manzanomaa88@univie.ac.at

In collaboration with Anouk Willemsen (Uniersity of Vienna), we sequenced high-quality genomes of protists known as hosts of giant viruses (GVs). Matching of codon usage preferences is often used to predict virus-host pairs. Our analyses revealed that in GVs, codon usage alone is a poor predictor of known pairs. Why? well, GVs have complex genomes… They encode few to complete tRNA sets and even genes from the translational machinery (e.g. tRNA–ligases). The host immune system may also play a role, driving viral codon usage away from its own. Moreover, its replication site (nuclear vs. cytoplasmatic) could also play a role. Finally, by analyzing the new amoebal genomes, we discovered viral integrations (potentially from GVs) into some of them, indicating historical infections. Most notably some inserted major capsid proteins seem to potentially encode for intact proteins (work in progress)…

Reference: 10.1101/2024.09.23.614596
*Version of record: 10.1093/gbe/evae271

Very happy the first group project SymBirth: Development of an artificial symbiont’s birth has been funded by the FWF’s 1000 ideas program. This program aims to fund “[…] completely new, high-risk, or particularly original research ideas that go beyond our current scientific understanding. The focus is on seed funding for forward-looking topics that have high transformative potential for science and research.”

In this project, we will study symbiont transmission in the European turtle leech Placobdella costata and related leeches. Using what we learn about this unknown process, we will undertake our ultimate goal of triggering a symbiont replacement event in this species. If accomplished, this project will result in the development of a highly promising model system for the study of the triggering of an obligate symbiotic lifestyle in bacteria.

After many years in the making (and an eternal cycle of adding new data….) our work on the discordance among phylogenomic datasets in is out!

Relationships between subfamilies remain contentious in both mitochondrial and nuclear phylogenies. Topologies obtained with Buchnera appear fully resolved but exhibit some discordance with host phylogenies at deep evolutionary scales and conflict with views on the evolution of aphid morphology. BUT…. further sampling (we had to stop at some point for this study) and sequence-independent analyses, such as male morphology and chromosomal structure, might help piece out some difficult-to-solve/contentious relationships.

This was a great collaboration with friends and work colleagues Emmanuelle Jousselin and Armelle Cœur d’acier (CBGP, france).

Reference: 10.1101/2024.04.12.589189
*Version of record: 10.1093/zoolinnean/zlae098

Pluralibacter now joins the (very) selected group of genera from which obligate nutritional symbionts of leeches have evolved from. As the previously known Providencia, this novel symbiont displays strong genome reduction w/convergent retention of B vitamin biosynthetic pathways. This discovery was surprising, as no change in bacteriome structure is observed (in leeches new symbiont=new bacteriome). Genomic features from the novel symbiont suggest it likely represents a symbiont replacement event, but future work should help clarify symbiont turnover in this leech genus.

This was a great collaboration with friends and work colleagues Alejandro Oceguera Figueroa (IB UNAM, Mexico) and Sebastian Kvist (Naturhistoriska riksmuseet, Sweden).

Reference: 10.1101/2023.12.21.572949
*Version of record: 10.1128/spectrum.04286-23

Another year of the International FISH course, where participants bring challenging samples and we help them design and apply the best strategy possible to analyse and get the most out of their samples. Always interesting to get to know what people are trying to FISH (often really difficult samples) and meet some good scientists. Until next one!

Back from a great FEMS 2023 edition. This year, a symbiosis session was organised by Martin Kaltenpoth (MPI – Jena). There was a great line-up of speakers as well as really nice posters. It was also good to catch up with some old friends and hear about the research they are doing on animal-microbe symbioses. I presented my work on leech-microbe symbiosis and was glad to spark interest in these very understudied organisms through people approaching me after the talk and throughout the conference. As a plus, I samples some local predatory leeches! Until next one!

Another year of the GRS/GRC animal-microbe symbioses meeting! As always great science all-around. As chair of the GRS meeting, got to read great abstracts, visit posters and interact with a bunch of scientists in their Masters, PhD, and Postdoc stages. At the GRC, co-chaired by Thomas Bosch (University Kiel, Germany) and Martin Kaltenpoth (MPI – Jena, Germany), the larger group of symbiosis-driven researchers joined us for even more days of research and fun! I got to present my work on leech nutritional endosymbionts and the evolution of their funky genomes. As a bonus, got my selfie with Takema, ten years or so since we first met in Krakow.

Can’t wait to hopefully be able to join to the 2025 edition!

