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

An Evolutionary-Focused Review of the Holosporales (Alphaproteobacteria): Diversity, Host Interactions, and Taxonomic Re-ranking as Holosporineae Subord. Nov

The order Holosporales is a broad and ancient lineage of bacteria obligatorily associated with eukaryotic hosts, mostly protists. Significantly, this is similar to other evolutionary distinct bacterial lineages (e.g. Rickettsiales and Chlamydiae). Here, we provide a detailed and comprehensive account on the current knowledge on the Holosporales. First, acknowledging the up-to-date phylogenetic reconstructions and recent nomenclatural proposals, we reevaluate their taxonomy, thus re-ranking them as a suborder, i.e. Holosporineae, within the order Rhodospirillales. Then, we examine the phylogenetic diversity of the Holosporineae, presenting the 20 described genera and many yet undescribed sub-lineages, as well as the variety of the respective environments of provenance and hosts, which belong to several different eukaryotic supergroups. Noteworthy representatives of the Holosporineae are the infectious intranuclear Holospora, the host manipulator 'Caedimonas', and the farmed shrimp pathogen 'Candidatus Hepatobacter'. Next, we put these bacteria in the broad context of the whole Holosporineae, by comparing with the available data on the least studied representatives, including genome sequences. Accordingly, we reason on the most probable evolutionary trajectories for host interactions, host specificity, and emergence of potential pathogens in aquaculture and possibly humans, as well as on future research directions to investigate those many open points on the Holosporineae.

Hepatincolaceae (Alphaproteobacteria) are Distinct From Holosporales and Independently Evolved to Associate With Ecdysozoa

The Hepatincolaceae (Alphaproteobacteria) are a group of bacteria that inhabit the gut of arthropods and other ecdysozoans, associating extracellularly with microvilli. Previous phylogenetic studies, primarily single-gene analyses, suggested their relationship to the Holosporales, which includes intracellular bacteria in protist hosts. However, the genomics of Hepatincolaceae is still in its early stages. In this study, the number of available Hepatincolaceae genomes was increased to examine their evolutionary and functional characteristics. It was found that the previous phylogenetic grouping with Holosporales was incorrect due to sequence compositional biases and that Hepatincolaceae form an independent branch within the Hepatincolaceae. This led to a reinterpretation of their features, proposing a new evolutionary scenario that involves an independent adaptation to host association compared to the Holosporales, with distinct specificities. The Hepatincolaceae exhibit greater nutritional flexibility, utilising various molecules available in the host gut and thriving in anaerobic conditions. However, they have a less complex mechanism for modulating host interactions, which are likely less direct than those of intracellular bacteria. In addition, representatives of Hepatincolaceae show several lineage-specific traits related to differences in host species and life conditions.

"Candidatus Intestinibacterium parameciiphilum"-member of the "Candidatus Paracaedibacteraceae" family (Alphaproteobacteria, Holosporales) inhabiting the ciliated protist Paramecium

Protists frequently host diverse bacterial symbionts, in particular those affiliated with the order Holosporales (Alphaproteobacteria). All characterised members of this bacterial lineage have been retrieved in obligate association with a wide range of eukaryotes, especially multiple protist lineages (e.g. amoebozoans, ciliates, cercozoans, euglenids, and nucleariids), as well as some metazoans (especially arthropods and related ecdysozoans). While the genus Paramecium and other ciliates have been deeply investigated for the presence of symbionts, known members of the family "Candidatus Paracaedibacteraceae" (Holosporales) are currently underrepresented in such hosts. Herein, we report the description of "Candidatus Intestinibacterium parameciiphilum" within the family "Candidatus Paracaedibacteraceae", inhabiting the cytoplasm of Paramecium biaurelia. This novel bacterium is almost twice as big as its relative "Candidatus Intestinibacterium nucleariae" from the opisthokont Nuclearia and does not present a surrounding halo. Based on phylogenetic analyses of 16S rRNA gene sequences, we identified six further potential species-level lineages within the genus. Based on the provenance of the respective samples, we investigated the environmental distribution of the representatives of "Candidatus Intestinibacterium" species. Obtained results are consistent with an obligate endosymbiotic lifestyle, with protists, in particular freshwater ones, as hosts. Thus, available data suggest that association with freshwater protists could be the ancestral condition for the members of the "Candidatus Intestinibacterium" genus.

