Symbiotic bacteria of the gall-inducing mite Fragariocoptes setiger (Eriophyoidea) and phylogenomic resolution of the eriophyoid position among Acari

Phylogenomics resolves the higher-level phylogeny of herbivorous eriophyoid mites (Acariformes: Eriophyoidea)

BACKGROUND

Eriophyoid mites (Eriophyoidea) are among the largest groups in the Acariformes; they are strictly phytophagous. The higher-level phylogeny of eriophyoid mites, however, remains unresolved due to the limited number of available morphological characters-some of them are homoplastic. Nevertheless, the eriophyoid mites sequenced to date showed highly variable mitochondrial (mt) gene orders, which could potentially be useful for resolving the higher-level phylogenetic relationships.

RESULTS

Here, we sequenced and compared the complete mt genomes of 153 eriophyoid mite species, which showed 54 patterns of rearranged mt gene orders relative to that of the hypothetical ancestor of arthropods. The shared derived mt gene clusters support the monophyly of eriophyoid mites (Eriophyoidea) as a whole and the monophylies of six clades within Eriophyoidea. These monophyletic groups and their relationships were largely supported in the phylogenetic trees inferred from mt genome sequences as well. Our molecular dating results showed that Eriophyoidea originated in the Triassic and diversified in the Cretaceous, coinciding with the diversification of angiosperms.

CONCLUSIONS

This study reveals multiple molecular synapomorphies (i.e. shared derived mt gene clusters) at different levels (i.e. family, subfamily or tribe level) from the complete mt genomes of 153 eriophyoid mite species. We demonstrated the use of derived mt gene clusters in unveiling the higher-level phylogeny of eriophyoid mites, and underlines the origin of these mites and their co-diversification with angiosperms.

Microbiome and plant cell transformation trigger insect gall induction in cassava

Several specialised insects can manipulate normal plant development to induce a highly organised structure known as a gall, which represents one of the most complex interactions between insects and plants. Thus far, the mechanism for insect-induced plant galls has remained elusive. To study the induction mechanism of insect galls, we selected the gall induced by Iatrophobia brasiliensis (Diptera: Cecidomyiidae) in cassava (Euphorbiaceae: Manihot esculenta Crantz) as our model. PCR-based molecular markers and deep metagenomic sequencing data were employed to analyse the gall microbiome and to test the hypothesis that gall cells are genetically transformed by insect vectored bacteria. A shotgun sequencing discrimination approach was implemented to selectively discriminate between foreign DNA and the reference host plant genome. Several known candidate insertion sequences were identified, the most significant being DNA sequences found in bacterial genes related to the transcription regulatory factor CadR, cadmium-transporting ATPase encoded by the cadA gene, nitrate transport permease protein (nrtB gene), and arsenical pump ATPase (arsA gene). In addition, a DNA fragment associated with ubiquitin-like gene E2 was identified as a potential accessory genetic element involved in gall induction mechanism. Furthermore, our results suggest that the increased quality and rapid development of gall tissue are mostly driven by microbiome enrichment and the acquisition of critical endophytes. An initial gall-like structure was experimentally obtained in M. esculenta cultured tissues through inoculation assays using a Rhodococcus bacterial strain that originated from the inducing insect, which we related to the gall induction process. We provide evidence that the modification of the endophytic microbiome and the genetic transformation of plant cells in M. esculenta are two essential requirements for insect-induced gall formation. Based on these findings and having observed the same potential DNA marker in galls from other plant species (ubiquitin-like gene E2), we speculate that bacterially mediated genetic transformation of plant cells may represent a more widespread gall induction mechanism found in nature.

Atypically Shaped Setae in Gall Mites (Acariformes, Eriophyoidea) and Mitogenomics of the Genus Leipothrix Keifer (Eriophyidae)

