Filip Husnik

Okinawa Institute of Science and Technology | OIST · Evolution, Cell Biology, and Symbiosis Unit

The smallest reported bacterial genome belongs to Tremblaya princeps, a symbiont of Planococcus citri mealybugs (PCIT). Tremblaya PCIT not only has a 139 kb genome, but possesses its own bacterial endosymbiont, Moranella endobia. Genome and transcriptome sequencing, including genome sequencing from a Tremblaya lineage lacking intracellular bacteria...

Significance Mealybugs are plant sap-sucking insects with a nested symbiotic arrangement, where one bacterium lives inside another bacterium, which together live inside insect cells. These two bacteria, along with genes transferred from other bacteria to the insect genome, allow the insect to survive on its nutrient-poor diet. Here, we show that th...

Bacteria influence eukaryotic biology as parasitic, commensal or beneficial symbionts. Aside from these organismal interactions, bacteria have also been important sources of new genetic sequences through horizontal gene transfer (HGT) for eukaryotes. In this Review, we focus on gene transfers from bacteria to eukaryotes, discuss how horizontally tr...

Animals are common hosts of mutualistic, commensal and pathogenic microorganisms. Blood-feeding parasites feed on a diet that is nutritionally unbalanced and thus often rely on symbionts to supplement essential nutrients. However, they are also of medical importance as they can be infected by pathogens such as bacteria, protists or viruses that tak...

Endosymbioses between bacteria and eukaryotes are enormously important in ecology and evolution, and as such are intensely studied. Despite this, the range of investigated hosts is narrow in the context of the whole eukaryotic tree of life: most of the information pertains to animal hosts, while most of the diversity is found in unicellular protist...

Haplozoans are intestinal parasites of marine annelids with bizarre traits, including a differentiated and dynamic trophozoite stage that resembles the scolex and strobila of tapeworms. Described originally as "Mesozoa", comparative ultrastructural data and molecular phylogenetic analyses have shown that haplozoans are aberrant dinoflagellates; how...

Symbiosis between prokaryotes and microbial eukaryotes (protists) has broadly impacted both evolution and ecology. Endosymbiosis led to mitochondria and plastids, the latter spreading across the tree of eukaryotes by subsequent rounds of endosymbiosis. Present-day endosymbionts in protists remain both common and diverse, although what function they...

Poster explaining the science-art exhibition displayed at OIST from March 25th to 31st about the floating star sand Hoshizuna.

Variations in toxicity of the benthic dinoflagellate Ostreopsis Schmidt 1901 have been attributed to specific molecular clades, biogeography of isolated strains, and the associated bacterial community. Here, we attempted to better understand the biodiversity and the basic biology influencing toxin production of Ostreopsis. Nine clonal cultures were...

Understanding the order and importance of events through which endosymbionts transition into cellular organelles (organellogenesis) is central to hypotheses about the origin of the eukaryotic cell. A new study on host-symbiont integration in a unicellular eukaryote reveals host-derived cell-division proteins that are targeted to the cell envelope o...

Comparing obligate endosymbionts with their free-living relatives is a powerful approach to investigate the evolution of symbioses, and it has led to the identification of several genomic traits consistently associated with the establishment of symbiosis. ‘ Candidatus Nebulobacter yamunensis’ is an obligate bacterial endosymbiont of the ciliate Eup...

Two new mealybug species (Hemiptera: Coccomorpha: Pseudococcidae), namely, Dysmicoccus kunaw Tanaka sp. nov. and Phenacoccus miruku Tanaka & Choi sp. nov., collected in Japan, are described based on the morphological characteristics of the adult females. Dysmicoccus kunaw resembles D. trispinosus (Hall 1923) and D. furcillosus Williams 2004, but...

Prokaryotic genomes are usually densely packed with intact and functional genes. However, in certain contexts, such as after recent ecological shifts or extreme population bottlenecks, broken and non-functional gene fragments can quickly accumulate and form a substantial fraction of the genome. Identification of these broken genes, called pseudogen...

