species is growing in status as a major agricultural pest. We compared 37 Australian M. persicae populations with other populations, including 21 field populations from China and 15 clones from the UK, France, Italy, Greece, USA, Spain, South Korea, Chile, Japan and Zimbabwe. No secondary endosymbionts were identified in M. persicae samples outside of China, despite samples covering a wide geographic range and being collected from several host plant families. We detected two secondary endosymbionts (Rickettsia, Spiroplasma) in Chinese samples, although diversity appeared lower than detected in a recent study. We also found very high clonal diversity in Chinese samples based on DNA microsatellite markers in comparison with lower clonal diversity from Australia. These patterns may indicate a higher diversity of secondary endosymbionts (and clonal diversity) in the native range of M. persicae when compared to its invasive range.

A highly divergent Wolbachia with a tiny genome in an insect-parasitic tylenchid nematode

Wolbachia symbionts are the most successful host-associated microbes on the planet, infecting arthropods and nematodes. Their role in nematodes is particularly enigmatic, with filarial nematode species either 100% infected and dependent on symbionts for reproduction and development, or not at all infected. We have discovered a highly divergent strain of Wolbachia in an insect-parasitic tylenchid nematode, Howardula sp., in a nematode clade that has not previously been known to harbour Wolbachia. While this nematode is 100% infected with Wolbachia, we did not detect it in related species. We sequenced the Howardula symbiont (wHow) genome and found that it is highly reduced, comprising only 550 kilobase pairs of DNA, approximately 35% smaller than the smallest Wolbachia nematode symbiont genomes. The wHow genome is a subset of all other Wolbachia genomes and has not acquired any new genetic information. While it has lost many genes, including genes involved in cell wall synthesis and cell division, it has retained the entire haem biosynthesis pathway, suggesting that haem supplementation is critical. wHow provides key insights into our understanding of what are the lower limits of Wolbachia cells, as well as the role of Wolbachia symbionts in the biology and convergent evolution of diverse parasitic nematodes.

Establishment of Wolbachia infection in Aedes aegypti from Pakistan via embryonic microinjection and semi-field evaluation of general fitness of resultant mosquito population

Background

Dengue is a mosquito-borne viral disease that is mainly spread by Aedes aegypti. It is prevalent on five continents, predominantly in tropical and sub-tropical zones across the world. Wolbachia bacteria have been extensively used in vector control strategies worldwide. The focus of the current study was to obtain a natural population of Ae. aegypti harbouring Wolbachia and to determine the impact of this bacteria on the new host in a semi-field environment.

Methods

Wolbachia-infected Aedes albopictus was collected from the city of Lahore, Punjab, Pakistan, and Wolbachia were successfully introduced into laboratory-reared Ae. aegypti via embryonic microinjection. The stable vertical transmission of wAlbB in the host population was observed for eight generations, and the impact of Wolbachia on the general fitness of the host was evaluated in semi-field conditions.

Results

In the laboratory and semi-field experiments, wAlbB Wolbachia presented a strong cytoplasmic incompatibility (CI) effect, evidenced as zero egg hatching, in crosses between Wolbachia-infected males and wild (uninfected) females of Ae. aegypti. Wolbachia infection had no noticeable impact on the general fitness (P > 0.05), fecundity, body size (females and males) and mating competitiveness of the new host, Ae. aegypti. However, there was a significant decrease in female fertility (egg hatch) (P < 0.001). In addition, under starvation conditions, there was a remarkable decrease (P < 0.0001) in the life span of Wolbachia-infected females compared to uninfected females (4 vs. > 5 days, respectively).

Conclusions

Wolbachia strain wAlbB has a great potential to control the dengue vector in Ae. aegypti populations by producing 100% CI with a limited burden on its host in natural field conditions. This strain can be used as a biological tool against vector-borne diseases.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s13071-022-05317-4.

A Margulian View of Symbiosis and Speciation: the Nasonia Wasp System

Species are fundamental units of biology that exemplify lineage diversification, while symbiosis of microbes and macrobial hosts exemplify lineage unification between the domains of life. While these conceptual differences between speciation and symbiosis often dominate the narrative of the respective fields, Lynn Margulis argued for interconnection between these two subdisciplines of biology in a manner that left a legacy for scholars and students alike to pursue, detail, and discover. The Margulian perspective has always been that host evolutionary processes such as speciation are more impacted by microbial symbioses than typically appreciated. In this article, we present and review the case system that she long envisioned, one in which layers of microbial symbiosis reduce species interbreeding and assist species diversification among a closely related group of small, metallic green, parasitoid wasps from the genus Nasonia.