The setae in Eriophyoidea are filiform, slightly bent and thickened near the base. Confocal microscopy indicates that their proximal and distal parts differ in light reflection and autofluorescence. Approximately 50 genera have atypically shaped setae: bifurcated, angled or swollen. These modifications are known in the basal part of prosomal setae u', ft', ft″, d, v, bv, ve, sc and caudal setae h2. We assessed the distribution of atypically shaped setae in Eriophyoidea and showed that they are scattered in different phylogenetic lineages. We hypothesized that the ancestral setae of eriophyoid mites were bifurcated before later simplifying into filiform setae. We also proposed that hypo-furcating setae are a synapomorphy that unites Eriophyoidea with Nematalycidae. We analyzed four new mitochondrial genomes of Leipothrix, the largest genus with bifurcated d, and showed that it is monophyletic and has a unique mitochondrial gene order with translocated trnK. We exclude Cereusacarus juniperensisn. comb. Xue and Yin, 2020 from Leipothrix and transfer five Epitrimerus spp. to Leipothrix: L. aegopodii (Liro 1941) n. comb., L. femoralis (Liro 1941) n. comb., L. geranii (Liro 1941) n. comb., L. ranunculi (Liro 1941) n. comb., and L. triquetra (Meyer 1990) n. comb.

A review of the molecular mechanisms of acaricide resistance in mites and ticks

The Arachnida subclass of Acari comprises many harmful pests that threaten agriculture as well as animal health, including herbivorous spider mites, the bee parasite Varroa, the poultry mite Dermanyssus and several species of ticks. Especially in agriculture, acaricides are often used intensively to minimize the damage they inflict, promoting the development of resistance. Beneficial predatory mites used in biological control are also subjected to acaricide selection in the field. The development and use of new genetic and genomic tools such as genome and transcriptome sequencing, bulked segregant analysis (QTL mapping), and reverse genetics via RNAi or CRISPR/Cas9, have greatly increased our understanding of the molecular genetic mechanisms of resistance in Acari, especially in the spider mite Tetranychus urticae which emerged as a model species. These new techniques allowed to uncover and validate new resistance mutations in a larger range of species. In addition, they provided an impetus to start elucidating more challenging questions on mechanisms of gene regulation of detoxification associated with resistance.

Deuterogyny and the Association of Two Vagrant Eriophyoid Mites (Acariformes, Eriophyoidea) with the Host-plant Generative Organs of Two Broad-leaved Trees in North-West Russia

Phytoparasitic mites of the superfamily Eriophyoidea Nalepa live and feed on mature leaf surfaces, between leaf bud scales, and (though less commonly) on flowers or fruits. In this study, we focused on the seasonal associations of two eriophyoid species, Shevtchenkella serrata (Nalepa 1892) with the Norway maple tree (Acer platanoides L.), and Brevulacus reticulatus Manson 1984 with the common oak (Quercus robur L.). These species have complex life cycles with two morphologically different, seasonal female forms, the protogyne and deutogyne. In B. reticulatus, both forms retain all the major generic characteristics but in S. serrata only the protogynes conform to the diagnosis of Shevtchenkella, whereas the deutogynes have the typical traits of Anthocoptes. We confirmed the conspecificity of the protogynes and deutogynes of both eriophyoid species by sequencing a barcode fragment of the Cox1 gene from which we obtained four pairwise identical sequences: ON920305/ON920306 (S. serrata) and ON920307/ON920308 (B. reticulatus). In addition, taxonomical studies on Shevtchenkella and Brevulacus resulted in new synonymies and combinations: (1) Oxypleurites obtusus Roivainen 1947 is considered a deutogyne of S. serrata and treated as a junior synonym of S. serrata; (2) two rhyncaphytoptine species from North America are transferred from the genus Rhyncaphytoptus to Brevulacus: B. albus (Keifer 1959) comb. nov. and B. atlanticus (Keifer 1959) comb. nov.; and (3) one species, B. salicinus Soika et al. 2017, is excluded from Brevulacus and transferred to Rhyncaphytoptus: Rhyncaphytoptus salicinus (Soika et al. 2017) comb. nov. Apart from distinct morphological deuterogyny in S. serrata and B. reticulatus, we observed the persistent association of S. serrata with the generative organs of the maple tree, A. platanoides, leading to transmission to the next host generation via the seed-containing winged fruits (samaras) and subsequent colonization of seedlings. In B. reticulatus, similar synchronization with host-plant dispersal was not detected; however, in mid-summer, temporary colonization of immature acorns and feeding was observed. Additional studies conducted in various ecosystems and including different ecological groups of plants, especially anemochorous plants, are needed to estimate the frequency of the association of eriophyoids with plant generative organs, seeds and seedlings to better understand what role in mite ecology such associations may play.

