Biology subjects

Leisch, N.

Publications and source records attributed to Leisch, N..

12 recordsLinked to original sources

bioRxiv2026

A mobile optical coherence microscope for studying aquatic organisms in- and outside the laboratory

High-resolution, three-dimensional imaging of live organisms has largely depended on laboratory-bound microscopes, limiting quantitative analysis of morphology and dynamics to species that survive transport and thrive under lab-controlled conditions. Here we present a mobile optical coherence microscopy (OCM) platform that overcomes this constraint, delivering [~]2.5 {micro}m axial resolution, label-free, volumetric imaging of live aquatic organisms in both laboratory and remote field environments. We demonstrate the platform across a broad range of aquatic organisms from the lab and field, spanning multiple phyla - including cnidarians, poriferans, annelids, arthropods and echinoderms - resolving internal anatomy, tissue boundaries and organismal morphology at micrometer scale without fixation, fluorescent labeling, or specialized sample preparation. High-speed acquisition, with up to 250 kHz A-line rate and 7.7 Hz volume rate, further enabled morphodynamic imaging of live biological processes, including cellular aggregate motility, embryonic cell division, and organ-level peristaltic dynamics in intact, living animals. To demonstrate field deployability, the platform was operated during the EMBL TREC pan-European expedition, enabling on-site, label-free imaging of marine organisms and plankton immediately upon collection. By decoupling high-resolution volumetric imaging from fixed laboratory settings, mobile OCM opens a path toward field-ready quantitative morphological and dynamic phenotyping of aquatic life.

bioengineering↗

bioRxiv2026

An Advanced Mobile Laboratory to enable field-based microbial ecology and cell biology across scales

Microbial biodiversity is central to ecosystem function, yet mechanistic insights into the cell biology of environmental organisms remain limited. The underlying challenges are twofold: most microbes remain uncultivable, and a persistent gap exists between field sampling and laboratory analyses. Here, we introduce the Advanced Mobile Laboratory (AML), a field-deployable platform that integrates confocal microscopy, image-enabled cell sorting, and cryo-preparation for expansion and electron microscopy. This setup enables immediate, standardized processing and analysis of environmental communities directly at the sampling site. We demonstrate its capability using marine eukaryotic plankton, showing how the AML enables multiscale investigations, from live imaging of natural communities to enabling ultrastructural and single-cell omics analyses, while minimizing sample degradation and enabling on-site experimentation. By bringing high-end sample preparation and analytical capacity into the field, the AML enables studying life in its natural context to mechanistically understand lifes diversity in the environment.

cell biology↗

bioRxiv2025

Evolutionary history of the widespread association between placozoans and diverse Rickettsiales symbionts

Rickettsiales are an enigmatic clade of strictly host-associated bacteria with some very common phylotypes in aquatic habitats. Despite amplicon- and metagenomic sequencing-based observations, the roles of these aquatic Rickettsiales are still unknown, as their genomes feature both beneficial and parasitic traits. In placozoans, microscopy-based observations of intracellular and Rickettsia-like-organisms point to Rickettsiales as common and abundant symbionts. We therefore systematically studied the microbiomes of placozoans to understand the eco-evolutionary dynamics of their associated Rickettsiales. Single-animal metagenomics revealed a widespread association of placozoans with Rickettsiales from three clades of Ca. Midichloriaceae, which were present in all but two placozoan lineages. A comparative phylogenetic analysis of placozoans and their Rickettsiales symbionts revealed host species-specific switches among Rickettsiales clades in several placozoan lineages. Our combination of evolutionary analyses, genome annotations, and expression data indicate different functional roles of these Rickettsiales clades, with some clearly diverging from a classical parasitic lifestyle by the loss of all ATP scavenging machinery. One of placozoan lineages that lacked Ca. Midichloriaceae was instead associated with Rickettsiaceae symbionts, while another was completely devoid of Rickettsiales symbionts. Our imaging data of fibre cells entirely free of Rickettsiales underscores previously unrecognized variation in placozoan-microbe associations. Early-branching invertebrates, including placozoans as well as many corals, are gaining increasing traction as emerging models across the life sciences. Our data and analyses show that it is important to consider the specific endosymbiont groups and their ecology in a given host, as these symbionts likely influence the hosts cellular and organismal biology.