Novel evolutionary insights on the interactions of the Holosporales (Alphaproteobacteria) with eukaryotic hosts from comparative genomics

Holosporales are an alphaproteobacterial order engaging in obligate and complex associations with eukaryotes, in particular protists. The functional and evolutionary features of those interactions are still largely undisclosed. Here, we sequenced the genomes of two members of the species Bealeia paramacronuclearis (Holosporales, Holosporaceae) intracellularly associated with the ciliate protist Paramecium, which resulted in high correspondence. Consistent with the short-branched early-divergent phylogenetic position, Bealeia presents a larger functional repertoire than other Holosporaceae, comparable to those of other Holosporales families, particularly for energy metabolism and motility. Our analyses indicate that different Holosporales likely experienced at least partly autonomous genome reduction and adaptation to host interactions, for example regarding dependence on host biotin driven by multiple independent horizontal acquisitions of transporters. Among Alphaproteobacteria, this is reminiscent of the convergently evolved Rickettsiales, which however appear more diverse, possibly due to a probably more ancient origin. We identified in Bealeia and other Holosporales the plasmid-encoded putative genetic determinants of R-bodies, which may be involved in a killer trait towards symbiont-free hosts. While it is not clear whether these genes are ancestral or recently horizontally acquired, an intriguing and peculiar role of R-bodies is suggested in the evolution of the interactions of multiple Holosporales with their hosts.

'Candidatus Gromoviella agglomerans', a novel intracellular Holosporaceae parasite of the ciliate Paramecium showing marked genome reduction

Holosporales are an alphaproteobacterial lineage encompassing bacteria obligatorily associated with multiple diverse eukaryotes. For most representatives, little is known on the interactions with their hosts. In this study, we characterized a novel Holosporales symbiont of the ciliate Paramecium polycaryum. This bacterium inhabits the host cytoplasm, frequently forming quite large aggregates. Possibly due to such aggregates, host cells sometimes displayed lethal division defects. The symbiont was also able to experimentally stably infect another Paramecium polycaryum strain. The bacterium is phylogenetically related with symbionts of other ciliates and diplonemids, forming a putatively fast-evolving clade within the family Holosporaceae. Similarly to many close relatives, it presents a very small genome (<600 kbp), and, accordingly, a limited predicted metabolism, implying a heavy dependence on Paramecium, thanks also to some specialized membrane transporters. Characterized features, including the presence of specific secretion systems, are overall suggestive of a mild parasitic effect on the host. From an evolutionary perspective, a potential ancestral trend towards pronounced genome reduction and possibly linked to parasitism could be inferred, at least among fast-evolving Holosporaceae, with some lineage-specific traits. Interestingly, similar convergent features could be observed in other host-associated lineages, in particular Rickettsiales among Alphaproteobacteria.

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.

Epidemiology of Nucleus-Dwelling Holospora: Infection, Transmission, Adaptation, and Interaction with Paramecium

The chapter describes the exceptional symbiotic associations formed between the ciliate Paramecium and Holospora, highly infectious bacteria residing in the host nuclei. Holospora and Holospora-like bacteria (Alphaproteobacteria) are characterized by their ability for vertical and horizontal transmission in host populations, a complex biphasic life cycle, and pronounced preference for host species and colonized cell compartment. These bacteria are obligate intracellular parasites; thus, their metabolic repertoire is dramatically reduced. Nevertheless, they perform complex interactions with the host ciliate. We review ongoing efforts to unravel the molecular adaptations of these bacteria to their unusual lifestyle and the host's employment in the symbiosis. Furthermore, we summarize current knowledge on the genetic and genomic background of Paramecium-Holospora symbiosis and provide insights into the ecological and evolutionary consequences of this interaction. The diversity and occurrence of symbioses between ciliates and Holospora-like bacteria in nature is discussed in connection with transmission modes of symbionts, host specificity and compatibility of the partners. We aim to summarize 50 years of research devoted to these symbiotic systems and conclude trying to predict some perspectives for further studies.