Playing Peekaboo with a Master Manipulator: Metagenetic Detection and Phylogenetic Analysis of Wolbachia Supergroups in Freshwater Invertebrates

The infamous "master manipulators"-intracellular bacteria of the genus Wolbachia-infect a broad range of phylogenetically diverse invertebrate hosts in terrestrial ecosystems. Wolbachia has an important impact on the ecology and evolution of their host with documented effects including induced parthenogenesis, male killing, feminization, and cytoplasmic incompatibility. Nonetheless, data on Wolbachia infections in non-terrestrial invertebrates are scarce. Sampling bias and methodological limitations are some of the reasons limiting the detection of these bacteria in aquatic organisms. In this study, we present a new metagenetic method for detecting the co-occurrence of different Wolbachia strains in freshwater invertebrates host species, i.e., freshwater Arthropoda (Crustacea), Mollusca (Bivalvia), and water bears (Tardigrada) by applying NGS primers designed by us and a Python script that allows the identification of Wolbachia target sequences from the microbiome communities. We also compare the results obtained using the commonly applied NGS primers and the Sanger sequencing approach. Finally, we describe three supergroups of Wolbachia: (i) a new supergroup V identified in Crustacea and Bivalvia hosts; (ii) supergroup A identified in Crustacea, Bivalvia, and Eutardigrada hosts, and (iii) supergroup E infection in the Crustacea host microbiome community.

A new extremophile ostracod crustacean from the Movile Cave sulfidic chemoautotrophic ecosystem in Romania

Sulfidic cave ecosystems are remarkable evolutionary hotspots that have witnessed adaptive radiation of their fauna represented by extremophile species having particular traits. Ostracods, a very old group of crustaceans, exhibit specific morphological and ecophysiological features that enable them to thrive in groundwater sulfidic environments. Herein, we report a peculiar new ostracod species Pseudocandona movilaensis sp. nov. thriving in the chemoautotrophic sulfidic groundwater ecosystem of Movile Cave (Romania). The new species displays a set of homoplastic features specific for unrelated stygobitic species, e.g., triangular carapace in lateral view with reduced postero-dorsal part and simplification of limb chaetotaxy (i.e., loss of some claws and reduction of secondary male sex characteristics), driven by a convergent or parallel evolution during or after colonization of the groundwater realm. P. movilaensis sp. nov. thrives exclusively in sulfidic meso-thermal waters (21 °C) with high concentrations of sulphides, methane, and ammonium. Based on the geometric morphometrics-based study of the carapace shape and molecular phylogenetic analyses based on the COI marker (mtDNA), we discuss the phylogenetic relationship and evolutionary implication for the new species to thrive in groundwater sulfidic groundwater environments.

Two new Cypridopsinae Kaufmann, 1900 (Crustacea, Ostracoda) from southern Africa

Two new Cypridopsinae ostracods, Potamocyprismeissneri sp. nov. and Sarscypridopsisharundineti sp. nov. are described. Both were found only as asexual (all-female) populations in temporary waters of southern Africa. Potamocyprismeissneri was collected from a small pan in the North-West Province of South Africa. It is approximately 0.5 mm long and belongs to the species group with long swimming setae on the second antennae. However, the species has a somewhat isolated position in the genus owing to the conspicuously reticulated carapace, which is furthermore densely covered by prominent conuli with normal pores carrying long sensilla, as well as to the wide anterior and posterior flanges on the left valve. To allow identification of the new species in relation to its closest congeners, a key to the species of the genus Potamocypris Brady, 1870 from southern Africa is provided. The genus Sarscypridopsis McKenzie, 1977 mostly has an Afrotropical distribution with only few species occurring in other regions. Sarscypridopsisharundineti was collected from floodplains of the outskirts of the Okavango Delta in Botswana. It is approximately 0.4 mm long and can be distinguished from congeners mainly by the smaller and more oval-shaped valves. We conclude that southern African Cypridopsinae urgently need integrated taxonomic revision, by means of both morphological characters and DNA-sequence data.

Taxonomic classification of the bacterial endosymbiont Wolbachia based on next-generation sequencing: is there molecular evidence for its presence in tardigrades?