microbiology↗

bioRxiv2024

Charting the landscape of cytoskeletal diversity in microbial eukaryotes

Microbial eukaryotes are small and often resistant to standard labelling and imaging techniques, and therefore remain understudied - despite their critical ecological importance - with the exception of a few established models. Here, we use Ultrastructure Expansion Microscopy (U-ExM) to carry out high-resolution volumetric imaging of over 200 cultured planktonic eukaryotes across major lineages. By combining U-ExM with pan- and specific immuno-labelling, we reveal novel microtubule and centrin-containing elements and assign molecular identities to enigmatic cytoskeletal structures observed previously only by electron microscopy. Our investigation represents the first systematic survey of the extensive cytoskeletal diversity on display across the eukaryotic tree, including the major species groups of dinoflagellates, haptophytes, ciliates, euglenids, cryptomonads, and green algae. Our U-ExM approach extends to mixed environmental samples, paving the way for environmental cell biology at ultrastructural resolution and unprecedented scale, a crucial step towards understanding and protecting complex ecosystems in the face of biodiversity loss.

cell biology↗

bioRxiv2023

An intranuclear bacterial parasite of deep-sea musselsexpresses apoptosis inhibitors acquired from its host

Endozoicomonadaceae bacteria are widespread in many marine animals, and generally considered beneficial. Members of one clade, however, Candidatus Endonucleobacter, infect the nuclei of deep-sea mussels, where they replicate to [≥] 80,000 bacteria per nucleus and cause the nuclei to swell to 50 times their original size. How these parasites are able to persist in host nuclei without the cell undergoing apoptosis is not known. We show here that Ca. Endonucleobacter encodes and expresses 7-15 inhibitors of apoptosis (IAPs), proteins previously only known from animals and viruses. Dual RNA-seq transcriptomes of infected nuclei revealed parallel upregulation of Ca. Endonucleobacter IAPs and host caspases, suggesting an arms race between the parasite and host for control of apoptosis. Comparative phylogenetic analyses revealed that Ca. Endonucleobacter acquired IAPs repeatedly through horizontal gene transfer from their hosts in convergent acquisition, possibly mediated by herpes viruses that may infect both the parasite and the host.

microbiology↗

bioRxiv2021

Highly variable fidelity drives symbiont community composition in an obligate symbiosis

Multipartite symbioses, which involve intimate interactions among three or more species, have evolved independently numerous times in convergent evolution, and enable functional complexity and ecological flexibility. How stability is maintained in such relationships remains, however, poorly understood, and can only be fully understood by integrating processes across both micro- and macroevolutionary scales. In this study, we bridge these scales by examining the symbiotic communities of gutless marine oligochaetes - annelid worms that have become obligately dependent on their bacterial partners for nutrition and waste removal over the past 150 million years. Using metagenomic sequencing of 231 individuals from 63 host species, collected across 17 marine environments worldwide, we reconstructed host and symbiont phylogenies to investigate the composition, specificity, and evolutionary history of their symbiotic communities from the strain to genus level. Our results show that each gutless oligochaete harbors up to 10 symbiont species drawn from a restricted pool of 33 marine bacterial genera. Community composition was strongly shaped by host species at 90% explanatory power, and much less by geography or environment. Symbiont communities were highly stable within host species but shifted rapidly at short macroevolutionary scales as host species diverged. Ancestral state reconstructions revealed that the primary symbiont, Candidatus Thiosymbion, was an early and persistent acquisition, while secondary symbionts were gained multiple times through convergent evolution, enhancing the diversity and metabolic flexibility of the symbiotic communities. By linking fine-scale microevolutionary dynamics with broader macroevolutionary patterns, our study reveals how gutless oligochaetes achieve both stability and flexibility in their symbiotic partnerships - enabling long-term host dependency while driving innovation and adaptation. This evolutionary trajectory may underpin the ecological success and diversification of gutless oligochaetes in marine sediments, and may help explain the repeated emergence and persistence of other multipartite associations.

evolutionary biology↗

bioRxiv2020

Becoming symbiotic - the symbiont acquisition and the early development of bathymodiolin mussels