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

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 wTex, 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 wTex 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, wPni from aphids, wFol from springtails, and wCfeT 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 wCfeT, 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.

Molecular phylogeny of heritable symbionts and microbiota diversity analysis in phlebotominae sand flies and Culex nigripalpus from Colombia

Background

Secondary symbionts of insects include a range of bacteria and fungi that perform various functional roles on their hosts, such as fitness, tolerance to heat stress, susceptibility to insecticides and effects on reproduction. These endosymbionts could have the potential to shape microbial communites and high potential to develop strategies for mosquito-borne disease control.

Methodology/Principal findings

The relative frequency and molecular phylogeny of Wolbachia, Microsporidia and Cardinium were determined of phlebotomine sand flies and mosquitoes in two regions from Colombia. Illumina Miseq using the 16S rRNA gene as a biomarker was conducted to examine the microbiota. Different percentages of natural infection by Wolbachia, Cardinium, and Microsporidia in phlebotomines and mosquitoes were detected. Phylogenetic analysis of Wolbachia shows putative new strains of Lutzomyia gomezi (wLgom), Brumptomyia hamata (wBrham), and a putative new group associated with Culex nigripalpus (Cnig) from the Andean region, located in Supergroup A and Supergroup B, respectively. The sequences of Microsporidia were obtained of Pi. pia and Cx. nigripalpus, which are located on phylogeny in the IV clade (terrestrial origin). The Cardinium of Tr. triramula and Ps. shannoni were located in group C next to Culicoides sequences while Cardinium of Mi. cayennensis formed two putative new subgroups of Cardinium in group A. In total were obtained 550 bacterial amplicon sequence variants (ASVs) and 189 taxa to the genus level. The microbiota profiles of Sand flies and mosquitoes showed mainly at the phylum level to Proteobacteria (67.6%), Firmicutes (17.9%) and Actinobacteria (7.4%). High percentages of relative abundance for Wolbachia (30%-83%) in Lu. gomezi, Ev. dubitans, Mi. micropyga, Br. hamata, and Cx. nigripalpus were found. ASVs assigned as Microsporidia were found in greater abundance in Pi. pia (23%) and Cx. nigripalpus (11%). An important finding is the detection of Rickettsia in Pi. pia (58,8%) and Bartonella sp. in Cx. nigripalpus.

Conclusions/Significance

We found that Wolbachia infection significantly decreased the alpha diversity and negatively impacts the number of taxa on sand flies and Culex nigripalpus. The Principal Coordinate Analysis (PCoA) is consistent, which showed statistically significant differences (PERMANOVA, F = 2.4744; R2 = 0.18363; p-value = 0.007) between the microbiota of sand flies and mosquitoes depending on its origin, host and possibly for the abundance of some endosymbionts (Wolbachia, Rickettsia).

The secondary endosymbionts can positively influence the metabolism of many compounds essential for the survival of the insect vectors, provide resistance to pathogens and impact susceptibility to insecticides, as also the tolerance to heat stress. We provide information from new records of natural infection of secondary endosymbionts, such as Wolbachia, Cardinium, Microsporidia, Flavobacterium, and Rickettsia in phlebotomine sand flies and mosquitoes from Colombia. An important finding is the detection of Bartonella sp. in Cx. nigripalpus. Clear differences were found in the composition and diversity of microbiota at the intra-specific and interspecific levels in sand flies and Cx. nigripalpus, which may depend in the of the load of natural infection of endosymbionts (as Wolbachia), the geographical distribution and host.

Observations on a Novel Bacterial Pathogen of Root-Knot Nematodes (Meloidogyne spp.)

A novel Gram-negative pathogenic bacterium (BN) was discovered in second-stage juveniles (J2) of root-knot nematodes (RKN, Meloidogyne spp.). Mature bacteria showed a peculiar rod morphology characterized by four cells sequentially joined at septa. Mature rods measured 4–5 × 0.5–0.6 μm and were characterized by the emptying and tapering of both apical cells. The data showed an electron-dense external matrix forming a coating capsule involved in host attachment. The rods were not motile and packed in parallel inside the J2 body. After J2 penetration by adhering, germinating cells, the bacterium proliferated until the host body content was completely digested, producing a lethal disease. Parasitized hosts were recognized using light microscopy by a pale creamy-brown color assumed at parasitism completion. At death, the whole nematode body was filled with cells and only a few sclerotized esophageal structures (i.e., stylet, median bulb) remained visible. The BN cells were quickly released at host body rupture, suggesting that J2 infection occurs through passive adhesion of cells dispersed in soil. The bacterium appeared fastidious, as attempts to obtain pure cultures on common nutritive media failed.