Symbiotic systems vary in the degree to which the partners are bound to each other¹. At one extreme, there are intracellular endosymbionts in mutually obligate relationships with their host, often interpreted as mutualistic. The symbiosis between the betaproteobacterium Polynucleobacter and the ciliate Euplotes (clade B) challenges this view²: alth...

Gene transfer agents (GTAs) are virus-like structures that package and transfer prokaryotic DNA from donor to recipient prokaryotic cells. Here, we describe widespread GTA gene clusters in the highly reduced genomes of bacterial endosymbionts from microbial eukaryotes (protists). Homologs of the GTA capsid and portal complexes were initially found...

Marine benthic dinoflagellates within the genus Amphidinium were isolated from Guam and Okinawa. Isolated strains were identified to species-level using phylogenetic analyses of 28S rRNA and ITS-5.8S rRNA genes as well as microscopy. Of the six isolated strains, two were new species: A. pagoense sp. nov. and A. uduigamense sp. nov. Other isolates i...

The family ‘ Candidatus Midichloriaceae’ constitutes the most diverse but least studied lineage within the important order of intracellular bacteria Rickettsiales . Midichloriaceae endosymbionts are found in many hosts, including terrestrial arthropods, aquatic invertebrates, and protists. Representatives of the family are not documented to be path...

Prokaryotic genomes are generally gene dense and encode relatively few pseudogenes, or nonfunctional/inactivated remnants of genes. However, in certain contexts, such as recent ecological shifts or extreme population bottlenecks (such as those experienced by symbionts and pathogens), pseudogenes can quickly accumulate and form a substantial fractio...

Most of the genetic, cellular, and biochemical diversity of life rests within single-celled organisms — the prokaryotes (bacteria and archaea) and microbial eukaryotes (protists). Very close interactions, or symbioses, between protists and prokaryotes are ubiquitous, ecologically significant, and date back at least two billion years ago to the orig...

Phenotypic differences between sexes are often mediated by differential expression and alternative splicing of genes. However, the mechanisms that regulate these expression and splicing patterns remain poorly understood. The mealybug, Planococcus citri, displays extreme sexual dimorphism and exhibits an unusual instance of sex‐specific genomic impr...

The phylum Apicomplexa consists largely of obligate animal parasites that include the causative agents of human diseases such as malaria. Apicomplexans have also emerged as models to study the evolution of non-photosynthetic plastids, as they contain a relict chloroplast known as the apicoplast. The apicoplast offers important clues into how apicom...

Coolia Meunier 1919 from benthic assemblages of Hawai'i and Guam were isolated and clonal cultures were established from single cells. Cultures were identified to species-level based on 28S rRNA and ITS-5.8S rRNA genes and tested for toxicity. In Hawai'i, two strains of C. malayensis were isolated. In Guam, a high biodiversity was identified: four...

Phagocytosis is a fundamental process in marine ecosystems by which prey organisms are consumed and their biomass incorporated in food webs or remineralized. However, studies searching for the genes underlying this key ecological process in free-living phagocytizing protists are still scarce, in part due to the lack of appropriate ecological models...

Animals interact with a diverse array of both beneficial and detrimental microorganisms. In insects, these obligate symbioses in many cases allow feeding on nutritionally unbalanced diets. It is, however, still not clear how are obligate symbioses maintained at the cellular level for up to several hundred million years. Exact mechanisms driving hos...

Genome evolution in bacterial endosymbionts is notoriously extreme: the combined effects of strong genetic drift and unique selective pressures result in highly reduced genomes with distinctive adaptations to hosts [1-4]. These processes are mostly known from animal endosymbionts, where nutritional endosymbioses represent the best-studied systems....

Lower termites harbor in their hindgut complex microbial communities that are involved in the digestion of cellulose. Among these are protists, which are usually associated with specific bacterial symbionts found on their surface or inside their cells. While these form the foundations of a classic system in symbiosis research, we still know little...