Symbiotic associations between animals and microorganisms are widespread and have a profound impact on the ecology, behaviour, physiology, and evolution of the host. Research on deep-sea mussels of the genus Bathymodiolus has revealed how chemosynthetic symbionts sustain their host with energy, allowing them to survive in the nutrient-poor environment of the deep ocean. However, to date, we know little about the initial symbiont colonization and how this is integrated into the early development of these mussels. Here we analysed the early developmental life stages of B. azoricus, "B". childressi and B. puteoserpentis and the changes that occur once the mussels are colonized by symbionts. We combined synchrotron-radiation based {micro}CT, correlative light and electron microscopy and fluorescence in situ hybridization to show that the symbiont colonization started when the animal settled on the sea floor and began its metamorphosis into an adult animal. Furthermore, we observed aposymbiotic life stages with a fully developed digestive system which was streamlined after symbiont acquisition. This suggests that bathymodiolin mussels change their nutritional strategy from initial filter-feeding to relying on the energy provided by their symbionts. After [~]35 years of research on bathymodiolin mussels, we are beginning to answer fundamental ecological questions concerning their life cycle and the establishment of symbiosis.

zoology↗

bioRxiv2020

Kentrophoros magnus sp. nov. (Ciliophora, Karyorelictea), a new flagship species of marine interstitial ciliates

The karyorelictean ciliate Kentrophoros lacks a defined oral apparatus but has a dense coat of symbiotic bacteria that it consumes by phagocytosis. Body size, shape, and nuclear characters are variable in this genus. We formally describe a new species, K. magnus from Elba (Italy), which has unusual folding of its symbiont-bearing surface into pouch-like compartments, a body form that we term "pseudotrophosomal". K. magnus cells are large (2100 {+/-} 700 x 170 {+/-} 23 m in vivo), but contain only one micronucleus and two macronuclei, although these are much bigger than other Kentrophoros (widths 20 {+/-} 2.5 and 31 {+/-} 4.0 m respectively in K. magnus). We also present morphological observations on a close relative from Twin Cayes (Belize), which also has relatively large nuclei (micronuclei 13 {+/-} 1.5 m, mature macronuclei 20 {+/-} 2.8 m), but unlike K. magnus, it has on average 22 nuclei per cell, with different developmental stages of the macronuclei present simultaneously, and lacks pouch-like folding. Nuclear number and arrangement are important characters for karyorelicts. We suggest the use of a "nuclear formula" to simplify descriptions. Our discovery of large and morphologically distinctive new species underlines the incompleteness of our knowledge about meiofaunal ciliates.

microbiology↗

bioRxiv2019

Morphology of obligate ectosymbionts reveals Paralaxus gen. nov., a new circumtropical genus of marine stilbonematine nematodes

Stilbonematinae are a subfamily of conspicuous marine nematodes, distinguished by a coat of sulphur-oxidizing bacterial ectosymbionts on their cuticle. As most nematodes, the worm hosts have a simple anatomy and few taxonomically informative characters, and this has resulted in numerous taxonomic reassignments and synonymizations. Recent studies using a combination of morphological and molecular traits have helped to improve the taxonomy of Stilbonematinae but also raised questions on the validity of several genera. Here we describe a new circumtropically distributed genus Paralaxus (Stilbonematinae) with three species: Paralaxus cocos sp. nov., P. bermudensis sp. nov. and P. columbae sp. nov.. We used single worm metagenomes to generate host 18S rRNA and cytochrome oxidase I (COI) as well as symbiont 16S rRNA gene sequences. Intriguingly, COI alignments and primer matching analyses suggest that the COI is not suitxable for PCR-based barcoding approaches in Stilbonematinae as the genera have a highly diverse base composition and no conserved primer sites. The phylogenetic analyses of all three gene sets however confirm the morphological assignments and support the erection of the new genus Paralaxus as well as corroborate the status of the other stilbonematine genera. Paralaxus most closely resembles the stilbonematine genus Laxus in overlapping sets of diagnostic features but can be distinguished from Laxus by the morphology of the genus-specific symbiont coat. Our re-analyses of key parameters of the symbiont coat morphology as character for all Stilbonematinae genera show that with amended descriptions, including the coat, highly reliable genus assignments can be obtained.

