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Orthologous gene sets shared by species of Rickettsiales. Network graph showing orthologous gene sets shared by species of Rickettsiales at the order level (Rickettsiales), family level (Rickettsiaceae, Anaplasmataceae, Midichloriaceae), and genus level ("Ca. A. rohweri", "Ca. M. mitochondrii", "Ca. J. acanthamoeba", and "Ca. F. solitaria"). Numbers in black indicate shared gene sets between two compared organisms or families, or gene sets shared by an entire family sampled. Numbers in white indicate individual genes that were unique to a given organism. Orthologous gene families were identified using OrthoFinder
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Bacterial symbionts are integral to the health and homeostasis of invertebrate hosts. Notably, members of the Rickettsiales genus Wolbachia influence several aspects of the fitness and evolution of their terrestrial hosts, but few analogous partnerships have been found in marine systems. We report here the genome, phylogenetics, and biogeography of...
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... related genomes by aligning the draft genome to a reference from "Ca. Midichloriaceae" [50] (Fig. 2; Fig. S3). The assembled 1.28 Mb genome was estimated at 97.3% completion, with 1469 predicted genes, a coding density of 87.6% and a low GC content of 28.38% ( Fig. 2; Supplementary Table S2). Contamination was low as estimated by CheckM at 0.39% (Fig. S4), and completion was estimated at 97.3%, supported by the presence of tRNAs for all 20 proteinogenic amino acids. These genome features are characteristic of most Rickettsiales [18,20]. At 155 contigs, an N50 of 10,860 bp, and based on completeness and contamination estimates from CheckM, this genome is classified as a "High-Quality ...
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... on analysis of orthologous gene sets using OrthoFinder 2.2.3 (Fig. 4), "Candidatus A. rohweri" shares 188 gene clusters with other species of Rickettsiales, 327 gene clusters with only members of "Ca. Midichloriaceae" ("Ca. M. mitochondrii", "Ca. Fokinia solitaria", and "Ca. Jidaibacter acanthamoeba"), and encodes two unique gene clusters (genes that share a similar function, but are present only in the ...
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... related genomes by aligning the draft genome to a reference from "Ca. Midichloriaceae" [50] (Fig. 2; Fig. S3). The assembled 1.28 Mb genome was estimated at 97.3% completion, with 1469 predicted genes, a coding density of 87.6% and a low GC content of 28.38% ( Fig. 2; Supplementary Table S2). Contamination was low as estimated by CheckM at 0.39% (Fig. S4), and completion was estimated at 97.3%, supported by the presence of tRNAs for all 20 proteinogenic amino acids. These genome features are characteristic of most Rickettsiales [18,20]. At 155 contigs, an N50 of 10,860 bp, and based on completeness and contamination estimates from CheckM, this genome is classified as a "High-Quality ...
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... on analysis of orthologous gene sets using OrthoFinder 2.2.3 (Fig. 4), "Candidatus A. rohweri" shares 188 gene clusters with other species of Rickettsiales, 327 gene clusters with only members of "Ca. Midichloriaceae" ("Ca. M. mitochondrii", "Ca. Fokinia solitaria", and "Ca. Jidaibacter acanthamoeba"), and encodes two unique gene clusters (genes that share a similar function, but are present only in the ...
Citations
... The initial survey of immunetype systems in placozoans reveals the apparent simplicity of known metazoan immune complement [125]. With various bacteria located in fiber and other cell types [43,49,50,126], the underlying biology of these relationships is still unknown. ...
Placozoans are morphologically the simplest free-living animals. They represent a unique window of opportunities to understand both the origin of the animal organization and the rules of life for the system and synthetic biology of the future. However, despite more than 100 years of their investigations, we know little about their organization, natural habitats, and life strategies. Here, we introduce this unique animal phylum and highlight some directions vital to broadening the frontiers of the biomedical sciences. In particular, understanding the genomic bases of placozoan biodiversity, cell identity, connectivity, reproduction, and cellular bases of behavior are critical hot spots for future studies.
... Aquarickettsia rohweri was also included in the analysis (GCF_003953955.1) [70]. Coding sequence and genome size were plotted with ggplot2 (ver. ...