Whether mitochondria and plastids originated by endosymbiosis is no longer questioned, but we still do not understand the actual process of integration. Other, younger endosymbiotic systems are, however, relatively common. Traditionally, it was not clear whether these systems could be directly and informatively compared to organelles because they a...

Rhodophyta (red algae) is one of three lineages of Archaeplastida¹, a supergroup that is united by the primary endosymbiotic origin of plastids in eukaryotes2,3. Red algae are a diverse and species-rich group, members of which are typically photoautotrophic, but are united by a number of highly derived characteristics: they have relatively small in...

Genome evolution in bacterial endosymbionts is notoriously extreme: the combined effects of strong genetic drift and unique selective pressures result in highly reduced genomes with distinctive adaptations to hosts. These processes are mostly known from animal endosymbionts, where nutritional endosymbioses represent the best-studied systems. Howeve...

To date, sea slugs have been considered the only animals known to sequester functional algal plastids into their own cells, via a process called “kleptoplasty.” We report here, however, that endosymbionts in the marine flatworms Baicalellia solaris and Pogaina paranygulgus are isolated plastids stolen from diatoms. Ultrastructural data show that kl...

Members of the major candidate phylum Dependentiae (a.k.a. TM6) are widespread across diverse environments from showerheads to peat bogs; yet, with the exception of two isolates infecting amoebae, they are only known from metagenomic data. The limited knowledge of their biology indicates that they have a long evolutionary history of parasitism. Her...

Background: Animals interact with a diverse array of both beneficial and detrimental microorganisms. These interactions sometimes spark obligate symbioses where the host depends on beneficial bacteria for survival and reproduction. In insects, these obligate symbioses in many cases allow feeding on nutritionally unbalanced diets such as plant sap a...

Most of the diversity of microbial life is not available in culture, and as such we lack even a fundamental understanding of the biological diversity of several branches on the tree of life. One branch that is highly underrepresented is the candidate phylum TM6, also known as the Dependentiae. Their biology is known only from reduced genomes recove...

Horizontal gene transfer from bacteria to eukaryotes is the subject of much debate. A recent study reveals the instrumental role that the acquisition of bacterial nucleotide transporters played in the evolution of the ubiquitous, intracellular eukaryotic parasites, the microsporidia. Horizontal gene transfer from prokaryotes to eukaryotes is the su...

Phylogeny of Hippoboscoidea based on mitochondrial genes Phylogeny of Hippoboscoidea based on 15 mitochondrial genes. It includes figures of four mitochondrial genomes assembled and annotated in this study which were also used for phylogeny reconstruction.

Information about samples, primers, results, and GenBank sequences File includes five tables. Table 1 provides information about samples. Table 2 provides information about Primer names, sequences and products used for PCR amplification and sequencing. Table 3 summarizes results: detected endosymbionts, GC content of their 16S rDNA, and sequences a...

Phylogeny of Hippoboscoidea based on COI The phylogeny was reconstructed by BI analysis. Posterior probabilities and bootstrap support are printed upon branches, respectively (asterisk was used for very low or missing bootstrap branch support). Taxa labelled with voucher are newly sequenced in this study. Genomic COI sequences are labelled with rRN...

Phylogeny of Hippoboscoidea based on EF The phylogeny was reconstructed by BI analysis. Posterior probabilities and bootstrap support are printed upon branches, respectively (asterisk was used for very low or missing bootstrap branch support). Taxa labelled with voucher are newly sequenced in this study. Four main Hippoboscidae groups are colour co...

Phylogeny of Hippoboscoidea based on 16S rRNA The phylogeny was reconstructed by BI analysis. Posterior probabilities and bootstrap support are printed upon branches, respectively (asterisk was used for very low or missing bootstrap branch support). Taxa labelled with voucher are newly sequenced in this study. Genomic COI sequences are labelled wit...