Molecular Aspects of Gall Formation Induced by Mites and Insects

Recent publications on gall formation induced on the leaves of dicotyledonous flowering plants by eriophyoid mites (Eriophyoidea) and representatives of four insect orders (Diptera, Hemiptera, Hymenoptera, Lepidoptera) are analyzed. Cellular and molecular level data on the stimuli that induce and sustain the development of both mite and insect galls, the expression of host plant genes during gallogenesis, and the effects of these galling arthropods on photosynthesis are considered. A hypothesis is proposed for the relationship between the size of galls and the volume of secretions injected by a parasite. Multistep, varying patterns of plant gene expression and accompanying histo-morphological changes in the transformed gall tissues are apparent. The main obstacle to better elucidating the nature of the induction of gallogenesis is the impossibility of collecting a sufficient amount of saliva for analysis, which is especially important in the case of microscopic eriophyoids. The use of modern omics technologies at the organismal level has revealed a spectrum of genetic mechanisms of gall formation at the molecular level but has not yet answered the questions regarding the nature of gall-inducing agents and the features of events occurring in plant cells at the very beginning of gall growth.

Where Eriophyoidea (Acariformes) Belong in the Tree of Life

Over the past century and a half, the taxonomic placement of Eriophyoidea has been in flux. For much of this period, this group has been treated as a subtaxon within Trombidiformes. However, the vast majority of recent phylogenetic analyses, including almost all phylogenomic analyses, place this group outside Trombidiformes. The few studies that still place Eriophyoidea within Trombidiformes are likely to be biased by incomplete taxon/gene sampling, long branch attraction, the omission of RNA secondary structure in sequence alignment, and the inclusion of hypervariable expansion-contraction rRNA regions. Based on the agreement among a number of independent analyses that use a range of different datasets (morphology; multiple genes; mitochondrial/whole genomes), Eriophyoidea are almost certain to be closely related to Nematalycidae, a family of vermiform mites within Endeostigmata, a basal acariform grade. Much of the morphological evidence in support of this relationship was apparent after the discovery of Nematalycidae in the middle of the 20th century. However, this evidence has largely been disregarded until very recently, perhaps because of overconfidence in the placement of Eriophyoidea within Trombidiformes. Here, we briefly review and identify a number of biases, both molecular- and morphology-based, that can lead to erroneous reconstructions of the position of Eriophyoidea in the tree of life.

Genomic Assessment of the Contribution of the Wolbachia Endosymbiont of Eurosta solidaginis to Gall Induction

We explored the genome of the Wolbachia strain, wEsol, symbiotic with the plant-gall-inducing fly Eurosta solidaginis with the goal of determining if wEsol contributes to gall induction by its insect host. Gall induction by insects has been hypothesized to involve the secretion of the phytohormones cytokinin and auxin and/or proteinaceous effectors to stimulate cell division and growth in the host plant. We sequenced the metagenome of E. solidaginis and wEsol and assembled and annotated the genome of wEsol. The wEsol genome has an assembled length of 1.66 Mbp and contains 1878 protein-coding genes. The wEsol genome is replete with proteins encoded by mobile genetic elements and shows evidence of seven different prophages. We also detected evidence of multiple small insertions of wEsol genes into the genome of the host insect. Our characterization of the genome of wEsol indicates that it is compromised in the synthesis of dimethylallyl pyrophosphate (DMAPP) and S-adenosyl L-methionine (SAM), which are precursors required for the synthesis of cytokinins and methylthiolated cytokinins. wEsol is also incapable of synthesizing tryptophan, and its genome contains no enzymes in any of the known pathways for the synthesis of indole-3-acetic acid (IAA) from tryptophan. wEsol must steal DMAPP and L-methionine from its host and therefore is unlikely to provide cytokinin and auxin to its insect host for use in gall induction. Furthermore, in spite of its large repertoire of predicted Type IV secreted effector proteins, these effectors are more likely to contribute to the acquisition of nutrients and the manipulation of the host's cellular environment to contribute to growth and reproduction of wEsol than to aid E. solidaginis in manipulating its host plant. Combined with earlier work that shows that wEsol is absent from the salivary glands of E. solidaginis, our results suggest that wEsol does not contribute to gall induction by its host.