zoology↗

bioRxiv2019

Horizontal acquisition followed by expansion and diversification of toxin-related genes in deep-sea bivalve symbionts

Deep-sea bathymodioline mussels gain their nutrition from intracellular bacterial symbionts. Their sulfur-oxidizing (SOX) symbionts were recently shown to encode abundant toxin-related genes (TRGs) in their genomes, which may play a role in beneficial host-microbe interactions. Here, we compared TRGs in the genomes of SOX symbionts from 10 bathymodioline mussel and two sponge species to better understand their potential functions and evolutionary origins. Despite the close phylogenetic relatedness of these symbionts, the number and classes of encoded toxins varied greatly between host species. One of the TRG classes, YDs, has experienced gene expansions multiple times, suggesting that these genes are under adaptive selection. Some symbiont genomes contained secretion systems, which can play a role in host-microbe interactions. Both TRGs and secretion systems had a heterogeneous distribution, suggesting that these closely related bacteria have acquired different molecular mechanisms for interacting with the same family of animal hosts, possibly through convergent evolution.

microbiology↗

bioRxiv2019

The Trichoplax microbiome: the simplest animal lives in an intimate symbiosis with two intracellular bacteria

Summary paragraphPlacozoa is an enigmatic phylum of simple, microscopic, marine metazoans. Although intracellular bacteria have been found in all members of this phylum, almost nothing is known about their identity, location and interactions with their host. We used metagenomic and metatranscriptomic sequencing of single host individuals, plus metaproteomic and imaging analyses, to show that the placozoan Trichoplax H2 lives in symbiosis with two intracellular bacteria. One symbiont forms a new genus in the Midichloriaceae (Rickettsiales) and has a genomic repertoire similar to that of rickettsial parasites, but does not appear to express key genes for energy parasitism. Correlative microscopy and 3-D electron tomography revealed that this symbiont resides in an unusual location, the rough endoplasmic reticulum of its hosts internal fiber cells. The second symbiont belongs to the Margulisbacteria, a phylum without cultured representatives and not known to form intracellular associations. This symbiont lives in the ventral epithelial cells of Trichoplax, likely metabolizes algal lipids digested by its host, and has the capacity to supplement the placozoans nutrition. Our study shows that even the simplest animals known have evolved highly specific and intimate associations with symbiotic, intracellular bacteria, and highlights that symbioses with microorganisms are a basal trait of animal life.

microbiology↗

bioRxiv2018

Horizontal acquisition of a patchwork Calvin cycle by symbiotic and free-living Campylobacterota (formerly Epsilonproteobacteria)

Although the majority of known autotrophs use the Calvin-Benson-Bassham (CBB) cycle for carbon fixation, all currently described autotrophs from the Campylobacterota (previously Epsilonproteobacteria) use the reductive tricarboxylic acid cycle (rTCA) instead. We discovered campylobacterotal epibionts (\"Candidatus Thiobarba\") of deep-sea mussels that have acquired a complete CBB cycle and lost key genes of the rTCA cycle. Intriguingly, the phylogenies of campylobacterotal CBB genes suggest they were acquired in multiple transfers from Gammaproteobacteria closely related to sulfur-oxidizing endosymbionts associated with the mussels, as well as from Betaproteobacteria. We hypothesize that \"Ca. Thiobarba\" switched from the rTCA to a fully functional CBB cycle during its evolution, by acquiring genes from multiple sources, including co-occurring symbionts. We also found key CBB cycle genes in free-living Campylobacterota, suggesting that the CBB cycle may be more widespread in this phylum than previously known. Metatranscriptomics and metaproteomics confirmed high expression of CBB cycle genes in mussel-associated \"Ca. Thiobarba\". Direct stable isotope fingerprinting showed that \"Ca. Thiobarba\" has typical CBB signatures, additional evidence that it uses this cycle for carbon fixation. Our discovery calls into question current assumptions about the distribution of carbon fixation pathways across the tree of life, and the interpretation of stable isotope measurements in the environment.

microbiology↗