Obligate vertically-transmitted endo­­sym­­bi­onts are weird… Given their particular lifestyle and mode of inheritance, they have evolved all sorts of particular genomic features (small to tiny genomes, biased nucleotide composition, among others). These sort of weird critters not only live inside insects, but can be found widely spread across invertebrates with a nutrient restricted diet. Strict blood-feeding leeches have evolved these sort of symbionts, but little is known about their nature, identity and genomics. Thus, we set to further explore the Providencia–Haementeria symbiosis by expanding the genomic knowledge of this symbiont lineage.

In this latest work, we found that similarly to other long-term vertically transmitted symbionts, the Providencia siddallii ancestor evolved a small gene-dense mobile element-free genome (so far, pretty standard, right???). Most surprisingly, we found that a “rare” genetic code reassignment (11->4) evolved in the symbiont lineage associated to the mexican leech H. acuecueyetzin (fun fact! the specific epithet means “leech” in Nahuatl). This reassignment means that the STOP codon ‘UGA’ is now coding for tryptophan! Moreover, features form the symbiont genomes suggest an early stage of reassignment and an ancestral propensity for the P. siddallii bacteria to undergo such a reassignment, e.g. the ancestral accumulation of ‘UGA’ codons in essential genes.

This work was a great collaboration with my friends and long-lived colleagues Dr. Alejandro Oceguera Figueroa (Biology Institute, UNAM, Mexico) and Dr. Sebastian Kvist (Natural History Museum, Stockholm, Sweeden).

Reference: 10.1101/2023.03.27.534433
*Version of record: 10.1093/gbe/evad164

After many years of work, our paper on co-obligate symbioses across aphids is finally out! Aphids are a large family of hemipterans with around 5,200 species organised into 23 extant subfamilies. Most work relating to endosymbionts has been done on the Aphidinae (60% of diversity), where aphids typically host a single nutritional symbiont, Buchnera. However, previous evidence shows that, similarly to adelgids and pseudococcids, some aphids can host more than one obligate nutritional symbiont. These co-obligate symbioses exist in Lachninae and Periphyllus spp., but we know little of these associations across aphids.

In this work, we sought to explore the nature and evolution of these associations. To this goal, we performed 16S amplicon sequencing on a total of 223 aphid samples (147 species, 12 subfamilies). In addition, we newly sequenced the symbionts of 25 aphid species & re-assembled 20 more. We observed that, despite large-scale gene loss in Buchnera often being associated to the acquisition of a new co-obligate symbiont, these two processes can be decoupled: in fact, only a few losses can trigger the establishment of new multi-partite nutritional symbioses. In addition, B vitamins (mainly riboflavin, seem at the core of the evolution of these new co-obligate symbioses (in aphids), with the biosynthesis of biotin often also being taken-over by the new symbiont. In fact, some even bring a new nutrient to the mix, thiamin.

New co-obligate symbionts have most commonly evolved from bacterial taxa known to be facultative endosymbionts of aphids, stressing the facultative-to-obligate lifestyle shift. In conclusion, co-obligate symbioses have evolved anew at least 6 times across aphids, thus existing in upwards of 11% of aphid species (the number is way higher is you do not count the Aphidinae subfamily…).

This was the result of a long-term collaboration with friends and work colleagues Emmanuelle Jousselin and Armelle Cœur d’acier (CBGP, france).

Reference: 10.1101/2022.08.28.505559
*Version of record: 10.24072/pcjournal.278

Demodex folliculorum mites, members of the arachnid class, inhabit the skin of (almost) all humans and other mammals. They spend their whole lives as living as symbionts, cannot survive outside their host, and rarely have the opp. to outbreed. Sounds familiar? You’re right! just like bacterial endosymbionts do!

We found the genome of Demodex folliculorum holds several features of historical and ongoing genome reduction: 1) small compact genome, 2) widespread relaxed selection on genes, and 3) a staggering low amount of CDSs. In addition, rearrangement and changes in their Hox genes likely impacts their unique body plan such as the anterior and dorsal position of the penis and lack of segmentation. Lastly, the work shows Demodex is generally vertically transmitted and it indeed has an anus! and therefore have been wrongly blamed for many skin diseases attributed to the accumulation of faeces during their lifetime before release when Demodex died. This collaborative work has been published in the journal Molecular Biology and Evolution.

*Version of record: 10.1093/molbev/msac125

*** EDIT *** This work was also featured in a number of media outlets, among them EurekAlert! (AAAS), BBC, The Guardian, COSMOS, IFL Science, BIG Think, New York Post, Discover, The Telegraph, NPR, National Geographic España, Le Monde, Der Standard, APA, FOCUS, ORF, Krone, and Spektrum.