Integrative Taxonomy of the Gall Mite Nothopoda todeica n. sp. (Eriophyidae) from the Disjunct Afro-Australasian Fern Todea barbara: Morphology, Phylogeny, and Mitogenomics

Eriophyoidea is a group of phytoparasitic mites with poorly resolved phylogeny. Previous studies inferred Eriophyidae s.l. as the largest molecular clade of Eriophyoidea, and Nothopodinae as the basal divergence of Eriophyidae s.l. We investigate the morphology and molecular phylogeny of Nothopoda todeican. sp. (Nothopodinae, Nothopodini), associated with a disjunct Afro-Australasian fern Todea barbara (Osmundaceae) from South Africa. Our analyses (1) determine new erroneous sequences (KF782375, KF782475, KF782586) wrongly assigned to Nothopodinae instead of Phyllocoptinae, (2) confirm the basal position of Nothopodinae in Eriophyoidea s.l., (3) question the monophyly of the Colopodacini and Nothopodini tribes, and (4) show the nested position of African fern-associated Nothopoda within a clade dominated by Asian nothopodines from angiosperms, which implies (a) a secondary association of nothopodines with ferns and (b) no relation between geography (continents) and the phylogenetic relationships of Nothopodinae species. Finally, we obtained a first complete mitochondrial genome for Nothopodinae and revealed a new gene order in the mitogenome of N. todeican. sp., notably deviating from those in other investigated eriophyoids. Our results contribute to resolving the phylogeny of Eriophyoidea and provide an example of an integrative study of a new taxon belonging to an economically important group of acariform mites.

Endoparasitic Gall Mites: Two New Novophytoptus Species (Eriophyoidea, Phytoptidae) from Southern African Sedges (Cyperaceae, Carex) and New Hypotheses on the Phylogeny of Novophytoptines

Eriophyoid mites (Acariformes, Eriophyoidea) are microscopic chelicerates morphologically greatly preadapted to endoparasitism on plants. Members of at least six phylogenetically distant eriophyoid genera from two families homoplastically transitioned to endoparasitism and acquired the ability to penetrate under the plant epidermis and feed on parenchymatous cells, usually causing necrosis. Theoretically, endoparasites are expected to show patterns of codivergence with hosts more than ectoparasites. Novophytoptus Roivainen 1947 is the only eriophyoid genus comprising exclusively endoparasitic species living in subepidermal tissues of herbaceous monocots of three families of the order Poales: Cyperaceae, Juncaceae, and Poaceae. Here, we described two new endoparasitic species, N. limpopoensis n. sp. and N. zuluensis n. sp., from southern African sedges Carex spicatopaniculata Boeckeler ex C.B.Clarke and C. zuluensis C.B.Clarke, respectively, and investigated the Cox1 phylogeny of Novophytoptus. Contrary to expectations, molecular phylogenetics did not recover host-specific mite clades associated with Cyperaceae and Juncaceae, but revealed geographical groups of Novophytoptus species from Africa and Eurasia. Our results provide a substantial basis for future coevolutionary studies on novophytoptines, which will be possible when more species and sequences of Novophytoptus from geographically remote regions and from diverse hosts representing all major clades of Poales become available for analyses.

Macroevolutionary analyses point to a key role of hosts in diversification of the highly speciose eriophyoid mite superfamily

The superfamily Eriophyoidea includes >5000 named species of very small phytophagous mites. As for many groups of phytophagous invertebrates, factors responsible for diversification of eriophyoid mites are unclear. Here, we used an inferred phylogeny of 566 putative species of eriophyoid mites based on fragments of two mitochondrial genes and two nuclear genes to examine factors associated with their massive evolutionary diversification through time. Our dated phylogeny indicates a Carboniferous origin for gymnosperm-associated Eriophyoidea with subsequent diversification involving multiple host shifts to angiosperms-first to dicots, and then to monocots or shifts back to gymnosperms-beginning in the Cretaceous period when angiosperms diverged. Speciation rates increased more rapidly in the Eriophyidae + Diptilomiopidae (mostly infesting angiosperms) than in the Phytoptidae (mostly infesting gymnosperms). Phylogenetic signal, speciation rates, dispersal and vicariance results combined with inferred topologies show that hosts played a key role in the evolution of eriophyoid mites. Speciation constrained by hosts was probably the main driver behind eriophyoid mite diversification worldwide. We demonstrate monophyly of the Eriophyoidea, whereas all three families, most subfamilies, tribes, and most genera are not monophyletic. Our time-calibrated tree provides a framework for further evolutionary studies of eriophyoid mites and their interactions with host plants as well as taxonomic revisions above the species level.