The impact of microbiome in animal physiology is well appreciated, but characterization of animal-microbe symbiosis in marine environments remains a growing need. This study characterizes the microbial communities associated with the moon jellyfish Aurelia coerulea , first isolated from the East Pacific Ocean and has since been utilized as an experimental system. We find that the microbiome of this Pacific Aurelia culture is dominated by two taxa, a Mollicutes and Rickettsiales. The microbiome is stable across life stages, although composition varies. Mining the host sequencing data, we assembled the bacterial metagenome-assembled genomes (MAGs). The bacterial MAGs are highly reduced, and predict a high metabolic dependence on the host. Analysis using multiple metrics suggest that both bacteria are likely new species. We therefore propose the names Ca . Mariplasma lunae (Mollicutes) and Ca . Marinirickettsia aquamalans (Rickettsiales). Finally, comparison with studies of Aurelia from other geographical populations suggests the association with Ca . Mariplasma lunae occurs in Aurelia from multiple geographical locations. The low-diversity microbiome of Aurelia provides a relatively simple system to study host-microbe interactions.
... Rickettsiaceae and Anaplasma taceae are best studied and harbor invertebrate endosymbionts, human pathogens, and reproductive parasites (2)(3)(4)(5)(6)(7). Midichloriaceae contains some arthropod-associated bacteria of unknown vertebrate pathogenicity (8), but most species are described from protists (9)(10)(11)(12)(13)(14). Remarkably, Castelli and colleagues (15) described the first extracellu lar rickettsial species, "Candidatus Deianiraea vastatrix, " as a bacterium dependent on Paramecia and sharing many characteristics of the intracellular lifestyle. ...
Recent metagenome-assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. The discovery of basal lineages (novel families Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles exposed an evolutionary timepoint for the transition to host dependency, which seemingly occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for later-evolving rickettsial pathogens. MAG analysis also substantially increased diversity for the genus Rickettsia and delineated a sister lineage (the novel genus Tisiphia) that stands to inform on the emergence of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages illuminates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, indicating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role in shaping the rvh effector landscape, as evinced by the discovery of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can yield insight into pathogen effector origins, particularly how effector architectures might become tailored to the discrete host cell functions of different eukaryotic hosts.
IMPORTANCE
While rickettsioses are deadly vector-borne human diseases, factors distinguishing Rickettsia pathogens from the innumerable bevy of environmental rickettsial endosymbionts remain lacking. Recent metagenome-assembled genome (MAG) studies revealed evolutionary timepoints for rickettsial transitions to host dependency. The rvh type IV secretion system was likely repurposed from congener killing in basal extracellular species to parasitizing host cells in later-evolving pathogens. Our analysis of MAG diversity for over two dozen rvh effectors unearthed their presence in some non-pathogens. However, most effectors were found in multiple divergent forms with variable architectures, indicating gene duplication and recombination-fashioned effector repertoires of Rickettsia pathogens. Lateral gene transfer substantially shaped pathogen effector arsenals, evinced by the discovery of effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchanges between Rickettsia and Legionella species. Our study exemplifies how MAGs yield insight into pathogen effector origins and evolutionary processes tailoring effectors to eukaryotic host cell biology.
... Rickettsiales are consistently found in Acropora spp. [83][84][85][86][87] and corals globally [88]. This taxon is thought to be associated with white band disease [89] with genomic signatures of pathogenicity [88], though Casas et al. [83] found Rickettsiales to be widespread in both healthy and diseased A. cervicornis and A. palmata in the Caribbean. ...
... [83][84][85][86][87] and corals globally [88]. This taxon is thought to be associated with white band disease [89] with genomic signatures of pathogenicity [88], though Casas et al. [83] found Rickettsiales to be widespread in both healthy and diseased A. cervicornis and A. palmata in the Caribbean. The absence of Rickettsiales in the viable bacterial community of A. loripes in contrast to their abundance in the untreated condition implies that they were predominately dead cells or exDNA. ...
Background
Nucleic acid-based analytical methods have greatly expanded our understanding of global prokaryotic diversity, yet standard metabarcoding methods provide no information on the most fundamental physiological state of bacteria, viability. Scleractinian corals harbour a complex microbiome in which bacterial symbionts play critical roles in maintaining health and functioning of the holobiont. However, the coral holobiont contains both dead and living bacteria. The former can be the result of corals feeding on bacteria, rapid swings from hyper- to hypoxic conditions in the coral tissue, the presence of antimicrobial compounds in coral mucus, and an abundance of lytic bacteriophages.