'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.

Newly introduced Cardinium endosymbiont reduces microbial diversity in the rice brown planthopper Nilaparvata lugens

Symbiotic microorganisms in invertebrates play vital roles in host ecology and evolution. Cardinium, a common intracellular symbiont, is transinfected into the important agricultural pest Nilaparvata lugens (rice brown planthopper) to regulate its reproduction, but how this impacts its microbial community is unknown. Here, we characterized the bacterial microbiota from N. lugens, with or without Cardinium, at different developmental stages and in various adult tissues using 16S ribosomal ribonucleic acid (16S rRNA) gene sequencing. Upon infection with Cardinium, we found that microbial diversity in the different developmental stages of N. lugens (especially females), and in female midguts and male testes, was lower than that in the uninfected control. There was a negative correlation between Cardinium and most related genera and between Bacteroidetes and Proteobacteria. Although the microbial structure varied during Cardinium infection, Acinetobacter spp. were a core microbiome genus. The Cardinium infection enhanced the relative density of midgut-associated Acinetobacter spp., with both bacteria exhibiting tissue-specific tropism. In addition, this infection caused the changes of main microbial functions in N. lugens. These results offer insights into the effects of alien (i.e. newly introduced from other organism) Cardinium infection on N. lugens-associated microbiotas, aiding in the development of transinfected endosymbionts for pest control.

Gall-Inducing Parasites: Convergent and Conserved Strategies of Plant Manipulation by Insects and Nematodes

Gall-inducing insects and nematodes engage in sophisticated interactions with their host plants. These parasites can induce major morphological and physiological changes in host roots, leaves, and other tissues. Sedentary endoparasitic nematodes, root-knot and cyst nematodes in particular, as well as gall-inducing and leaf-mining insects, manipulate plant development to form unique organs that provide them with food from feeding cells. Sometimes, infected tissues may undergo a developmental switch resulting in the formation of aberrant and spectacular structures (clubs or galls). We describe here the complex interactions between these plant-reprogramming sedentary endoparasites and their infected hosts, focusing on similarities between strategies of plant manipulation. We highlight progress in our understanding of the host plant response to infection and focus on the nematode and insect molecules secreted in planta. We suggest thatlooking at similarities may identify convergent and conserved strategies and shed light on the promise they hold for the development of new management strategies in agriculture and forestry.

Stable Establishment of Cardinium spp. in the Brown Planthopper Nilaparvata lugens despite Decreased Host Fitness

The brown planthopper Nilaparvata lugens (Hemiptera) is a major pest of rice crops in Asia. Artificial transinfections of Wolbachia have recently been used for reducing host impacts, but transinfections have not yet been undertaken with another important endosymbiont, Cardinium This endosymbiont can manipulate the reproduction of hosts through phenotypes such as cytoplasmic incompatibility (CI), which is strong in the related white-backed planthopper, Sogatella furcifera (Hemiptera). Here, we stably infected N. lugens with Cardinium from S. furcifera and showed that it exhibits perfect maternal transmission in N. lugens The density of Cardinium varied across developmental stages and tissues of the transinfected host. Cardinium did not induce strong CI in N. lugens, likely due to its low density in testicles. The infection did decrease fecundity and hatching rate in the transinfected host, but a decrease in fecundity was not apparent when transinfected females mated with Wolbachia-infected males. The experiments show the feasibility of transferring Cardinium endosymbionts across hosts, but the deleterious effects of Cardinium on N. lugens limit its potential to spread in wild populations of N. lugens in the absence of strong CI.IMPORTANCE In this study we established a Cardinium-infected N. lugens line that possessed complete maternal transmission. Cardinium had a widespread distribution in tissues of N. lugens, and this infection decreased the fecundity and hatching rate of the host. Our findings emphasize the feasibility of transinfection of Cardinium in insects, which expands the range of endosymbionts that could be manipulated for pest control.