We used high-throughput sequencing of 16S rRNA to test whether tardigrade species are infected with Wolbachia parasites. We applied SILVA and Greengenes databases that allowed taxonomic classification of bacterial sequences to OTUs. The results obtained from both databases differed considerably in the number of OTUs, and only the Greengenes database allowed identification of Wolbachia (infection was also supported by comparison of sequences to NCBI database). The putative bacterial endosymbiont Wolbachia was discovered only in adult eutardigrades, while bacteria identified down to the order Rickettsiales were detected in both eutardigrade eggs and adult specimens. Nevertheless, the frequency of Wolbachia in the bacterial communities of the studied eutardigrades was low. Similarly, in our positive control, i.e., a fairy shrimp Streptocephalus cafer, which was found to be infected with Wolbachia in our previous study using Sanger sequencing, only the Rickettsiales were detected. We also carried out phylogenetic reconstruction using Wolbachia sequences from the SILVA and Greengenes databases, Alphaproteobacteria putative endosymbionts and Rickettsiales OTUs obtained in previous studies on the microbial community of tardigrades, and Rickettsiales and Wolbachia OTUs obtained in the current study. Our discovery of Wolbachia in tardigrades can fuel new research to uncover the specifics of this interaction.

Detection of bacterial endosymbionts in freshwater crustaceans: the applicability of non-degenerate primers to amplify the bacterial 16S rRNA gene

Bacterial endosymbionts of aquatic invertebrates remain poorly studied. This is at least partly due to a lack of suitable techniques and primers for their identification. We designed a pair of non-degenerate primers which enabled us to amplify a fragment of ca. 500 bp of the 16S rRNA gene from various known bacterial endosymbiont species. By using this approach, we identified four bacterial endosymbionts, two endoparasites and one uncultured bacterium in seven, taxonomically diverse, freshwater crustacean hosts from temporary waters across a wide geographical area. The overall efficiency of our new WOLBSL and WOLBSR primers for amplification of the bacterial 16S rRNA gene was 100%. However, if different bacterial species from one sample were amplified simultaneously, sequences were illegible, despite a good quality of PCR products. Therefore, we suggest using our primers at the first stage of bacterial endosymbiont identification. Subsequently, genus specific primers are recommended. Overall, in the era of next-generation sequencing our method can be used as a first simple and low-cost approach to identify potential microbial symbionts associated with freshwater crustaceans using simple Sanger sequencing. The potential to detected bacterial symbionts in various invertebrate hosts in such a way will facilitate studies on host-symbiont interactions and coevolution.

Sieve-type pore canals in the Timiriaseviinae-A contribution to the comparative morphology and the systematics of the Limnocytheridae (Ostracoda, Crustacea)

Examination of normal pore canals, especially sieve-type pore canals, in living and fossil representatives of ten genera of the family Limnocytheridae, subfamily Timiriaseviinae, has revealed important diversity of structure. These complex pore canals have been studied via high-resolution scanning electron microscopy (the Cartographic Method) and analysed via the application of newly devised indices to assess patterns of consistency and variation in both detailed structure of individual pores and of their distribution on the calcified valve. The timiriaseviine taxa are compared with species of the genera Limnocythere, sub-family Limnocytherinae and Cyprideis (family Cytherideidae). The relationship between the living animal and its aquatic environment is discussed in the light of previous studies and of new evidence herein. The importance of normal pore canals for systematics is highlighted by the recognition and definition of the new tribe Gomphodellini Danielopol, Cabral Lord nov. tribe, subfamily Timiriaseviinae, family Limnocytheridae.

