A new Cardinium group of bacteria found in Achipteria coleoptrata (Acari: Oribatida)

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.

One to host them all: genomics of the diverse bacterial endosymbionts of the spider Oedothorax gibbosus

Bacterial endosymbionts of the groups Wolbachia, Cardinium and Rickettsiaceae are well known for their diverse effects on their arthropod hosts, ranging from mutualistic relationships to reproductive phenotypes. Here, we analysed a unique system in which the dwarf spider Oedothorax gibbosus is co-infected with up to five different endosymbionts affiliated with Wolbachia, 'Candidatus Tisiphia' (formerly Torix group Rickettsia), Cardinium and Rhabdochlamydia. Using short-read genome sequencing data, we show that the endosymbionts are heterogeneously distributed among O. gibbosus populations and are frequently found co-infecting spider individuals. To study this intricate host-endosymbiont system on a genome-resolved level, we used long-read sequencing to reconstruct closed genomes of the Wolbachia, 'Ca. Tisiphia' and Cardinium endosymbionts. We provide insights into the ecology and evolution of the endosymbionts and shed light on the interactions with their spider host. We detected high quantities of transposable elements in all endosymbiont genomes and provide evidence that ancestors of the Cardinium, 'Ca. Tisiphia' and Wolbachia endosymbionts have co-infected the same hosts in the past. Our findings contribute to broadening our knowledge about endosymbionts infecting one of the largest animal phyla on Earth and show the usefulness of transposable elements as an evolutionary 'contact-tracing' tool.

Isolation and characterization culturable microbes on the surface of ‘Granny Smith’ apples treated with electrolyzed water during cold storage

Response of culturable microbes on the surface of apples treated with slightly alkaline electrolyzed water (SAIEW) is largely unexplored. Thus, the aim of this study was to characterize culturable microbes on the surface of SAIEW treated 'Granny Smith' apples using conventional and molecular approach. Results showed that SAIEW treatments and storage duration influenced culturable microbes isolated from the surface of 'Granny Smith' apples stored at 5 °C for 21 days. Enterobacterial repetitive intergenic consensus (ERIC-PCR) analysis distinctively identified 27 groups of bacteria from 56 plate isolates. Using random amplified polymorphic DNA (RAPD-PCR) typing and RAPD1283 primers, 10 distinct band patterns were identified from 30 fungal isolates. Sequencing of 16S rRNA and intergenic spacer (ITS1 and ITS4) region, identified eight bacteria and four fungi, respectively, to species level. Study showed that SAIEW treatment inhibited growth of Staphylococcus epidermidis, S. capitis, Ochrobactrum soli, and Aspergillus inuii on the surface apples during storage.

Graphical abstract

Supplementary Information

The online version contains supplementary material available at 10.1007/s10068-022-01148-2.

Wolbachia supergroup E found in Hypochthonius rufulus (Acari: Oribatida) in Poland

Data on the spread of intracellular bacteria in oribatid mites (Acari: Oribatida) are scarce. Our work fills a gap in the research on endosymbionts in this group of invertebrates and provides information on Wolbachia infection in Hypochthonius rufulus (Acari: Oribatida) from soil, litter and moss sample collected in south-eastern Poland. This is the first report of Wolbachia in H. rufulus. Phylogeny based on the analysis of the 16S rRNA, gatB, fbpA, gltA, ftsZ and hcpA gene sequences revealed that Wolbachia from H. rufulus represented supergroup E and was related to bacterial endosymbionts of Collembola. The unique sequence within Wolbachia supergroup E was detected for the 16S rRNA gene of the bacteria from H. rufulus. The sequences of Wolbachia 16S rRNA and housekeeping genes have been deposited in publicly available databases and are an important source of molecular data for comparative studies.

First report of Wolbachia in Damaeus onustus (Acari: Oribatida)

Purpose

Little is known about the distribution and phylogeny of bacterial endosymbionts in oribatid mites (Acari: Oribatida). Thus, we undertook the issue of occurrence of these microbial symbionts in this arthropod group.