Results
By combining propidium monoazide (PMA) treatment with high-throughput sequencing on six coral species (Acropora loripes, A. millepora, A. kenti, Platygyra daedalea, Pocillopora acuta, and Porites lutea) we were able to obtain information on bacterial communities with little noise from non-viable microbial DNA. Metabarcoding of the 16S rRNA gene showed significantly higher community evenness (85%) and species diversity (31%) in untreated compared with PMA-treated tissue for A. loripes only. While PMA-treated coral did not differ significantly from untreated samples in terms of observed number of ASVs, > 30% of ASVs were identified in untreated samples only, suggesting that they originated from cell-free/non-viable DNA. Further, the bacterial community structure was significantly different between PMA-treated and untreated samples for A. loripes and P. acuta indicating that DNA from non-viable microbes can bias community composition data in coral species with low bacterial diversity.
Conclusions
Our study is highly relevant to microbiome studies on coral and other host organisms as it delivers a solution to excluding non-viable DNA in a complex community. These results provide novel insights into the dynamic nature of host-associated microbiomes and underline the importance of applying versatile tools in the analysis of metabarcoding or next-generation sequencing data sets.
Supplementary Information
The online version contains supplementary material available at 10.1186/s40793-023-00541-6.
... 10 This loss of rugosity and microhabitats led to an overall reduction in biodiversity within Caribbean reef ecosystems. 31,96 Studies suggest that the disease associated with mortality of A. palmata and A. cervicornis in the 1980s and 1990s, white band disease, is caused by a transmissible agent, but the cause has not been identified and there are few reports of microscopic changes 46,68,111 associated with the progression of this disease. More recently, Caribbean reefs have undergone marked coral losses due to a newer disease, stony coral tissue loss disease (SCTLD), which is identified by the appearance of (usually) multifocal, rapid tissue loss affecting a consistent pattern of multiple (>24) species, but sparing acroporids. ...
Stony corals (Scleractinia) are in the Phylum Cnidaria (cnidae referring to various types of stinging cells). They may be solitary or colonial, but all secrete an external, supporting aragonite skeleton. Large, colonial members of this phylum are responsible for the accretion of coral reefs in tropical and subtropical waters that form the foundations of the most biodiverse marine ecosystems. Coral reefs worldwide, but particularly in the Caribbean, are experiencing unprecedented levels of disease, resulting in reef degradation. Most coral diseases remain poorly described and lack clear case definitions, while the etiologies and pathogenesis are even more elusive. This introductory guide is focused on reef-building corals and describes basic gross and microscopic lesions in these corals in order to serve as an invitation to other veterinary pathologists to play a critical role in defining and advancing the field of coral pathology.
... Bootstrap values based on percentage agreement with resampled ASV tables (B). Klinges et al., 2019). Notably, the unidentified phylum was found to account for 12.98% of the total prokaryotic abundance in coral Porites. ...
Coral-associated microbial communities play a vital role in underpinning the health and resilience of reef ecosystems. Previous studies have demonstrated that the microbial communities of corals are affected by multiple factors, mainly focusing on host species and geolocation. However, up-to-date, insight into how the coral microbiota is structured by vast geographic distance with rich taxa is deficient. In the present study, the coral microbiota in six stony coral species collected from the coastal area of three countries, including United States of America (USA), Australia and Fiji, was used for analysis. It was found that the geographic influence on the coral microbiota was stronger than the coral host influence, even though both were significant. Interestingly, the contribution of the deterministic process to bacterial community composition increased as geographical distance grew. A total of 65 differentially abundant features of functions in coral microbial communities were identified to be associated with three geolocations. While in the same coastal area of USA, the similar relationship of coral microbiota was consistent with the phylogenetic relationship of coral hosts. In contrast to the phylum Proteobacteria, which was most abundant in other coral species in USA, Cyanobacteria was the most abundant phylum in Orbicella faveolata . The above findings may help to better understand the multiple natural driving forces shaping the coral microbial community to contribute to defining the healthy baseline of the coral microbiome.
... Supplementary Table S1 suggests that we can improve on this. High prevalence in healthy corals does not negate a microbe's pathogenic potential (Shaver et al., 2017;Klinges et al., 2019), and even common commensals or mutualists may turn into pathogens under certain conditions (Seyedsayamdost et al., 2011). Multidisciplinary approaches are already underway to tackle these questions (Bourne et al., 2016;Barreto et al., 2021), including in studies of coral-algal interactions (Roach et al., 2020). ...