Redefinition of the Genus Typhlocypris Vejdovský, 1882 (Ostracoda, Candonidae)

The taxonomy of the genus Typhlocypris Vejdovský, 1882 is reviewed. New morphological information on Typhlocypris eremita (Vejdovský, 1882), the type species of the genus, is provided, and a new reference material is presented. The generic diagnosis is emended with details derived from the developmental trajectory of the valves, from the juvenile stage A-3 to the adult. Those criteria clearly differentiate Typhlocypris from the related genus Pseudocandona Kaufmann, 1900. As here redefined, Typhlocypris is a phylogentic lineage of the subfamily Candoninae containing extant species presently living in aquatic subterranean habitats and fossil species recovered from non-marine Late Palaeogene to Neogene and Quaternary deposits in Europe and western Asia. The type species of Typhlocypris is considered a metaspecies, taxonomically treated as T. eremita (sensu lato), which includes populations resembling the newly designated reference material. The homeomorphic triangular valve shape of the Candoninae is discussed. Careful examination of the valve morphology of Typhlocypris combined with the analysis of limb traits helps to distinguish representatives of this genus from unrelated phylogenetic groups presenting similar triangularly shaped valves. It is emphasised that for a useful description of Typhlocypris taxa both transmitted light and scanning electron microscopy are necessary.

On the Leptocytheridae Ostracods of the Long-Lived Lake Ohrid: A Reappraisal of their Taxonomic Assignment and Biogeographic Origin

Leptocythere karamani Klie, one of few non-marine species of the family Leptocytheridae (Ostracoda), is redescribed from specimens recently collected from the long-lived Lake Ohrid on the Albanian-Macedonian border. Detailed morphologies of valves and limbs of this species were compared with those of other Ohrid-Prespa leptocytherids, of some recent marine representatives of the genera Leptocythere Sars and Callistocythere Ruggieri from the Mediterranean, Irish and Baltic seas as well as with that of fossil non-marine species from the Miocene palaeo-Lake Pannon belonging to the genera Amnicythere Devoto and Euxinocythere Stancheva. Comparison with other species of Leptocytheridae inhabiting fresh to brackish waters of the Black-Azov, Caspian and Aral seas were also carried out using descriptions provided in the literature. Based on the comparative morphological studies it is shown that L. karamani and other Ohrid leptocytherids have a number of characters distinguishing them from other members of the genus Leptocythere but demonstrating a relationship with species of the genus Amnicythere. The most reliable of these characters are: a) anterior valve vestibulum from where mostly uni-ramified pore canals start, b) the entomodont hinge type with a strong anterior anti-slip tooth, a smooth posterior anti-slip bar on the left valve, and c) the hemipenis with underdeveloped lateral lobe and reduced clasping organ. From this strong evidence, the Ohrid leptocytherid species are allocated to the genus Amnicythere. Finally, a biogeographic scenario on the origin of the Ohrid leptocytherids is proposed which matches the "Lake Pannon derivate hypothesis". Close relationship of the Ohrid Amnicythere species with the non-marine leptocytherid taxa from the Neogene lakes of Central and Eastern Europe and with extant taxa from the Black and Caspian seas may indicate that the Ohrid Amnicythere derived from Lake Pannon species which were able to colonise lakes in Southern Europe through a stepping-stone process and subsequently to adapt to freshwater environment.

Exceptional cryptic diversity and multiple origins of parthenogenesis in a freshwater ostracod

The persistence of asexual reproduction in many taxa depends on a balance between the origin of new asexual lineages and the extinction of old ones. This turnover determines the diversity of extant asexual populations and so influences the interaction between sexual and asexual modes of reproduction. Species with mixed reproduction, like the freshwater ostracod (Crustacea) morphospecies Eucypris virens, are a good model to examine these dynamics. This species is also a geographic parthenogen, in which sexual females and males co-exist with asexual females in the circum-Mediterranean area only, whereas asexual females occur all over Europe. A molecular phylogeny of E. virens based on the mitochondrial COI and 16S fragments is presented. It is characterised by many distinct clusters of haplotypes which are either exclusively sexual or asexual, with only one exception, and are often separated by deep branches. Analysis of the phylogeny reveals an astonishing cryptic diversity, which indicates the existence of a species complex with more than 40 cryptic taxa. We therefore suggest a revision of the single species status of E. virens. The phylogeny indicates multiple transitions from diverse sexual ancestor populations to asexuality. Although many transitions appear to be ancient, we argue that this may be an artefact of the existence of unsampled or extinct sexual lineages.