Methods

We used PCR technique for detection of Wolbachia in Damaeus onustus. Phylogenetic analysis of the bacterium was conducted based on the 16S rDNA sequence.

Results

To the best of our knowledge, we present a novel finding of Wolbachia infection in the sexually reproducing oribatid mite, D. onustus. The presence of uninfected individuals (ca. 93%) suggests that the bacteria do not function as primary symbionts. A comparison of the bacterial 710-bp 16S rDNA sequence detected in the oribatid mite with the sequences deposited in GenBank revealed its 92–93% similarity to the 16S rDNA sequences of Wolbachia identified in some springtails (Collembola) and Bryobia sp. mite. Bacteria from D. onustus showed phylogenetic relationships with Wolbachia from springtails, Megalothorax minimus and Neelus murinus, which were included by other authors into a separate Wolbachia clade.

Conclusion

Our finding suggests that the strains of Wolbachia from D. onustus may form a new Wolbachia supergroup.

First Evidence of Intracellular Bacteria Cardinium in Thermophilic Mite Microzetorchestes emeryi (Acari: Oribatida): Molecular Screening of Bacterial Endosymbiont Species

We undertook the issue of the distribution of intracellular bacteria among Oribatida (Acari). Six genera of bacteria were detected by PCR and Sanger DNA sequencing: Wolbachia, Cardinium, Rickettsia, Spiroplasma, Arsenophonus, and Hamiltonella. Our research, for the first time, revealed the presence of Cardinium in Microzetorchestes emeryi in two subpopulations separated from each other by 300 m. The percentages of infected animals were the same in both subpopulations-ca. 20%. The identity of 16S rDNA sequences of Cardinium between these two subpopulations of M. emeryi was 97%. Phylogenetic analysis showed that the Cardinium in M. emeryi was clustered into the group A. The occurrence of M. emeryi in Poland has not been reported before and our report is the first one. Cardinium maybe help the thermophilic M. emeryi to adapt to low temperatures in the Central Europe.

Detection of a new bacterium of the family Holosporaceae (Alphaproteobacteria: Holosporales) associated with the oribatid mite Achipteria coleoptrata

We detected an unknown bacterium in Achipteria coleoptrata (Acari: Oribatida). Its 16S rDNA gene sequence showed 89% identity to the endosymbiont “Candidatus Nucleicultrix amoebiphila” from amoebae and “Candidatus Gortzia sp.” from ciliates. Phylogenetic analysis revealed that the microorganism is a member of the family Holosporaceae, order Holosporales of Alphaproteobacteria. Its occurrence in Oribatida is enigmatic. It cannot be excluded that it is a symbiont of Oribatida as well as it is an endosymbiont of a smaller, even unicellular, organisms living inside the mite. The issue of the occurrence of this microorganism is interesting and further research is needed to gain the knowledge of its role and the nature of bacterium-host interaction.

Wolbachia of phylogenetic supergroup E identified in oribatid mite Gustavia microcephala (Acari: Oribatida)

Heritable endosymbionts have been observed in arthropod and nematode hosts. The most-known among them is Wolbachia. Although the bacterium was previously identified in oribatid mites (Acari: Oribatida), it was not assigned to any phylogenetic group. Endosymbionts have a profound influence on their hosts, playing various functions that affect invertebrate's biology such as changing the way of reproduction. Oribatida provide the very unique examples of groups in which even whole families appear to be thelytokous, so we considered that it is worth to investigate the occurrence of endosymbiotic microorganisms in oribatid mites, especially that the knowledge on the symbionts occurrence in this invertebrate group is negligible. We report for the first time Wolbachia in oribatid mite Gustavia microcephala. The sequences of 16S rDNA, gltA, and ftsZ genes of the endosymbiont from the mite showed the highest similarity to Wolbachia found in Collembola. Phylogenetic analysis based on single gene and concatenated alignments of three genes revealed that the bacteria from G. microcephala and Collembola were related and clustered together with supergroup E. Relatively close relationship of Wolbachia from oribatid and collembolan hosts might mean at the evolutionary scale that horizontal transfer of bacteria between these two groups of invertebrates may take place.