Tropical reefs are commonly transitioning from coral to macroalgal dominance, but the role of macroalgae in coral decline remains inadequately understood. A growing body of research suggests that algae may harm corals via disruptions to the homeostasis of the coral holobiont, including resident microbial communities, but the processes that mediate these potential microbial effects and the spatial scales at which they operate are uncertain. Resolving the relative importance and context dependencies of microbially-mediated algal-coral competition is critical for understanding and predicting coral dynamics as reefs further degrade. In this review, we examine the current state of knowledge surrounding algal impacts on corals via disruption of their microbiomes, with a particular focus on the mechanisms hypothesized to mediate microbial effects, the scales at which they are thought to operate, and the evidence from laboratory- and field-based studies for their existence and ecological relevance in the wild. Lastly, we highlight challenges for further advancing the field.
... species (Bryopsidales), sampled in the Pacific and North Sea at 18.0 and 32.4 psu [63]. Intracellular Rickettsiales have already been detected in coral host tissue (Candidatus 'Aquarickettsia rohweri'; [72]) and in two Symbiodiniaceae microalgal strains, Cladocopium goreaui and Durusdinium glynii, which are isolated from the corals Acropora tenuis and Porites lobata, respectively [50]. The AB1 lineage highlighted here within cultured Ostreobium thalli was also detected in multiple Symbiodiniaceae cultures (propagated from an isolate from Acropora tenuis coral; [73]). ...
... Indeed, many (5) but not all seven bacterial taxa identified here as core Ostreobium microbiota were also found within the field collected corals, and/or have also been documented within skeleton assemblages of several coral species: Rhodospirillaceae ASV16 ( [52], this study), Kiloniellaceae [54], Hyphomonadaceae ASV57 (this study), Candidatus 'Amoebophilus' ( [54], this study), and Rickettsiales_AB1 lineage ( [72], this study). ...
Microscopic filaments of the siphonous green algae Ostreobium (Ulvophyceae, Bryopsidales) colonize and dissolve the calcium carbonate skeletons of coral colonies in reefs of contrasted salinities. Here, we analyzed their bacterial community’s composition and plasticity in response to salinity. Multiple cultures of Pocillopora coral-isolated Ostreobium strains from two distinct rbcL lineages representative of IndoPacific environmental phylotypes were pre-acclimatized (>9 months) to three ecologically relevant reef salinities: 32.9, 35.1, and 40.2 psu. Bacterial phylotypes were visualized for the first time at filament scale by CARD-FISH in algal tissue sections, within siphons, at their surface or in their mucilage. Ostreobium-associated microbiota, characterized by bacterial 16S rDNA metabarcoding of cultured thalli and their corresponding supernatants, were structured by host genotype (Ostreobium strain lineage), with dominant Kiloniellaceae or Rhodospirillaceae (Alphaproteobacteria, Rhodospirillales) depending on Ostreobium lineage, and shifted Rhizobiales’ abundances in response to the salinity increase. A small core microbiota composed of seven ASVs (~1.5% of thalli ASVs, 19–36% cumulated proportions) was persistent across three salinities in both genotypes, with putative intracellular Amoebophilaceae and Rickettsiales_AB1, as well as Hyphomonadaceae and Rhodospirillaceae also detected within environmental (Ostreobium-colonized) Pocillopora coral skeletons. This novel knowledge on the taxonomic diversity of Ostreobium bacteria paves the way to functional interaction studies within the coral holobiont.
... The Rickettsiales are a group of obligate intracellular bacteria that can be parasitic, symbiotic, or commensal with a diverse host range [64,65]. Rickettsiales are known to be pathogenic to many animals including humans and can also be found in cnidarians, including corals (Gorgonia ventalina, Orbicella annularis, and Orbicella faveolate), Hydrozoa (Hydra oligactis), and other jellyfish (Cyanea capillata) [66,67]. The Rickettsiales were detected in a high relative sequence abundance in most of the tissues and especially in the gonads (where they were~60-80% of sequences) and therefore could potentially be an important member of the jellyfish microbiome. ...