Phylogeny of Hippoboscidae based on COI The phylogeny was reconstructed by BI analysis. Posterior probabilities and bootstrap support are printed upon branches, respectively (asterisk was used for very low or missing bootstrap branch support). Taxa labelled with voucher are newly sequenced in this study. Genomic COI sequences are labelled with rRNA...

Phylogeny of Hippoboscidae based on 16S rRNA The phylogeny was reconstructed by BI analysis. Posterior probabilities and bootstrap support are printed upon branches, respectively (asterisk was used for very low or missing bootstrap branch support). Taxa labelled with voucher are newly sequenced in this study. Three main families of Hippoboscidae ar...

Information about raw sequences acquired in this study It provides information about raw sequences acquired in this study and their accession numbers.

Raw sequences acquired in this study File includes raw sequences acquired in this study: symbiont 16S rRNA, Wolbachia MLST, host 16S rRNA, host elongation factor, and host cytochrome oxidase subunit I.

Phylogeny of Hippoboscoidea based on concatenation of 16S rRNA, EF, and COI The phylogeny was reconstructed by BI analysis. Posterior probabilities and bootstrap support are printed upon branches, respectively (asterisk was used for very low or missing bootstrap branch support). Taxa labelled with voucher are newly sequenced in this study. Four mai...

Phylogeny of Hippoboscidae based on EF The phylogeny was reconstructed by BI analysis. Posterior probabilities and bootstrap support are printed upon branches, respectively (asterisk was used for very low or missing bootstrap branch support). Taxa labelled with voucher are newly sequenced in this study. Three main families of Hippoboscidae are colo...

Phylogeny of Arsenophonus within entire Hippoboscoidea based on 16S rRNA Posterior probabilities and bootstrap support are printed upon branches, respectively (asterisk was used for very low or missing bootstrap branch support). Taxa labelled with voucher are newly sequenced in this study. Genomic sequences are labelled with rRNA. Dark blue boxes r...

Phylogeny of all Arsenophonus bacteria based on 16S rRNA Posterior probabilities and bootstrap support are printed upon branches, respectively (asterisk was used for very low or missing bootstrap branch support). Taxa labelled with voucher are newly sequenced in this study. Genomic sequences are labelled with rRNA.

Symbiotic interactions between insects and bacteria are ubiquitous and form a continuum from loose facultative symbiosis to greatly intimate and stable obligate symbiosis. In blood-sucking insects living exclusively on vertebrate blood, obligate endosymbionts are essential for hosts and hypothesized to supplement B-vitamins and cofactors missing fr...

Legionellaceae are intracellular bacteria known as important human pathogens. In the environment, they are mainly found in biofilms associated with amoebas. In contrast to the gammaproteobacterial family Enterobacteriaceae, which established a broad spectrum of symbioses with many insect taxa, the only instance of legionella-like symbiont has been...

Spirotrichonymphea is a class of hypermastigote parabasalids defined by their spiral rows of many flagella. They are obligate hindgut symbionts of lower termites. Despite more than 100 years of morphological and ultrastructural study, the group remains poorly characterised by molecular data and the phylogenetic positions and taxonomic validity of m...

Symbiotic interactions between insects and bacteria are ubiquitous and form a continuum from loose facultative symbiosis to greatly intimate and stable obligate symbiosis. In blood-sucking insects living exclusively on vertebrate blood, obligate endosymbionts are essential for hosts and hypothesized to supplement B-vitamins and cofactors missing fr...

Symbiotic interactions between insects and bacteria are ubiquitous and form a continuum from loose facultative symbiosis to greatly intimate and stable obligate symbiosis. In blood-sucking insects living exclusively on vertebrate blood, obligate endosymbionts are essential for hosts and hypothesized to supplement B-vitamins and cofactors missing fr...

Legionellaceae are intracellular bacteria known as important pathogens of man. In the environment, they are mainly found in biofilms associated with amoebas. In contrast to another gammaproteobacterial family Enterobacteriaceae which established a broad spectrum of symbioses with many insect taxa, the only instance of legionella-like symbiont has b...