A New Webbing Aberoptus Species from South Africa Provides Insight in Silk Production in Gall Mites (Eriophyoidea)

Arthropods include a high diversity of lineages adapted for silk production. Several species of microscopic phytophagous mites of the hyperdiverse superfamily Eriophyoidea spin web; however, the origin of their silk is unknown. We described a new web-spinning mite, Aberoptus schotiae n. sp., collected from leaves of Schotia brachypetala (Fabaceae) in South Africa and showed that it has a complex life cycle, including two morphotypes of adults and nymphs. Molecular phylogenetic analyses and 28S sequence comparison showed conspecificity of heteromorphic females and rejected synonymy of Aberoptus and Aceria proposed by previous authors. For the first time, we provided SEM images of the web nests and, using a set of different microscopic techniques, described the silk-producing anal secretory apparatus (ASA) of Aberoptus. It comprises two pairs of anal glands (hypertrophied in web-spinning females), three cuticular sacs and a rectal tube leading to the anal opening. This is a unique case (analogy) of anal silk secretion in Chelicerata previously reported only in Serianus (Pseudoscorpiones). Recent findings of rudimentary ASA in distant eriophyoid lineages and the results of this study transform the current paradigm of exoticism of web-spinning eriophyoid taxa into the concept of synapomorphic specialization of the hindgut for excreting the anal gland secretions in Eriophyoidea.

Anatomy of the miniature four-legged mite Achaetocoptes quercifolii (Arachnida: Acariformes: Eriophyoidea)

Miniaturization is one of the important trends in the evolution of terrestrial arthropods. In order to study adaptations to microscopic sizes, the anatomy of the smallest insects was previously studied, but not the anatomy of the smallest mites. Some of the smallest mites are Eriophyidae. In this study we describe for the first time the anatomy of the mite Achaetocoptes quercifolii, which is about 115 μm long. For this purpose, we used light, scanning, and transmission electron microscopy and performed 3D reconstructions. The anatomy of A. quercifolii is compared with the anatomy of larger representatives of Eriophyoidea. Despite the small size of the studied species, there is no considerable simplification of its anatomy compared to larger four-legged mites. A. quercifolii has a number of miniaturization effects similar to those found in microinsects: a strong increase in the relative volume of the reproductive system, an increase in the relative volume of the brain, reduction in the number and size of cells of the nervous system. As in some larger four-legged mites, A. quercifolii undergoes midgut lysis at the stage of egg production. On the other hand, in A. quercifolii a greater number of opisthosomal muscles are preserved than in larger gall-forming four-legged mites.

One-way ticket to the blue: A large-scale, dated phylogeny revealed asymmetric land-to-water transitions in acariform mites (Acari: Acariformes)