Amplicon sequencing of the 16S rRNA gene is extensively used to characterize bacterial communities, including those living in association with eukaryotic hosts. Deciding which region of the 16S rRNA gene to analyze and selecting the appropriate PCR primers remains a major decision when initiating any new microbiome study. Based on a detailed literature survey of studies focusing on cnidarian microbiomes, we compared three commonly used primers targeting different hypervariable regions of the 16S rRNA gene, V1V2, V3V4, and V4V5, using the jellyfish Rhopilema nomadica as a model. Although all primers exhibit a similar pattern in bacterial community composition, the performance of the V3V4 primer set was superior to V1V2 and V4V5. The V1V2 primers misclassified bacteria from the Bacilli class and exhibited low classification resolution for Rickettsiales, which represent the second most abundant 16S rRNA gene sequence in all the primers. The V4V5 primer set detected almost the same community composition as the V3V4, but the ability of these primers to also amplify the eukaryotic 18S rRNA gene may hinder bacterial community observations. However, after overcoming the challenges possessed by each one of those primers, we found that all three of them show very similar bacterial community dynamics and compositions. Nevertheless, based on our results, we propose that the V3V4 primer set is potentially the most suitable for studying jellyfish-associated bacterial communities. Our results suggest that, at least for jellyfish samples, it may be feasible to directly compare microbial community estimates from different studies, each using different primers but otherwise similar experimental protocols. More generally, we recommend specifically testing different primers for each new organism or system as a prelude to large-scale 16S rRNA gene amplicon analyses, especially of previously unstudied host–microbe associations.
... Historically, most research focussed on arthropod-vectored pathogens of vertebrates and humans (e.g., Anaplasma spp., Ehrlichia spp., Orientia tsutsugamushi, Rickettsia spp.) as well as Wolbachia spp., reproductive parasites of arthropods [4,5]. However, this paradigm has shifted in recent years and it is now established that members of both orders are widespread symbionts of arthropods [6,7], protists [8][9][10][11][12][13][14][15][16], corals [17], marine worms [18] and algae [19]. The appreciation of the ecological diversity of these bacteria has also led to the recent recognition of the Holosporales as a separate order, containing many taxa that had previously been considered basal or neglected Rickettsiales [20][21][22]. ...
... This obligate intracellular lifestyle has resulted in highly streamlined genomes with often reduced metabolic capacities. For instance, several pathways that are considered essential for most organisms across the tree of life (e.g., glycolysis, TCA cycle) are incomplete or missing in numerous members of the Rickettsiales and Holosporales [13,14,16,17,25,26], highlighting their dependence on the host to scavenge nutrients and precursors. Therefore, these taxa represent ideal models to investigate evolutionary trajectories from free-living to strictly intracellular bacteria. ...
... depending on the Hepatincola strain), the major facilitator superfamily (MFS, N = 9-11), sodium ion:proton antiporters (N = 7-8), sugar specific PTS (N = 4-5), drug/metabolite transporters (DMT, N = 4-5), multidrug/oligosaccharidyl-lipid/polysaccharide (MOP) flippase (N = 3), proton/sodium ion:glutamate/aspartate symporters (N = 2) and a sodium ion:nucleoside symporter of the Concentrative Nucleoside Transporter (CNT) family (N = 1). In contrast, we did not identify any tlc ADP/ATP translocases, which are thought to enable the import of ATP from the host cytosol in several Rickettsiales and Holosporales bacteria [12,[14][15][16][17]. Each strain also has 3-4 porins and four beta barrel-containing outer membrane proteins, which allow the diffusion of larger molecules in and out of the cell. ...
The order Holosporales (Alphaproteobacteria) encompasses obligate intracellular bacterial symbionts of diverse Eukaryotes. These
bacteria have highly streamlined genomes and can have negative fitness effects on the host. Herein, we present a comparative
analysis of the first genome sequences of ‘Ca. Hepatincola porcellionum’, a facultative symbiont occurring extracellularly in the
midgut glands of terrestrial isopods. Using a combination of long-read and short-read sequencing, we obtained the complete
circular genomes of two Hepatincola strains and an additional metagenome-assembled draft genome. Phylogenomic analysis
validated its phylogenetic position as an early-branching family-level clade relative to all other established Holosporales families
associated with protists. A 16S rRNA gene survey revealed that this new family encompasses diverse bacteria associated with both
marine and terrestrial host species, which expands the host range of Holosporales bacteria from protists to several phyla of the
Ecdysozoa (Arthropoda and Priapulida). Hepatincola has a highly streamlined genome with reduced metabolic and biosynthetic
capacities as well as a large repertoire of transmembrane transporters. This suggests that this symbiont is rather a nutrient
scavenger than a nutrient provider for the host, likely benefitting from a nutrient-rich environment to import all necessary
metabolites and precursors. Hepatincola further possesses a different set of bacterial secretion systems compared to protistassociated
Holosporales, suggesting different host-symbiont interactions depending on the host organism.