Blood-sucking lice of the genus Polyplax harbour two bacterial endosymbionts, one from family Legionellales and the other from family Neisseriales. Fylogenetic and genomic analyses reveal typical features of endosymbiotic bacteria and coevolution history with the host. In the genome of the endosymbiont from family Legionellales I found operon, whic...

Candidatus Arsenophonus lipopteni (Enterobacteriaceae, Gammaproteobacteria) is an obligate intracellular symbiont of the blood feeding deer ked, Lipoptena cervi (Diptera: Hippoboscidae). The bacteria reside in specialized cells derived from host gut epithelia (bacteriocytes) forming a compact symbiotic organ (bacteriome). Compared to the closely re...

Manure from dairy farms has been shown to contain diverse tetracycline resistance genes that are transferable to soil. Here, we focus on conjugative plasmids that may spread tetracycline resistance at a conventional dairy farm. We performed exogenous plasmid isolation from cattle feces using chlortetracycline for transconjugant selection. The trans...

Stable endosymbiosis of a bacterium into a host cell promotes cellular and genomic complexity. The mealybug Planococcus citri has two bacterial endosymbionts; remarkably, the gammaproteobacterium Moranella endobia lives in the cytoplasm of the betaproteobacterium Tremblaya princeps. These two bacteria, along with genes horizontally transferred from...

Symbiosis between insects and bacteria resulted in a variety of arrangements, genomic modifications and metabolic interconnections. Here, we present genomic, phylogenetic and morphological characteristics of a symbiotic system associated with Melophagus ovinus, a member of the blood-feeding family Hippoboscidae. The system comprises four unrelated...

Symbiosis is well known to influence bacterial symbiont genome evolution and has recently been shown to shape eukaryotic host genomes. Intriguing patterns of host genome evolution, including remarkable numbers of gene duplications, have been observed in the pea aphid, a sap-feeding insect that relies on a bacterial endosymbiont for amino acid provi...

Source DNA is available from John McCutcheon (john.mccutcheon@umontana.edu).

Bacteria of the genus Sodalis live in symbiosis with various groups of insects. The best known member of this group, a secondary symbiont of tsetse flies Sodalis glossinidius, has become one of the most important models in investigating establishment and evolution of insect-bacteria symbiosis. It represents a bacterium in the early/intermediate sta...

Phylogenetic trees derived from groEL aminoacid matrix under ML in PhyML. Bootstrap values are indicated by the numbers at the nodes. New Sodalis lineages added in this study are printed in red. Values under 50 are not shown. (EPS)

List of primers used in this study. (DOC)

List of 16 S rDNA sequences used for phylogenetic inference. (DOC)

List of groEL sequences used for phylogenetic inference. (DOC)

16 S rDNA tree derived by ML method in PhyML. Bootstrap values are indicated by the numbers at the nodes. New Sodalis lineages added in this study are printed in red. Values under 50 are not shown. (EPS)

List of spaPQR sequences used for phylogenetic inference. (DOC)

List of sequences acquired in this study. (DOC)

Characteristics of particular datasets. (DOC)

Additional phylogenetic trees.

Summary of 20 studies on symbionts phylogeny.

List of the taxa and orthologous genes used in the study.

All phylogenetic trees derived from AT-GC and SF datasets. A rar file of all phylogenetic trees obtained under BI, ML and MP from 11 AT/GC datasets, and under ML from five slow-fasted datasets. Trees are in phylip and nexus formats and can be viewed, for example, in TreeView http://taxonomy.zoology.gla.ac.uk/rod/treeview.html or Mesquite http://mes...

Additional phylogenetic trees inferred from CAT and CAT+GTR unconverged chains.

The bacterial family Enterobacteriaceae gave rise to a variety of symbiotic forms, from the loosely associated commensals, often designated as secondary (S) symbionts, to obligate mutualists, called primary (P) symbionts. Determination of the evolutionary processes behind this phenomenon has long been hampered by the unreliability of phylogenetic r...