Acariform mites are an ancient and megadiverse lineage that may have experienced a complex pattern of invasions into terrestrial and aquatic habitats. These among-realm transitions may relate to periods of turmoil in Earth's history or be simply results of uneven biodiversity patterns across habitats. Here, we inferred a dated, representative acariform phylogeny (five genes, 9,200 bp aligned, 367 terminals belonging to 150 ingroup plus 15 outgroup families, 23 fossil calibration points) which was used to infer transitions between marine/freshwater/terrestrial habitats. We detected four unambiguous transitions from terrestrial to freshwater habitats (Hydrozetes, Naiadacarus, Fusohericia, Afronothrus, Homocaligus); one from freshwater to marine (Pontarachnidae), and four from marine to brackish or freshwater transitions (all among Halacaridae: Acarothrix; Halacarellus petiti; Copidognathus sp.; clade Limnohalacarus + Soldanellonyx + Porohalacarus + Porolohmannella). One transition to the sea was inferred ambiguously with respect to the ancestor being either terrestrial or freshwater (Hyadesiidae), and another must be most carefully examined by adding potential related taxa (Selenoribatidae + Fortuyniidae). Finally, we inferred a single, remarkable transition from aquatic to terrestrial habitats involving early evolution of the large and ecologically diverse lineage: the ancestor of the Halacaridae + Parasitengona clade was probably freshwater given our dataset, thus making terrestrial Parasitengona secondarily terrestrial. Overall, our results suggested a strong asymmetry in environmental transitions: the majority occurred from terrestrial to aquatic habitats. This asymmetry is probably linked to mites' biological properties and uneven biodiversity patterns across habitats rather than Earth's geological history. Since the land holds more acariform diversity than water habitats, a shift from the former is more likely than from the latter. We inferred the following relationships: alicid endeostigmatid + eriophyoid (Alycidae, (Nanorchestidae, (Nematalycidae, Eriophyoidea))) being sister group to the remaining Acariformes: (proteonematalycid Endeostigmata, alicorhagiid Endeostigmata, Trombidiformes, Oribatida (including Astigmata)). Trombidiform relationships had several novel rearrangements: (i) traditional Eupodina lacked support for the inclusion of Bdelloidea; (ii) Teneriffidae, traditionally placed among Anystina, was consistently recovered in a clade including Heterostigmata in Eleutherengona; (iii) several lineages, such as Adamystidae, Paratydeidae, Caeculidae and Erythracaridae, were recovered in a large clade along other Anystina and Eleutherengona, suggesting single origins of several fundamental character states, such as the reduction of the cheliceral fixed digit and development of the palpal thumb-claw complex.

First rhyncaphytoptine mite (Eriophyoidea, Diptilomiopidae) parasitizing American hazelnut (Corylus americana): molecular identification, confocal microscopy, and phylogenetic position

The plant genus Corylus is an economically important crop, valued especially for its nuts. Numerous pathogens and harmful phytophagous arthropods are known to damage hazelnuts. We report on a new eriophyoid mite, Rhyncaphytoptus corylivagrans n. sp., and the first record of Coptophylla lamimani both collected from leaves of American hazelnut (Corylus americana) in North Carolina, USA. Including our new data, the complex of eriophyoids from Corylus comprises 15 species from three families: Phytoptidae (2 spp.), Eriophyidae (11 spp.), and Diptilomiopidae (2 spp.). We obtained sequences of three genes (Cox1, D1-D5 28S, and ITS1-5.8S-ITS2), applied BLAST and tree-based approaches for identification of R. corylivagrans n. sp., and performed the first molecular phylogenetic analysis focused on Rhyncaphytoptinae. Among the three genes, Cox1 showed better power when used for BLAST searches. Combined molecular phylogenetic analyses inferred R. corylivagrans n. sp. as sister to R. betulae, determined several moderately supported host-specific lineages of rhyncaphytoptines, and indicated a close relationship of the new species with members of the genus Rhinotergum. In two Rhinotergum spp. from Rosaceae, confocal microscopy revealed a new structure, the needle-like anterior process of the prodorsal shield, which is absent in R. corylivagrans n. sp. Additionally, the elements of the anal secretory apparatus presumably associated with silk-production and hypothesized as a synapomorphy of Eriophyoidea, were detected in the new species, providing the first documented report of this structure in Diptilomiopidae. Our study contributes to knowledge on the biodiversity of phytoparasites associated with hazelnuts and calls for future comparative phylogenetics of Diptilomiopidae.

The secret life of insect-associated microbes and how they shape insect-plant interactions

Insects are associated with a plethora of different microbes of which we are only starting to understand their role in shaping insect–plant interactions. Besides directly benefitting from symbiotic microbial metabolism, insects obtain and transmit microbes within their environment, making them ideal vectors and potential beneficiaries of plant diseases and microbes that alter plant defenses. To prevent damage, plants elicit stress-specific defenses to ward off insects and their microbiota. However, both insects and microbes harbor a wealth of adaptations that allow them to circumvent effective plant defense activation. In the past decades, it has become apparent that the enormous diversity and metabolic potential of insect-associated microbes may play a far more important role in shaping insect–plant interactions than previously anticipated. The latter may have implications for the development of sustainable pest control strategies. Therefore, this review sheds light on the current knowledge on multitrophic insect–microbe–plant interactions in a rapidly expanding field of research.