The draft genome of strain cCpun from biting midges confirms insect Cardinium are not a monophyletic group and reveals a novel gene family expansion in a symbiont

Background

It is estimated that 13% of arthropod species carry the heritable symbiont Cardinium hertigii. 16S rRNA and gyrB sequence divides this species into at least four groups (A–D), with the A group infecting a range of arthropods, the B group infecting nematode worms, the C group infecting Culicoides biting midges, and the D group associated with the marine copepod Nitocra spinipes. To date, genome sequence has only been available for strains from groups A and B, impeding general understanding of the evolutionary history of the radiation. We present a draft genome sequence for a C group Cardinium, motivated both by the paucity of genomic information outside of the A and B group, and the importance of Culicoides biting midge hosts as arbovirus vectors.

Methods

We reconstructed the genome of cCpun, a Cardinium strain from group C that naturally infects Culicoides punctatus, through Illumina sequencing of infected host specimens.

Results

The draft genome presented has high completeness, with BUSCO scores comparable to closed group A Cardinium genomes. Phylogenomic analysis based on concatenated single copy core proteins do not support Cardinium from arthropod hosts as a monophyletic group, with nematode Cardinium strains nested within the two groups infecting arthropod hosts. Analysis of the genome of cCpun revealed expansion of a variety of gene families classically considered important in symbiosis (e.g., ankyrin domain containing genes), and one set—characterized by DUF1703 domains—not previously associated with symbiotic lifestyle. This protein group encodes putative secreted nucleases, and the cCpun genome carried at least 25 widely divergent paralogs, 24 of which shared a common ancestor in the C group. The genome revealed no evidence in support of B vitamin provisioning to its haematophagous host, and indeed suggests Cardinium may be a net importer of biotin.

Discussion

These data indicate strains of Cardinium within nematodes cluster within Cardinium strains found in insects. The draft genome of cCpun further produces new hypotheses as to the interaction of the symbiont with the midge host, in particular the biological role of DUF1703 nuclease proteins that are predicted as being secreted by cCpun. In contrast, the coding content of this genome provides no support for a role for the symbiont in provisioning the host with B vitamins.

Phylogenetic analysis based on the 16S rDNA, gltA, gatB, and hcpA gene sequences of Wolbachia from the novel host Ceratozetes thienemanni (Acari: Oribatida)

We determined the occurrence of intracellular endosymbionts (Wolbachia, Cardinium, Arsenophonus, Rickettsia, Spiroplasma, Hamiltonella, flavobacteria, and microsporidia) in oribatid mites (Acari: Oribatida) with the use of PCR technique. For the first time we looked for and detected Wolbachia in parthenogenetic oribatid mite Ceratozetes thienemanni Willmann, 1943. The 16S rDNA, gatB, hcpA, and gltA sequences of Wolbachia in C. thienemanni showed the highest similarity (≥ 90%) to the genes of Wolbachia from springtails (Collembola) and oribatid mite Gustavia microcephala. We found the unique sequence 5'-GGGGTAATGGCC-3' in 16S rDNA of Wolbachia from C. thienemanni and collembolan representing group E. The phylogeny of Wolbachia based on the analysis of single genes as well as concatenated alignments of four bacterial loci showed that the bacteria from C. thienemanni belonged to Wolbachia group E, like the endosymbionts from springtail hosts and G. microcephala. Considering coexisting of representatives of Oribatida and Collembola in the same soil habitat and similar food, it is possible that the source of Wolbachia infection was the same. Residues of dead invertebrates could be in organic matter of their soil food, so the scenario of infection transferred by eating of remains of soil cohabitates is also possible. It could explain the similarity and relationship of the Wolbachia in these two arthropod groups. Oribatid mite C. thienemanni is a parthenogenetic mite which is a unique feature in the genus Ceratozetes. Moreover, this species, within the entire genus Ceratozetes, is characterized by the most northerly distribution. It is difficult to determine either it is parthenogenesis or the presence of endosymbionts that are in some way responsible for this kind of evolutionary success. Maybe we are dealing here with a kind of synergy of both factors?